From 20fc9b6a66de6204bfcd2e96c63ba59cd8d24953 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 19 Jan 2023 10:34:05 +0000
Subject: [PATCH 001/203] bumped RoxygenNote in DESCRIPTION

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index c490d11..241630f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -36,7 +36,7 @@ Suggests:
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 Depends: 
     R (>= 2.10)

From 091f93f6363277a63d450e76349de0728935c1ee Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 19 Jan 2023 10:35:06 +0000
Subject: [PATCH 002/203] removed tidyverse dependency from DESCRIPTION

---
 DESCRIPTION | 1 -
 1 file changed, 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 241630f..94648c8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -28,7 +28,6 @@ Imports:
     stringr,
     tibble,
     tidyr,
-    tidyverse,
     urltools
 Suggests:
     devtools, 

From b9313e083e7bf2c0baca6e0bc753a1c6de0ce85e Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 19 Jan 2023 16:53:22 +0000
Subject: [PATCH 003/203] added testing infrastructure and a test for get_cases
 to run locally (skipped by default)

---
 tests/testthat.R                | 12 +++++
 tests/testthat/test-get_cases.R | 95 +++++++++++++++++++++++++++++++++
 2 files changed, 107 insertions(+)
 create mode 100644 tests/testthat.R
 create mode 100644 tests/testthat/test-get_cases.R

diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 0000000..7427e8c
--- /dev/null
+++ b/tests/testthat.R
@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/tests.html
+# * https://testthat.r-lib.org/reference/test_package.html#special-files
+
+library(testthat)
+library(godataR)
+
+test_check("godataR")
diff --git a/tests/testthat/test-get_cases.R b/tests/testthat/test-get_cases.R
new file mode 100644
index 0000000..631b19c
--- /dev/null
+++ b/tests/testthat/test-get_cases.R
@@ -0,0 +1,95 @@
+test_that("get_cases works as expected", {
+  skip("get_cases requires API call")
+
+  res <- get_cases(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id,
+    method = "export",
+    batch_size = 50000,
+    wait = 2,
+    file.type = "json"
+  )
+
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(13L, 357L))
+  expect_true(
+    all(c(
+      "id", "visualId", "dateOfReporting", "isDateOfReportingApproximate",
+      "createdAt", "createdBy", "updatedAt", "updatedBy", "deleted",
+      "deletedAt", "createdOn", "firstName", "middleName", "lastName", "gender",
+      "occupation", "dob", "classification", "wasContact", "dateBecomeCase",
+      "wasCase", "dateOfInfection", "dateOfOnset", "riskLevel", "riskReason",
+      "outcomeId", "dateOfOutcome", "documents", "type", "dateRanges",
+      "transferRefused", "addresses", "safeBurial", "dateOfBurial",
+      "isDateOfOnsetApproximate", "numberOfExposures", "numberOfContacts",
+      "burialLocationId", "burialLocationId Identifiers",
+      "burialLocationId Location geographical level",
+      "burialLocationId Parent location", "burialPlaceName",
+      "investigationStatus", "dateInvestigationCompleted", "vaccinesReceived",
+      "pregnancyStatus", "responsibleUserId", "age.years", "age.months"
+    ) %in% colnames(res))
+  )
+
+  expect_true(
+    all(grepl(pattern = "^questionnaireAnswers", x = colnames(res)[50:357]))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "character", "character", "logical", "character",
+      "character", "character", "character", "logical", "logical", "character",
+      "character", "character", "character", "character", "character",
+      "character", "character", "logical", "character", "logical", "character",
+      "character", "character", "character", "character", "character", "list",
+      "character", "list", "logical", "list", "logical", "logical", "logical",
+      "integer", "integer", "logical", "list", "list", "list", "logical",
+      "character", "logical", "list", "character", "character", "integer",
+      "integer", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "list", "list", "list",
+      "list", "list", "list", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "list", "list", "list",
+      "list", "list", "list", "list", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "logical",
+      "list", "list", "list", "list", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "list", "logical", "logical", "list", "logical", "logical",
+      "logical", "list", "logical", "list", "logical", "list", "logical",
+      "list", "logical", "list", "logical", "list", "logical", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "logical", "list", "logical", "list",
+      "logical", "logical", "logical", "logical", "list", "logical", "logical",
+      "logical", "logical", "list", "logical", "list", "logical", "list",
+      "list", "logical", "list", "logical", "list", "logical", "list",
+      "logical", "list", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "list", "list", "list"))
+})

From a9a59491d0e5a419282fb92e202324bf0385f87c Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 19 Jan 2023 16:53:45 +0000
Subject: [PATCH 004/203] added testthat to DESCRIPTION

---
 DESCRIPTION | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 94648c8..ef8a27d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -30,8 +30,8 @@ Imports:
     tidyr,
     urltools
 Suggests:
-    devtools, 
-    testthat
+    devtools,
+    testthat (>= 3.0.0)
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
@@ -39,3 +39,4 @@ RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 Depends: 
     R (>= 2.10)
+Config/testthat/edition: 3

From f72716993a68627824a13c90011486bc33ca4f04 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 19 Jan 2023 16:54:44 +0000
Subject: [PATCH 005/203] linted style of get_cases

---
 R/get_cases.R | 90 ++++++++++++++++++++++++++++++++-------------------
 1 file changed, 57 insertions(+), 33 deletions(-)

diff --git a/R/get_cases.R b/R/get_cases.R
index 41b8e39..616fe73 100644
--- a/R/get_cases.R
+++ b/R/get_cases.R
@@ -22,17 +22,27 @@
 #'    be the default if you are using Go.Data version 2.38.1
 #'    or newer.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here.
+#' Don't forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
-#' @param outbreak_id The id number for the outbreak for which you want to download data.
-#' @param method The method to download data. `method="export"` is the preferred and default method for Go.Data version 2.38.1 or later. See Details.
-#' @param batch_size If `method="batches"`, then `batch_size` specifies the number of records to retrieve in each iteration.
-#' @param wait If `method="export"`, then `wait` is the number of seconds to wait in between iterations of checking the status of the export.
-#' @param file.type If `method="export"`, then `file.type` determines Whether the resulting data frame should contain nested fields (`file.type="json"`, the default) or an entirely flat data structure (`file.type="csv"`)
+#' @param outbreak_id The id number for the outbreak for which you want to
+#' download data.
+#' @param method The method to download data. `method="export"` is the
+#' preferred and default method for Go.Data version 2.38.1 or later.
+#' See Details.
+#' @param batch_size If `method = "batches"`, then `batch_size` specifies the
+#' number of records to retrieve in each iteration.
+#' @param wait If `method = "export"`, then `wait` is the number of seconds to
+#' wait in between iterations of checking the status of the export.
+#' @param file.type If `method = "export"`, then `file.type` determines Whether
+#' the resulting data frame should contain nested fields (`file.type = "json"`,
+#' the default) or an entirely flat data structure (`file.type = "csv"`)
 #'
 #' @return
-#' Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+#' Returns a data frame. Some fields, such as addresses, hospitalization
+#' history, and questionnaire fields may require further unnesting. See
+#' `\link[tidyr]{nest}` for assitance with unnesting.
 #' @export
 #'
 #' @examples
@@ -56,22 +66,32 @@
 #' @importFrom purrr pluck
 
 
-get_cases <- function(url=url,
-                      username=username,
-                      password=password,
-                      outbreak_id=outbreak_id,
-                      method=c("export","batch"),
-                      batch_size=50000,
-                      wait=2,
-                      file.type=c("json","csv")) {
+get_cases <- function(url = url,
+                      username = username,
+                      password = password,
+                      outbreak_id = outbreak_id,
+                      method = c("export", "batch"),
+                      batch_size = 50000,
+                      wait = 2,
+                      file.type = c("json", "csv")) {
 
   #Check that outbreak_id is active
-  if (outbreak_id != get_active_outbreak(url=url, username=username, password=password)) {
-    set_active_outbreak(url=url, username=username, password=password, outbreak_id=outbreak_id)
+  active_outbreak_id <- get_active_outbreak(
+    url = url,
+    username = username,
+    password = password
+  )
+  if (outbreak_id != active_outbreak_id) {
+    set_active_outbreak(
+      url = url,
+      username = username,
+      password = password,
+      outbreak_id = outbreak_id
+    )
   }
 
   #Set default method based on current version of Go.Data
-  version.check <- check_godata_version(url=url)
+  version.check <- check_godata_version(url = url)
   if (!version.check) {
     method <- "batches" #Older version of Go.Data can only use the batch method
   } else if (missing(method)) {
@@ -81,14 +101,16 @@ get_cases <- function(url=url,
 
   if (method == "batches") {
 
-    api_call_n <- paste0(url, "api/outbreaks/",outbreak_id,"/cases/count")
-    api_call_get <- paste0(url, "api/outbreaks/",outbreak_id,"/cases")
-    df <- batch_downloader(url=url,
-                           username=username,
-                           password=password,
-                           api_call_n=api_call_n,
-                           api_call_get=api_call_get,
-                           batch_size=batch_size)
+    api_call_n <- paste0(url, "api/outbreaks/", outbreak_id, "/cases/count")
+    api_call_get <- paste0(url, "api/outbreaks/", outbreak_id, "/cases")
+    df <- batch_downloader(
+      url = url,
+      username = username,
+      password = password,
+      api_call_n = api_call_n,
+      api_call_get = api_call_get,
+      batch_size = batch_size
+    )
 
   } else if (method == "export") {
 
@@ -96,13 +118,15 @@ get_cases <- function(url=url,
     if (missing(file.type)) file.type <- "json"
 
     #Submit an export request to the system
-    api_call_request <- paste0(url,"api/outbreaks/",outbreak_id,"/cases/export")
-    df <- export_downloader(url=url,
-                            username=username,
-                            password=password,
-                            api_call_request=api_call_request,
-                            file.type = file.type,
-                            wait = wait)
+    api_call_request <- paste0(url, "api/outbreaks/", outbreak_id, "/cases/export")
+    df <- export_downloader(
+      url = url,
+      username = username,
+      password = password,
+      api_call_request = api_call_request,
+      file.type = file.type,
+      wait = wait
+    )
 
 
   }

From 976d73fd8a4017036263fc0b0b5c28b1ed312b37 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 19 Jan 2023 17:04:54 +0000
Subject: [PATCH 006/203] changed file.type argument and variables to snake
 case

---
 R/get_cases.R | 31 +++++++++++++++----------------
 1 file changed, 15 insertions(+), 16 deletions(-)

diff --git a/R/get_cases.R b/R/get_cases.R
index 616fe73..4688289 100644
--- a/R/get_cases.R
+++ b/R/get_cases.R
@@ -10,7 +10,7 @@
 #'    Go.Data. This method relies on the GET outbreak/{id}/cases
 #'    API endpoint. Records are then retrieved in batches
 #'    based on `batch_size` and appended together into
-#'    a final dataset. `method="batches"` will be the default and
+#'    a final dataset. `method = "batches"` will be the default and
 #'    only available method for Go.Data version 2.38.0 or older.
 #'
 #' `method="export"` will only work on Go.Data versions
@@ -18,7 +18,7 @@
 #'    outbreak/{id}/cases/export API endpoint. An export
 #'    request is submitted to the server, and then when the
 #'    export is ready, it will be downloaded. Due to better
-#'    performance and more options, `method="export"` will
+#'    performance and more options, `method = "export"` will
 #'    be the default if you are using Go.Data version 2.38.1
 #'    or newer.
 #'
@@ -28,16 +28,16 @@
 #' @param password The password for your Go.Data login
 #' @param outbreak_id The id number for the outbreak for which you want to
 #' download data.
-#' @param method The method to download data. `method="export"` is the
+#' @param method The method to download data. `method = "export"` is the
 #' preferred and default method for Go.Data version 2.38.1 or later.
 #' See Details.
 #' @param batch_size If `method = "batches"`, then `batch_size` specifies the
 #' number of records to retrieve in each iteration.
 #' @param wait If `method = "export"`, then `wait` is the number of seconds to
 #' wait in between iterations of checking the status of the export.
-#' @param file.type If `method = "export"`, then `file.type` determines Whether
-#' the resulting data frame should contain nested fields (`file.type = "json"`,
-#' the default) or an entirely flat data structure (`file.type = "csv"`)
+#' @param file_type If `method = "export"`, then `file_type` determines Whether
+#' the resulting data frame should contain nested fields (`file_type = "json"`,
+#' the default) or an entirely flat data structure (`file_type = "csv"`)
 #'
 #' @return
 #' Returns a data frame. Some fields, such as addresses, hospitalization
@@ -73,7 +73,7 @@ get_cases <- function(url = url,
                       method = c("export", "batch"),
                       batch_size = 50000,
                       wait = 2,
-                      file.type = c("json", "csv")) {
+                      file_type = c("json", "csv")) {
 
   #Check that outbreak_id is active
   active_outbreak_id <- get_active_outbreak(
@@ -91,8 +91,8 @@ get_cases <- function(url = url,
   }
 
   #Set default method based on current version of Go.Data
-  version.check <- check_godata_version(url = url)
-  if (!version.check) {
+  version_check <- check_godata_version(url = url)
+  if (!version_check) {
     method <- "batches" #Older version of Go.Data can only use the batch method
   } else if (missing(method)) {
     method <- "export" # For new versions of Go.Data, default to export method
@@ -114,22 +114,21 @@ get_cases <- function(url = url,
 
   } else if (method == "export") {
 
-    #Default value of file.type is "json"
-    if (missing(file.type)) file.type <- "json"
+    # Default value of file_type is "json"
+    if (missing(file_type)) file_type <- "json"
 
     #Submit an export request to the system
-    api_call_request <- paste0(url, "api/outbreaks/", outbreak_id, "/cases/export")
+    api_call_request <- paste0(
+      url, "api/outbreaks/", outbreak_id, "/cases/export"
+    )
     df <- export_downloader(
       url = url,
       username = username,
       password = password,
       api_call_request = api_call_request,
-      file.type = file.type,
+      file_type = file_type,
       wait = wait
     )
-
-
   }
-
   return(df)
 }

From 56417f463ed067c4cbece30edb12658fcfa965f0 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 19 Jan 2023 17:05:18 +0000
Subject: [PATCH 007/203] updated get_cases documentation

---
 man/get_cases.Rd | 30 ++++++++++++++++++++----------
 1 file changed, 20 insertions(+), 10 deletions(-)

diff --git a/man/get_cases.Rd b/man/get_cases.Rd
index ca96123..6009004 100644
--- a/man/get_cases.Rd
+++ b/man/get_cases.Rd
@@ -12,28 +12,38 @@ get_cases(
   method = c("export", "batch"),
   batch_size = 50000,
   wait = 2,
-  file.type = c("json", "csv")
+  file_type = c("json", "csv")
 )
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here.
+Don't forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
 \item{password}{The password for your Go.Data login}
 
-\item{outbreak_id}{The id number for the outbreak for which you want to download data.}
+\item{outbreak_id}{The id number for the outbreak for which you want to
+download data.}
 
-\item{method}{The method to download data. \code{method="export"} is the preferred and default method for Go.Data version 2.38.1 or later. See Details.}
+\item{method}{The method to download data. \code{method = "export"} is the
+preferred and default method for Go.Data version 2.38.1 or later.
+See Details.}
 
-\item{batch_size}{If \code{method="batches"}, then \code{batch_size} specifies the number of records to retrieve in each iteration.}
+\item{batch_size}{If \code{method = "batches"}, then \code{batch_size} specifies the
+number of records to retrieve in each iteration.}
 
-\item{wait}{If \code{method="export"}, then \code{wait} is the number of seconds to wait in between iterations of checking the status of the export.}
+\item{wait}{If \code{method = "export"}, then \code{wait} is the number of seconds to
+wait in between iterations of checking the status of the export.}
 
-\item{file.type}{If \code{method="export"}, then \code{file.type} determines Whether the resulting data frame should contain nested fields (\code{file.type="json"}, the default) or an entirely flat data structure (\code{file.type="csv"})}
+\item{file_type}{If \code{method = "export"}, then \code{file_type} determines Whether
+the resulting data frame should contain nested fields (\code{file_type = "json"},
+the default) or an entirely flat data structure (\code{file_type = "csv"})}
 }
 \value{
-Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+Returns a data frame. Some fields, such as addresses, hospitalization
+history, and questionnaire fields may require further unnesting. See
+\verb{\link[tidyr]\{nest\}} for assitance with unnesting.
 }
 \description{
 A function to retrieve the case data for a
@@ -47,7 +57,7 @@ are two methods for downloading the data:
 Go.Data. This method relies on the GET outbreak/{id}/cases
 API endpoint. Records are then retrieved in batches
 based on \code{batch_size} and appended together into
-a final dataset. \code{method="batches"} will be the default and
+a final dataset. \code{method = "batches"} will be the default and
 only available method for Go.Data version 2.38.0 or older.
 
 \code{method="export"} will only work on Go.Data versions
@@ -55,7 +65,7 @@ only available method for Go.Data version 2.38.0 or older.
 outbreak/{id}/cases/export API endpoint. An export
 request is submitted to the server, and then when the
 export is ready, it will be downloaded. Due to better
-performance and more options, \code{method="export"} will
+performance and more options, \code{method = "export"} will
 be the default if you are using Go.Data version 2.38.1
 or newer.
 }

From 70bf9823dddd4b6b5b3be36d7541fde12ffae694 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 19 Jan 2023 17:13:09 +0000
Subject: [PATCH 008/203] remove imports that are not used in get_cases

---
 R/get_cases.R | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/R/get_cases.R b/R/get_cases.R
index 4688289..c8b69a3 100644
--- a/R/get_cases.R
+++ b/R/get_cases.R
@@ -57,15 +57,6 @@
 #'                    password=password,
 #'                    outbreak_id=outbreak_id)
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @import tibble
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
-
-
 get_cases <- function(url = url,
                       username = username,
                       password = password,

From 987cd451901ed8006858018687269283b20ef5e4 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 08:21:38 +0000
Subject: [PATCH 009/203] changed get_cases output from data frame to tibble

---
 R/get_cases.R                   | 12 +++++++-----
 man/get_cases.Rd                | 10 ++++++----
 tests/testthat/test-get_cases.R |  3 ++-
 3 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/R/get_cases.R b/R/get_cases.R
index c8b69a3..d04f0c6 100644
--- a/R/get_cases.R
+++ b/R/get_cases.R
@@ -52,10 +52,12 @@
 #' password <- "mypassword"
 #' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 #'
-#' cases <- get_cases(url=url,
-#'                    username=username,
-#'                    password=password,
-#'                    outbreak_id=outbreak_id)
+#' cases <- get_cases(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
 #' }
 get_cases <- function(url = url,
                       username = username,
@@ -121,5 +123,5 @@ get_cases <- function(url = url,
       wait = wait
     )
   }
-  return(df)
+  return(tibble::as_tibble(df))
 }
diff --git a/man/get_cases.Rd b/man/get_cases.Rd
index 6009004..aa28bbd 100644
--- a/man/get_cases.Rd
+++ b/man/get_cases.Rd
@@ -76,9 +76,11 @@ username <- "myemail@email.com"
 password <- "mypassword"
 outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 
-cases <- get_cases(url=url,
-                   username=username,
-                   password=password,
-                   outbreak_id=outbreak_id)
+cases <- get_cases(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
 }
 }
diff --git a/tests/testthat/test-get_cases.R b/tests/testthat/test-get_cases.R
index 631b19c..504cb8d 100644
--- a/tests/testthat/test-get_cases.R
+++ b/tests/testthat/test-get_cases.R
@@ -9,9 +9,10 @@ test_that("get_cases works as expected", {
     method = "export",
     batch_size = 50000,
     wait = 2,
-    file.type = "json"
+    file_type = "json"
   )
 
+  expect_s3_class(res, "tbl_df")
   expect_s3_class(res, "data.frame")
   expect_identical(dim(res), c(13L, 357L))
   expect_true(

From f32c6a31e71525dc38bf26e4c2ea9dbb95391198 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 08:56:41 +0000
Subject: [PATCH 010/203] linted get_active_outbreak

---
 R/get_active_outbreak.R | 39 ++++++++++++++++++++++++++-------------
 1 file changed, 26 insertions(+), 13 deletions(-)

diff --git a/R/get_active_outbreak.R b/R/get_active_outbreak.R
index a87b6a1..1b01f79 100644
--- a/R/get_active_outbreak.R
+++ b/R/get_active_outbreak.R
@@ -7,7 +7,8 @@
 #' housekeeping function used in many of the
 #' other `godataR` functions.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login.
 #'
@@ -20,9 +21,11 @@
 #' username <- "myemail@email.com"
 #' password <- "mypassword"
 #'
-#' active_outbreak_id <- get_active_outbreak(url=url,
-#'                                           username=username,
-#'                                           password=password)
+#' active_outbreak_id <- get_active_outbreak(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
 #' }
 #' @importFrom magrittr %>%
 #' @import dplyr
@@ -30,17 +33,27 @@
 #' @import httr
 #' @importFrom jsonlite fromJSON
 
-get_active_outbreak <- function(url=url,
-                                username=username,
-                                password=password) {
+get_active_outbreak <- function(url = url,
+                                username = username,
+                                password = password) {
 
-  users <- GET(paste0(url,"api/users",
-                          "?access_token=",get_access_token(url=url, username=username, password=password))) %>%
-    content(as="text") %>%
-    fromJSON(flatten=TRUE)
+  users <- GET(
+    paste0(
+      url,
+      "api/users",
+      "?access_token=",
+      get_access_token(
+        url = url,
+        username = username,
+        password = password
+      )
+    )
+  ) %>%
+    content(as = "text") %>%
+    fromJSON(flatten = TRUE)
 
-  active.outbreak <- users$activeOutbreakId[users$email==username]
+  active_outbreak <- users$activeOutbreakId[users$email == username]
 
-  return(active.outbreak)
+  return(active_outbreak)
 
 }

From fc26e4c751519c5ed80d71b32ddee144b7e72478 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 08:57:19 +0000
Subject: [PATCH 011/203] added tests for get_active_outbreak (skipped by
 default)

---
 tests/testthat/test-get_active_outbreak.R | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 tests/testthat/test-get_active_outbreak.R

diff --git a/tests/testthat/test-get_active_outbreak.R b/tests/testthat/test-get_active_outbreak.R
new file mode 100644
index 0000000..d000c2f
--- /dev/null
+++ b/tests/testthat/test-get_active_outbreak.R
@@ -0,0 +1,17 @@
+test_that("get_active_outbreak works as expected", {
+  skip("get_active_outbreak requires API call")
+
+  res <- get_active_outbreak(
+    url = url,
+    username = username,
+    password = password
+  )
+
+  expect_type(res, "character")
+  # character string can contain alphanumeric characters
+  expect_true(grepl(pattern = "[:alphanum:]", x = res))
+  # character string can contain punctuation marks
+  expect_true(grepl(pattern = "[:punct:]", x = res))
+  # character string cannot contain spaces
+  expect_false(grepl(pattern = "\\s", x = res))
+})

From ceb3a7f1e2761242067185a9ea3d79e199da84d1 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 08:59:44 +0000
Subject: [PATCH 012/203] removed pipes from get_active_outbreak

---
 R/get_active_outbreak.R | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/R/get_active_outbreak.R b/R/get_active_outbreak.R
index 1b01f79..05db1bb 100644
--- a/R/get_active_outbreak.R
+++ b/R/get_active_outbreak.R
@@ -32,12 +32,12 @@
 #' @import tidyr
 #' @import httr
 #' @importFrom jsonlite fromJSON
-
 get_active_outbreak <- function(url = url,
                                 username = username,
                                 password = password) {
 
-  users <- GET(
+
+  godata_url <- GET(
     paste0(
       url,
       "api/users",
@@ -48,9 +48,11 @@ get_active_outbreak <- function(url = url,
         password = password
       )
     )
-  ) %>%
-    content(as = "text") %>%
-    fromJSON(flatten = TRUE)
+  )
+
+  url_content <- content(godata_url, as = "text")
+
+  users <- fromJSON(url_content, flatten = TRUE)
 
   active_outbreak <- users$activeOutbreakId[users$email == username]
 

From 6f3066565058102f231f50dc07881345d59a3dbf Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 09:02:15 +0000
Subject: [PATCH 013/203] used explicit namespace instead of import in
 get_active_outbreak

---
 R/get_active_outbreak.R | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

diff --git a/R/get_active_outbreak.R b/R/get_active_outbreak.R
index 05db1bb..2df6c04 100644
--- a/R/get_active_outbreak.R
+++ b/R/get_active_outbreak.R
@@ -27,17 +27,11 @@
 #'   password = password
 #' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @importFrom jsonlite fromJSON
 get_active_outbreak <- function(url = url,
                                 username = username,
                                 password = password) {
 
-
-  godata_url <- GET(
+  godata_url <- httr::GET(
     paste0(
       url,
       "api/users",
@@ -50,12 +44,11 @@ get_active_outbreak <- function(url = url,
     )
   )
 
-  url_content <- content(godata_url, as = "text")
+  url_content <- httr::content(godata_url, as = "text")
 
-  users <- fromJSON(url_content, flatten = TRUE)
+  users <- jsonlite::fromJSON(url_content, flatten = TRUE)
 
   active_outbreak <- users$activeOutbreakId[users$email == username]
 
   return(active_outbreak)
-
 }

From 5cf6e5d7b6cf29fd6a4162f736d5a53c36824080 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 09:07:36 +0000
Subject: [PATCH 014/203] added comments to get_active_outbreak

---
 R/get_active_outbreak.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/R/get_active_outbreak.R b/R/get_active_outbreak.R
index 2df6c04..b28509f 100644
--- a/R/get_active_outbreak.R
+++ b/R/get_active_outbreak.R
@@ -31,6 +31,7 @@ get_active_outbreak <- function(url = url,
                                 username = username,
                                 password = password) {
 
+  # get request to go.data
   godata_url <- httr::GET(
     paste0(
       url,
@@ -44,10 +45,13 @@ get_active_outbreak <- function(url = url,
     )
   )
 
+  # unpack request as character string
   url_content <- httr::content(godata_url, as = "text")
 
+  # converts JSON string into data frame
   users <- jsonlite::fromJSON(url_content, flatten = TRUE)
 
+  # subset to active user
   active_outbreak <- users$activeOutbreakId[users$email == username]
 
   return(active_outbreak)

From f0606a1bf61c3d50b341e7bf446a1535d973f574 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 09:10:00 +0000
Subject: [PATCH 015/203] updated get_active_outbreak documentation

---
 man/get_active_outbreak.Rd | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/man/get_active_outbreak.Rd b/man/get_active_outbreak.Rd
index 1d93daa..185500c 100644
--- a/man/get_active_outbreak.Rd
+++ b/man/get_active_outbreak.Rd
@@ -7,7 +7,8 @@
 get_active_outbreak(url = url, username = username, password = password)
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
@@ -30,8 +31,10 @@ url <- "https://MyGoDataServer.com/"
 username <- "myemail@email.com"
 password <- "mypassword"
 
-active_outbreak_id <- get_active_outbreak(url=url,
-                                          username=username,
-                                          password=password)
+active_outbreak_id <- get_active_outbreak(
+  url = url,
+  username = username,
+  password = password
+)
 }
 }

From 00cca1b5bd308beffa96ec40965c532aa6e345e3 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 09:23:57 +0000
Subject: [PATCH 016/203] linted check_godata_version

---
 R/check_godata_version.R | 35 ++++++++++++++++++-----------------
 1 file changed, 18 insertions(+), 17 deletions(-)

diff --git a/R/check_godata_version.R b/R/check_godata_version.R
index 8557dae..1520530 100644
--- a/R/check_godata_version.R
+++ b/R/check_godata_version.R
@@ -5,7 +5,8 @@
 #' This is a housekeeping function used in
 #' many of the other `godataR` functions.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #'
 #' @return Boolean, where `TRUE` indicates version 2.38.1 or later.
 #' @examples
@@ -15,33 +16,33 @@
 #' }
 #' @importFrom magrittr %>%
 #' @importFrom stringr str_split
-check_godata_version <- function(url=url) {
+check_godata_version <- function(url = url) {
 
   # Get Current Version of Go.Data
-  gd.version <- get_godata_version(url=url)
+  gd_version <- get_godata_version(url = url)
 
   # Convert string to vector of 3 numbers
-  gd.version <- str_split(gd.version, "[.]") %>%
+  gd_version <- str_split(gd_version, "[.]") %>%
     unlist() %>%
     as.numeric()
 
   # Check if 2.38.1 or later
   # Should be TRUE if it is version 2.38.1 or later &
   # FALSE if version 2.38.0 or earlier
-  if (gd.version[1] < 2) {
-    after.2.38.1 <- FALSE
-  } else if (gd.version[1]==2 & gd.version[2] < 38) {
-    after.2.38.1 <- FALSE
-  } else if (gd.version[1]==2 & gd.version[2]==38 & gd.version[3]<1) {
-    after.2.38.1 <- FALSE
-  } else if (gd.version[1]==2 & gd.version[2]==38 & gd.version[3]>=1) {
-    after.2.38.1 <- TRUE
-  } else if (gd.version[1]==2 & gd.version[2]>38) {
-    after.2.38.1 <- TRUE
-  } else if (gd.version[1]>2) {
-    after.2.38.1 <- TRUE
+  if (gd_version[1] < 2) {
+    after_2_38_1 <- FALSE
+  } else if (gd_version[1] == 2 && gd_version[2] < 38) {
+    after_2_38_1 <- FALSE
+  } else if (gd_version[1] == 2 && gd_version[2] == 38 && gd_version[3] < 1) {
+    after_2_38_1 <- FALSE
+  } else if (gd_version[1] == 2 && gd_version[2] == 38 && gd_version[3] >= 1) {
+    after_2_38_1 <- TRUE
+  } else if (gd_version[1] == 2 && gd_version[2] > 38) {
+    after_2_38_1 <- TRUE
+  } else if (gd_version[1] > 2) {
+    after_2_38_1 <- TRUE
   }
 
-  return(after.2.38.1)
+  return(after_2_38_1)
 
 }

From 8ad29dc5861263616ffae5d8b8cdd7a6dc210b1b Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 09:24:12 +0000
Subject: [PATCH 017/203] updated documentation for check_godata_version

---
 man/check_godata_version.Rd | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/man/check_godata_version.Rd b/man/check_godata_version.Rd
index 42bbb5c..0a1b413 100644
--- a/man/check_godata_version.Rd
+++ b/man/check_godata_version.Rd
@@ -7,7 +7,8 @@
 check_godata_version(url = url)
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 }
 \value{
 Boolean, where \code{TRUE} indicates version 2.38.1 or later.

From b6dc35d88728b3e08ff7bdbafec8cbc5d4c4656b Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 09:24:35 +0000
Subject: [PATCH 018/203] added test for check_godata_version (skipped by
 default)

---
 tests/testthat/test-check_godata_version.R | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 tests/testthat/test-check_godata_version.R

diff --git a/tests/testthat/test-check_godata_version.R b/tests/testthat/test-check_godata_version.R
new file mode 100644
index 0000000..823650a
--- /dev/null
+++ b/tests/testthat/test-check_godata_version.R
@@ -0,0 +1,5 @@
+test_that("check_godata_version works as expected", {
+  skip("check_godata_version requires API call")
+
+  expect_true(check_godata_version(url = url))
+})

From 2833b13d7293237ff2ea95463200b03f925e6d6f Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 09:26:43 +0000
Subject: [PATCH 019/203] removed pipes from check_godata_version

---
 R/check_godata_version.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/check_godata_version.R b/R/check_godata_version.R
index 1520530..d6407ba 100644
--- a/R/check_godata_version.R
+++ b/R/check_godata_version.R
@@ -22,9 +22,9 @@ check_godata_version <- function(url = url) {
   gd_version <- get_godata_version(url = url)
 
   # Convert string to vector of 3 numbers
-  gd_version <- str_split(gd_version, "[.]") %>%
-    unlist() %>%
-    as.numeric()
+  gd_version <- str_split(gd_version, "[.]")
+
+  gd_version <- as.numeric(unlist(gd_version))
 
   # Check if 2.38.1 or later
   # Should be TRUE if it is version 2.38.1 or later &

From d1833a51a9a1b47abfd7169926484c4647e72393 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 09:30:44 +0000
Subject: [PATCH 020/203] used explicit namespace instead of import for
 check_godata_version

---
 NAMESPACE                | 1 -
 R/check_godata_version.R | 6 ++----
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 500a962..6c64574 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -42,5 +42,4 @@ import(urltools)
 importFrom(jsonlite,fromJSON)
 importFrom(magrittr,"%>%")
 importFrom(purrr,pluck)
-importFrom(stringr,str_split)
 importFrom(utils,read.csv)
diff --git a/R/check_godata_version.R b/R/check_godata_version.R
index d6407ba..00d8d15 100644
--- a/R/check_godata_version.R
+++ b/R/check_godata_version.R
@@ -12,17 +12,15 @@
 #' @examples
 #' \dontrun{
 #' url <- "https://MyGoDataServer.com/"
-#' check_godata_version(url=url)
+#' check_godata_version(url = url)
 #' }
-#' @importFrom magrittr %>%
-#' @importFrom stringr str_split
 check_godata_version <- function(url = url) {
 
   # Get Current Version of Go.Data
   gd_version <- get_godata_version(url = url)
 
   # Convert string to vector of 3 numbers
-  gd_version <- str_split(gd_version, "[.]")
+  gd_version <- stringr::str_split(gd_version, "[.]")
 
   gd_version <- as.numeric(unlist(gd_version))
 

From fb6581ff4d9395e21542e811b5da933dfc679310 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 09:31:07 +0000
Subject: [PATCH 021/203] updated documentation for check_godata_version

---
 man/check_godata_version.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/check_godata_version.Rd b/man/check_godata_version.Rd
index 0a1b413..46c6dff 100644
--- a/man/check_godata_version.Rd
+++ b/man/check_godata_version.Rd
@@ -22,6 +22,6 @@ many of the other \code{godataR} functions.
 \examples{
 \dontrun{
 url <- "https://MyGoDataServer.com/"
-check_godata_version(url=url)
+check_godata_version(url = url)
 }
 }

From f73a5244a54dfa79bff4c9db2a7109cfde0dea50 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 10:09:48 +0000
Subject: [PATCH 022/203] reduce cyclomatic complexity of check_godata_version

---
 R/check_godata_version.R | 19 ++++++-------------
 1 file changed, 6 insertions(+), 13 deletions(-)

diff --git a/R/check_godata_version.R b/R/check_godata_version.R
index 00d8d15..8cdd754 100644
--- a/R/check_godata_version.R
+++ b/R/check_godata_version.R
@@ -28,19 +28,12 @@ check_godata_version <- function(url = url) {
   # Should be TRUE if it is version 2.38.1 or later &
   # FALSE if version 2.38.0 or earlier
   if (gd_version[1] < 2) {
-    after_2_38_1 <- FALSE
+    return(FALSE)
   } else if (gd_version[1] == 2 && gd_version[2] < 38) {
-    after_2_38_1 <- FALSE
-  } else if (gd_version[1] == 2 && gd_version[2] == 38 && gd_version[3] < 1) {
-    after_2_38_1 <- FALSE
-  } else if (gd_version[1] == 2 && gd_version[2] == 38 && gd_version[3] >= 1) {
-    after_2_38_1 <- TRUE
-  } else if (gd_version[1] == 2 && gd_version[2] > 38) {
-    after_2_38_1 <- TRUE
-  } else if (gd_version[1] > 2) {
-    after_2_38_1 <- TRUE
+    return(FALSE)
+  } else if (gd_version[1] == 2 && gd_version[2] == 38 && gd_version[3] == 0) {
+    return(FALSE)
+  } else {
+    return(TRUE)
   }
-
-  return(after_2_38_1)
-
 }

From f6d894f0b7f19c4adfa570de77be22b92f527a7a Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 10:29:02 +0000
Subject: [PATCH 023/203] linted get_godata_version

---
 R/get_godata_version.R | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/R/get_godata_version.R b/R/get_godata_version.R
index 0ae96e0..260c7ee 100644
--- a/R/get_godata_version.R
+++ b/R/get_godata_version.R
@@ -5,7 +5,8 @@
 #' housekeeping function used in many of the
 #' other `godataR` functions.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #'
 #' @return string
 #' @export
@@ -13,22 +14,22 @@
 #' @examples
 #' \dontrun{
 #' url <- "https://MyGoDataServer.com/"
-#' get_godata_version(url=url)
+#' get_godata_version(url = url)
 #' }
 #' @import httr
 #' @importFrom jsonlite fromJSON
 #' @importFrom magrittr %>%
 
-get_godata_version <- function(url=url) {
+get_godata_version <- function(url = url) {
 
-  version.request <- GET(paste0(url,"api/system-settings/version"))
+  version_request <- GET(paste0(url, "api/system-settings/version"))
 
-  if (version.request$status_code==200) {
-    version <- content(version.request, as="text") %>%
-      fromJSON(flatten=TRUE)
+  if (version_request$status_code == 200) {
+    version <- content(version_request, as = "text") %>%
+      fromJSON(flatten = TRUE)
     return(version$version)
   } else {
-    stop(paste0("Error ",version.request$status_code))
+    stop(paste0("Error ", version_request$status_code))
   }
 
 }

From e1f79720e8388d85e0032333ff2c1f6765462c41 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 10:29:29 +0000
Subject: [PATCH 024/203] added test for get_godata_version (skipped by
 default)

---
 tests/testthat/test-get_godata_version.R | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 tests/testthat/test-get_godata_version.R

diff --git a/tests/testthat/test-get_godata_version.R b/tests/testthat/test-get_godata_version.R
new file mode 100644
index 0000000..6a8e862
--- /dev/null
+++ b/tests/testthat/test-get_godata_version.R
@@ -0,0 +1,13 @@
+test_that("get_godata_versions works as expected", {
+  skip("get_godata_version requires API call")
+
+  res <- get_godata_version(url = url)
+
+  expect_type(res, "character")
+  # character string can contain digits
+  expect_true(grepl(pattern = "\\d",x = res))
+  # character string can contain full stops
+  expect_true(grepl(pattern = ".", x = res))
+  # character string cannot contain alphabetic characters
+  expect_false(grepl(pattern = "[:alpha:]", x = res))
+})

From 95511f175cabb2caab6a45c90fc1841488a2fe2a Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 10:29:48 +0000
Subject: [PATCH 025/203] updated documentation for get_godata_version

---
 man/get_godata_version.Rd | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/man/get_godata_version.Rd b/man/get_godata_version.Rd
index 809e38f..db8cd2a 100644
--- a/man/get_godata_version.Rd
+++ b/man/get_godata_version.Rd
@@ -7,7 +7,8 @@
 get_godata_version(url = url)
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 }
 \value{
 string
@@ -21,6 +22,6 @@ other \code{godataR} functions.
 \examples{
 \dontrun{
 url <- "https://MyGoDataServer.com/"
-get_godata_version(url=url)
+get_godata_version(url = url)
 }
 }

From fefc74e642f89dbf580de26d088cc7038a09af2e Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 10:32:47 +0000
Subject: [PATCH 026/203] removed pipe from get_godata_version

---
 R/get_godata_version.R | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/R/get_godata_version.R b/R/get_godata_version.R
index 260c7ee..d4c8c7f 100644
--- a/R/get_godata_version.R
+++ b/R/get_godata_version.R
@@ -19,17 +19,15 @@
 #' @import httr
 #' @importFrom jsonlite fromJSON
 #' @importFrom magrittr %>%
-
 get_godata_version <- function(url = url) {
 
   version_request <- GET(paste0(url, "api/system-settings/version"))
 
   if (version_request$status_code == 200) {
-    version <- content(version_request, as = "text") %>%
-      fromJSON(flatten = TRUE)
+    version <- content(version_request, as = "text")
+    version <- fromJSON(version, flatten = TRUE)
     return(version$version)
   } else {
     stop(paste0("Error ", version_request$status_code))
   }
-
 }

From 6d5a167843c4756ff31079594820b8b5422d9d17 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 10:34:18 +0000
Subject: [PATCH 027/203] used explicit namespace instead of import in
 get_godata_version

---
 R/get_godata_version.R | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/R/get_godata_version.R b/R/get_godata_version.R
index d4c8c7f..375cabc 100644
--- a/R/get_godata_version.R
+++ b/R/get_godata_version.R
@@ -16,16 +16,13 @@
 #' url <- "https://MyGoDataServer.com/"
 #' get_godata_version(url = url)
 #' }
-#' @import httr
-#' @importFrom jsonlite fromJSON
-#' @importFrom magrittr %>%
 get_godata_version <- function(url = url) {
 
-  version_request <- GET(paste0(url, "api/system-settings/version"))
+  version_request <- httr::GET(paste0(url, "api/system-settings/version"))
 
   if (version_request$status_code == 200) {
-    version <- content(version_request, as = "text")
-    version <- fromJSON(version, flatten = TRUE)
+    version <- httr::content(version_request, as = "text")
+    version <- jsonlite::fromJSON(version, flatten = TRUE)
     return(version$version)
   } else {
     stop(paste0("Error ", version_request$status_code))

From 25edbda79d4b3f638c846581b1771307f1eed845 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 11:36:59 +0000
Subject: [PATCH 028/203] linted batch_downloader

---
 R/batch_downloader.R | 71 ++++++++++++++++++++++++++++++++------------
 1 file changed, 52 insertions(+), 19 deletions(-)

diff --git a/R/batch_downloader.R b/R/batch_downloader.R
index 86e4af6..2051e66 100644
--- a/R/batch_downloader.R
+++ b/R/batch_downloader.R
@@ -2,15 +2,19 @@
 #'
 #' A housekeeping function to do batch downloads.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
 #' @param api_call_n The API url to get the number of records.
 #' @param api_call_get The API url to GET the records.
-#' @param batch_size Specifies the number of records to retrieve in each iteration.
+#' @param batch_size Specifies the number of records to retrieve in each
+#' iteration.
 #'
 #' @return
-#' Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+#' Returns a data frame. Some fields, such as addresses, hospitalization
+#' history, and questionnaire fields may require further unnesting. See
+#' `\link[tidyr]{nest}` for assitance with unnesting.
 #'
 #' @examples
 #' \dontrun{
@@ -41,44 +45,73 @@ batch_downloader <- function(url = url,
                              batch_size = batch_size) {
 
   #get total number of records
-  df_n <- GET(paste0(api_call_n),
-              add_headers(Authorization = paste("Bearer", get_access_token(url=url, username=username, password=password), sep = " "))) %>%
-    content(as="text") %>%
-    fromJSON(flatten=TRUE) %>%
+  df_n <- GET(
+    paste0(api_call_n),
+    add_headers(
+      Authorization = paste("Bearer", get_access_token(
+        url = url,
+        username = username,
+        password = password
+      ), sep = " "))) %>%
+    content(as = "text") %>%
+    fromJSON(flatten = TRUE) %>%
     unlist() %>%
     unname()
 
   #Import records in batches
   df <- tibble()
   batch_size <- batch_size # number of records to import per iteration
-  skip <-0
+  skip <- 0
   message("****************************")
 
   #Download records in batches, and then append them into a single dataset
   while (skip < df_n) {
 
     #Progress message
-    if (df_n <= batch_size) message(paste0("...downloading records 1 to ",df_n))
-    if (df_n > batch_size)     message(paste0("...downloading records ", as.character(skip+1, scientific = FALSE), " to ", format(skip+batch_size, scientific = FALSE)))
+    if (df_n <= batch_size) {
+      message(paste0("...downloading records 1 to ", df_n))
+    }
+    if (df_n > batch_size) {
+      message(
+        paste0(
+          "...downloading records ",
+          as.character(skip + 1, scientific = FALSE),
+          " to ",
+          format(skip + batch_size, scientific = FALSE)
+        )
+      )
+    }
 
     #fetch the batch of records
-    df.i <- GET(paste0(api_call_get,
-                       "?filter={%22limit%22:",format(batch_size, scientific = FALSE),",%22skip%22:",format(skip, scientific = FALSE),"}"),
-                add_headers(Authorization = paste("Bearer", get_access_token(url=url, username=username, password=password), sep = " "))) %>%
-      content(as='text') %>%
-      fromJSON( flatten=TRUE) %>%
+    df_i <- GET(
+      paste0(
+        api_call_get,
+        "?filter={%22limit%22:",
+        format(batch_size, scientific = FALSE),
+        ",%22skip%22:",
+        format(skip, scientific = FALSE),
+        "}"
+      ),
+      add_headers(
+        Authorization = paste("Bearer", get_access_token(
+          url = url,
+          username = username,
+          password = password),
+          sep = " ")
+      )
+    ) %>%
+      content(as = "text") %>%
+      fromJSON(flatten = TRUE) %>%
       as_tibble()
 
     #append the new batch of records to the existing data frame
     df <- df %>%
-      bind_rows(df.i)
+      bind_rows(df_i)
 
     #update numbers for the next iteration
     skip <- skip + batch_size
-    rm(df.i)
+    rm(df_i)
   }
   rm(batch_size, skip, df_n)
   return(df)
 }
-
-

From d75335fd3165755d978ed26a45651f20e5262d4c Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 11:37:23 +0000
Subject: [PATCH 029/203] added tests for batch_downloader

---
 tests/testthat/test-batch_downloader.R | 157 +++++++++++++++++++++++++
 1 file changed, 157 insertions(+)
 create mode 100644 tests/testthat/test-batch_downloader.R

diff --git a/tests/testthat/test-batch_downloader.R b/tests/testthat/test-batch_downloader.R
new file mode 100644
index 0000000..e7da9d4
--- /dev/null
+++ b/tests/testthat/test-batch_downloader.R
@@ -0,0 +1,157 @@
+test_that("batch_downloader works as expected", {
+  skip("batch_downloader requires API call")
+
+  api_call_n <- paste0(url, "api/outbreaks/", outbreak_id, "/cases/count")
+  api_call_get <- paste0(url, "api/outbreaks/", outbreak_id, "/cases")
+  res <- batch_downloader(
+    url = url,
+    username = username,
+    password = password,
+    api_call_n = api_call_n,
+    api_call_get = api_call_get,
+    batch_size = 50000
+  )
+
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(13L, 153L))
+  expect_identical(
+    colnames(res),
+    c("firstName", "gender", "wasContact", "safeBurial", "classification",
+      "investigationStatus", "riskLevel", "transferRefused", "vaccinesReceived",
+      "id", "outbreakId", "visualId", "lastName", "dob", "occupation",
+      "documents", "addresses", "dateOfReporting",
+      "isDateOfReportingApproximate", "dateOfLastContact", "dateOfOnset",
+      "dateRanges", "classificationHistory", "hasRelationships",
+      "relationshipsRepresentation", "numberOfExposures", "numberOfContacts",
+      "usualPlaceOfResidenceLocationId", "responsibleUserId", "createdAt",
+      "createdBy", "updatedAt", "updatedBy", "createdOn", "deleted",
+      "dateBecomeCase", "wasCase", "active", "followUpHistory",
+      "isDateOfOnsetApproximate", "outcomeId", "riskReason", "pregnancyStatus",
+      "dateOfOutcome", "dateOfInfection", "middleName",
+      "questionnaireAnswers.would_you_like_to_complete_who_basic_case_questionnaire",
+      "questionnaireAnswers.Case_WhichForm",
+      "questionnaireAnswers.report_test_reason",
+      "questionnaireAnswers.Comcond_present",
+      "questionnaireAnswers.patinfo_occuhcw",
+      "questionnaireAnswers.expo_travel",
+      "questionnaireAnswers.expo_visit_healthcare",
+      "questionnaireAnswers.patcourse", "questionnaireAnswers.Comcond_select",
+      "questionnaireAnswers.specify_places_and_dates_for_up_to_3_locations_below",
+      "questionnaireAnswers.expo_travel_country1",
+      "questionnaireAnswers.expo_travel_city1",
+      "questionnaireAnswers.expo_travel_date1",
+      "questionnaireAnswers.FA0_UniqueIDClustNumber",
+      "questionnaireAnswers.FA0_datacollector_name",
+      "questionnaireAnswers.FA0_datacollector_institution",
+      "questionnaireAnswers.FA0_datacollector_telephone",
+      "questionnaireAnswers.FA0_datacollector_email",
+      "questionnaireAnswers.FA0_caseidentifier_email",
+      "questionnaireAnswers.FA0_caseidentifier_socialnumber",
+      "questionnaireAnswers.FA0_case_countryresidence",
+      "questionnaireAnswers.FA0_respondent_ispatient",
+      "questionnaireAnswers.FA0_symptoms_caseshowssymptoms",
+      "questionnaireAnswers.FA0_respiratorysample_collectedYN",
+      "questionnaireAnswers.FA0_clinicalcomplications_ARDS",
+      "questionnaireAnswers.FA0_clinicalcomplications_pneumoniachestXray",
+      "questionnaireAnswers.FA0_symptom_fever",
+      "questionnaireAnswers.FA0_symptom_sorethroat",
+      "questionnaireAnswers.FA0_symptom_runnynose",
+      "questionnaireAnswers.FA0_symptom_cough",
+      "questionnaireAnswers.FA0_symptom_shortnessofbreath",
+      "questionnaireAnswers.FA0_symptom_vomiting",
+      "questionnaireAnswers.FA0_symptom_nausea",
+      "questionnaireAnswers.FA0_symptom_diarrhea",
+      "questionnaireAnswers.FA0_symptom_taste", "questionnaireAnswers.test",
+      "questionnaireAnswers.which_date_omicron_was_found",
+      "questionnaireAnswers.place_of_death",
+      "questionnaireAnswers.patinfo_occuhcw_country",
+      "questionnaireAnswers.patinfo_occuhcw_city",
+      "questionnaireAnswers.patinfo_occuhcw_name",
+      "questionnaireAnswers.country_2",
+      "questionnaireAnswers.city_2", "questionnaireAnswers.date_2",
+      "questionnaireAnswers.FA1_UniqueIDClustNumber",
+      "questionnaireAnswers.FA1_FurtherCaseClassification",
+      "questionnaireAnswers.FA1_datacollector_name",
+      "questionnaireAnswers.FA1_datacollector_institution",
+      "questionnaireAnswers.FA1_datacollector_telephone",
+      "questionnaireAnswers.FA1_datacollector_email",
+      "questionnaireAnswers.FA1_respondent_ispatient",
+      "questionnaireAnswers.FA1_caseidentifier_email",
+      "questionnaireAnswers.FA1_caseidentifier_socialnumber",
+      "questionnaireAnswers.FA1_case_countryresidence",
+      "questionnaireAnswers.FA1_case_nationality",
+      "questionnaireAnswers.FA1_case_ethnicity",
+      "questionnaireAnswers.FA1_case_responsiblehealthcentre",
+      "questionnaireAnswers.FA1_case_nurseryschoolcollege",
+      "questionnaireAnswers.FA1_carecentre_practicename",
+      "questionnaireAnswers.FA1_carecentre_treatingphysicianname",
+      "questionnaireAnswers.FA1_carecentre_casepartofoutbreak",
+      "questionnaireAnswers.FA1_carecentre_telephone",
+      "questionnaireAnswers.FA1_carecentre_fax",
+      "questionnaireAnswers.FA1_carecentre_address",
+      "questionnaireAnswers.FA1_symptoms_caseshowssymptoms",
+      "questionnaireAnswers.FA1_symptoms_healthfacilityvisitedYN",
+      "questionnaireAnswers.FA1_complications_mechanicalventilation",
+      "questionnaireAnswers.FA1_complications_ARDS",
+      "questionnaireAnswers.FA1_complications_acuterenalfailure",
+      "questionnaireAnswers.FA1_complications_cardiacfailure",
+      "questionnaireAnswers.FA1_complications_consumptivecoagulopathy",
+      "questionnaireAnswers.FA1_complications_pneumoniachestXray",
+      "questionnaireAnswers.FA1_complications_other",
+      "questionnaireAnswers.FA1_complications_EMOrequired",
+      "questionnaireAnswers.FA1_complications_hypotensionrequiringvasopressors",
+      "questionnaireAnswers.FA1_preexistingconditions_obesity",
+      "questionnaireAnswers.FA1_preexistingconditions_cancer",
+      "questionnaireAnswers.FA1_preexistingconditions_diabetes",
+      "questionnaireAnswers.FA1_preexistingconditions_HIVotherimmunedeficiency",
+      "questionnaireAnswers.FA1_preexistingconditions_heartdisease",
+      "questionnaireAnswers.FA1_preexistingconditions_asthmarequiringmedication",
+      "questionnaireAnswers.FA1_preexistingconditions_chroniclungdiseasenonasthma",
+      "questionnaireAnswers.FA1_preexistingconditions_chronicliverdisease",
+      "questionnaireAnswers.FA1_preexistingconditions_chronichaematologicaldisorder",
+      "questionnaireAnswers.FA1_preexistingconditions_chronickidneydisease",
+      "questionnaireAnswers.FA1_preexistingconditions_chronicneurological",
+      "questionnaireAnswers.FA1_preexistingconditions_organorbonemarrowrecipient",
+      "questionnaireAnswers.FA1_preexistingconditions_otherpreexistingcondition",
+      "questionnaireAnswers.FA1_healthcareinteractions_contactemergencynumber",
+      "questionnaireAnswers.FA1_priorXdayexposure_travelleddomestically",
+      "questionnaireAnswers.FA1_priorXdayexposure_travelledinternationally",
+      "questionnaireAnswers.FA1_priorXdayexposure_contactwithcase",
+      "questionnaireAnswers.FA1_priorXdayexposure_massgathering",
+      "questionnaireAnswers.FA1_priorXdayexposure_exposedtosimilarillness",
+      "questionnaireAnswers.FA1_priorXdayexposure_locationexposure",
+      "questionnaireAnswers.FA1_priorXdayexposure_inpatient",
+      "questionnaireAnswers.FA1_priorXdayexposure_outpatient",
+      "questionnaireAnswers.FA1_priorXdayexposure_traditionalhealer",
+      "questionnaireAnswers.FA1_formcompleted", "age.years", "age.months",
+      "duplicateKeys.name", "duplicateKeys.document",
+      "followUp.originalStartDate", "followUp.startDate", "followUp.endDate",
+      "followUp.status")
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "character", "logical", "logical", "character", "character",
+      "character", "logical", "list", "character", "character", "character",
+      "character", "character", "character", "list", "list", "character",
+      "logical", "character", "character", "list", "list", "logical", "list",
+      "integer", "integer", "character", "character", "character", "character",
+      "character", "character", "character", "logical", "character", "logical",
+      "logical", "list", "logical", "character", "character", "character",
+      "character", "character", "character", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "integer", "integer", "list",
+      "list", "character", "character", "character", "character")
+  )
+})

From 7749434c4a55411ce90c7bcb5b242a016f57e2f2 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 11:38:39 +0000
Subject: [PATCH 030/203] updated batch_downloader documentation

---
 R/batch_downloader.R    | 10 ++++++----
 man/batch_downloader.Rd | 20 +++++++++++++-------
 2 files changed, 19 insertions(+), 11 deletions(-)

diff --git a/R/batch_downloader.R b/R/batch_downloader.R
index 2051e66..b843b90 100644
--- a/R/batch_downloader.R
+++ b/R/batch_downloader.R
@@ -23,10 +23,12 @@
 #' password <- "mypassword"
 #' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 #'
-#' cases <- get_cases(url=url,
-#'                    username=username,
-#'                    password=password,
-#'                    outbreak_id=outbreak_id)
+#' cases <- get_cases(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
 #' }
 #' @importFrom magrittr %>%
 #' @import dplyr
diff --git a/man/batch_downloader.Rd b/man/batch_downloader.Rd
index e70e3de..dc6b191 100644
--- a/man/batch_downloader.Rd
+++ b/man/batch_downloader.Rd
@@ -14,7 +14,8 @@ batch_downloader(
 )
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
@@ -24,10 +25,13 @@ batch_downloader(
 
 \item{api_call_get}{The API url to GET the records.}
 
-\item{batch_size}{Specifies the number of records to retrieve in each iteration.}
+\item{batch_size}{Specifies the number of records to retrieve in each
+iteration.}
 }
 \value{
-Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+Returns a data frame. Some fields, such as addresses, hospitalization
+history, and questionnaire fields may require further unnesting. See
+\verb{\link[tidyr]\{nest\}} for assitance with unnesting.
 }
 \description{
 A housekeeping function to do batch downloads.
@@ -39,9 +43,11 @@ username <- "myemail@email.com"
 password <- "mypassword"
 outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 
-cases <- get_cases(url=url,
-                   username=username,
-                   password=password,
-                   outbreak_id=outbreak_id)
+cases <- get_cases(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
 }
 }

From 984d667961ad904d54c72fed5105d717d314255f Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 11:40:14 +0000
Subject: [PATCH 031/203] removed recursive argument defaults for
 batch_downloader

---
 R/batch_downloader.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/batch_downloader.R b/R/batch_downloader.R
index b843b90..700f0ac 100644
--- a/R/batch_downloader.R
+++ b/R/batch_downloader.R
@@ -39,12 +39,12 @@
 #' @importFrom purrr pluck
 #'
 #'
-batch_downloader <- function(url = url,
-                             username = username,
-                             password = password,
-                             api_call_n = api_call_n,
-                             api_call_get = api_call_get,
-                             batch_size = batch_size) {
+batch_downloader <- function(url,
+                             username,
+                             password,
+                             api_call_n,
+                             api_call_get,
+                             batch_size) {
 
   #get total number of records
   df_n <- GET(

From 0d54ffbaa05a0cc59d06f017ec061c115e778716 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 11:58:14 +0000
Subject: [PATCH 032/203] removed pipes from batch_downloader and renamed some
 variables

---
 R/batch_downloader.R | 42 ++++++++++++++++++++++--------------------
 1 file changed, 22 insertions(+), 20 deletions(-)

diff --git a/R/batch_downloader.R b/R/batch_downloader.R
index 700f0ac..96bcb89 100644
--- a/R/batch_downloader.R
+++ b/R/batch_downloader.R
@@ -46,19 +46,19 @@ batch_downloader <- function(url,
                              api_call_get,
                              batch_size) {
 
-  #get total number of records
-  df_n <- GET(
+  num_record_request <- GET(
     paste0(api_call_n),
     add_headers(
       Authorization = paste("Bearer", get_access_token(
         url = url,
         username = username,
         password = password
-      ), sep = " "))) %>%
-    content(as = "text") %>%
-    fromJSON(flatten = TRUE) %>%
-    unlist() %>%
-    unname()
+      ), sep = " ")))
+
+  num_record_content <- content(record_request, as = "text")
+
+  num_records <- fromJSON(record_content, flatten = TRUE)
+  num_records <- records$count
 
   #Import records in batches
   df <- tibble()
@@ -67,13 +67,13 @@ batch_downloader <- function(url,
   message("****************************")
 
   #Download records in batches, and then append them into a single dataset
-  while (skip < df_n) {
+  while (skip < num_records) {
 
     #Progress message
-    if (df_n <= batch_size) {
-      message(paste0("...downloading records 1 to ", df_n))
+    if (num_records <= batch_size) {
+      message(paste0("...downloading records 1 to ", num_records))
     }
-    if (df_n > batch_size) {
+    if (num_records > batch_size) {
       message(
         paste0(
           "...downloading records ",
@@ -85,7 +85,7 @@ batch_downloader <- function(url,
     }
 
     #fetch the batch of records
-    df_i <- GET(
+    record_request <- GET(
       paste0(
         api_call_get,
         "?filter={%22limit%22:",
@@ -101,19 +101,21 @@ batch_downloader <- function(url,
           password = password),
           sep = " ")
       )
-    ) %>%
-      content(as = "text") %>%
-      fromJSON(flatten = TRUE) %>%
-      as_tibble()
+    )
+
+    record_content <- content(cases_request, as = "text")
+
+    records <- fromJSON(cases_content, flatten = TRUE)
+
+    records <- as_tibble(cases)
 
     #append the new batch of records to the existing data frame
-    df <- df %>%
-      bind_rows(df_i)
+    df <- bind_rows(df, records)
 
     #update numbers for the next iteration
     skip <- skip + batch_size
-    rm(df_i)
+    rm(records)
   }
-  rm(batch_size, skip, df_n)
+  rm(batch_size, skip, num_records)
   return(df)
 }

From 8a9424feb66bfeb3a087c595201a9293e3267c17 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 12:03:29 +0000
Subject: [PATCH 033/203] used explicit namespace instead of import for
 batch_downloader

---
 R/batch_downloader.R | 31 +++++++++++--------------------
 1 file changed, 11 insertions(+), 20 deletions(-)

diff --git a/R/batch_downloader.R b/R/batch_downloader.R
index 96bcb89..6ea5ba0 100644
--- a/R/batch_downloader.R
+++ b/R/batch_downloader.R
@@ -30,15 +30,6 @@
 #'   outbreak_id = outbreak_id
 #' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @import tibble
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
-#'
-#'
 batch_downloader <- function(url,
                              username,
                              password,
@@ -46,22 +37,22 @@ batch_downloader <- function(url,
                              api_call_get,
                              batch_size) {
 
-  num_record_request <- GET(
+  num_record_request <- httr::GET(
     paste0(api_call_n),
-    add_headers(
+    httr::add_headers(
       Authorization = paste("Bearer", get_access_token(
         url = url,
         username = username,
         password = password
       ), sep = " ")))
 
-  num_record_content <- content(record_request, as = "text")
+  num_record_content <- httr::content(record_request, as = "text")
 
-  num_records <- fromJSON(record_content, flatten = TRUE)
+  num_records <- jsonlite::fromJSON(record_content, flatten = TRUE)
   num_records <- records$count
 
   #Import records in batches
-  df <- tibble()
+  df <- tibble::tibble()
   batch_size <- batch_size # number of records to import per iteration
   skip <- 0
   message("****************************")
@@ -85,7 +76,7 @@ batch_downloader <- function(url,
     }
 
     #fetch the batch of records
-    record_request <- GET(
+    record_request <- httr::GET(
       paste0(
         api_call_get,
         "?filter={%22limit%22:",
@@ -94,7 +85,7 @@ batch_downloader <- function(url,
         format(skip, scientific = FALSE),
         "}"
       ),
-      add_headers(
+      httr::add_headers(
         Authorization = paste("Bearer", get_access_token(
           url = url,
           username = username,
@@ -103,14 +94,14 @@ batch_downloader <- function(url,
       )
     )
 
-    record_content <- content(cases_request, as = "text")
+    record_content <- httr::content(cases_request, as = "text")
 
-    records <- fromJSON(cases_content, flatten = TRUE)
+    records <- jsonlite::fromJSON(cases_content, flatten = TRUE)
 
-    records <- as_tibble(cases)
+    records <- tibble::as_tibble(cases)
 
     #append the new batch of records to the existing data frame
-    df <- bind_rows(df, records)
+    df <- dplyr::bind_rows(df, records)
 
     #update numbers for the next iteration
     skip <- skip + batch_size

From a974cfbfb75b23f48e1bfa403516cc51e2364b8f Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 12:06:38 +0000
Subject: [PATCH 034/203] removed manual removing of variables in
 batch_downloader

---
 R/batch_downloader.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/batch_downloader.R b/R/batch_downloader.R
index 6ea5ba0..9d4dd35 100644
--- a/R/batch_downloader.R
+++ b/R/batch_downloader.R
@@ -107,6 +107,5 @@ batch_downloader <- function(url,
     skip <- skip + batch_size
     rm(records)
   }
-  rm(batch_size, skip, num_records)
   return(df)
 }

From f2165f8f68748344ef528dfd2a45ee21a238d37a Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 12:12:05 +0000
Subject: [PATCH 035/203] set to NULL rather than rm variable in
 batch_downloader

---
 R/batch_downloader.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/batch_downloader.R b/R/batch_downloader.R
index 9d4dd35..4152b7b 100644
--- a/R/batch_downloader.R
+++ b/R/batch_downloader.R
@@ -105,7 +105,7 @@ batch_downloader <- function(url,
 
     #update numbers for the next iteration
     skip <- skip + batch_size
-    rm(records)
+    records <- NULL
   }
   return(df)
 }

From a5ce035a19ab09b05c826bd2be08551038492da3 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 12:13:00 +0000
Subject: [PATCH 036/203] updated documentation for batch_downloader

---
 man/batch_downloader.Rd | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/man/batch_downloader.Rd b/man/batch_downloader.Rd
index dc6b191..c1f83c7 100644
--- a/man/batch_downloader.Rd
+++ b/man/batch_downloader.Rd
@@ -4,14 +4,7 @@
 \alias{batch_downloader}
 \title{Function to manage batch downloads}
 \usage{
-batch_downloader(
-  url = url,
-  username = username,
-  password = password,
-  api_call_n = api_call_n,
-  api_call_get = api_call_get,
-  batch_size = batch_size
-)
+batch_downloader(url, username, password, api_call_n, api_call_get, batch_size)
 }
 \arguments{
 \item{url}{Insert the base URL for your instance of Go.Data here. Don't

From 7e04fbc8feb6b82a68ce1f68f670ead206538d6b Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 12:17:34 +0000
Subject: [PATCH 037/203] fixed variable names in batch_downloader

---
 R/batch_downloader.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/batch_downloader.R b/R/batch_downloader.R
index 4152b7b..551fa90 100644
--- a/R/batch_downloader.R
+++ b/R/batch_downloader.R
@@ -46,10 +46,10 @@ batch_downloader <- function(url,
         password = password
       ), sep = " ")))
 
-  num_record_content <- httr::content(record_request, as = "text")
+  num_record_content <- httr::content(num_record_request, as = "text")
 
-  num_records <- jsonlite::fromJSON(record_content, flatten = TRUE)
-  num_records <- records$count
+  num_records <- jsonlite::fromJSON(num_record_content, flatten = TRUE)
+  num_records <- num_records$count
 
   #Import records in batches
   df <- tibble::tibble()
@@ -94,11 +94,11 @@ batch_downloader <- function(url,
       )
     )
 
-    record_content <- httr::content(cases_request, as = "text")
+    record_content <- httr::content(record_request, as = "text")
 
-    records <- jsonlite::fromJSON(cases_content, flatten = TRUE)
+    records <- jsonlite::fromJSON(record_content, flatten = TRUE)
 
-    records <- tibble::as_tibble(cases)
+    records <- tibble::as_tibble(records)
 
     #append the new batch of records to the existing data frame
     df <- dplyr::bind_rows(df, records)

From 2a0ab13adb72c00d90fe95dc3c9d527208b42afa Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 12:19:14 +0000
Subject: [PATCH 038/203] removed redundant assignment in batch_downloader

---
 R/batch_downloader.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/batch_downloader.R b/R/batch_downloader.R
index 551fa90..50fd60f 100644
--- a/R/batch_downloader.R
+++ b/R/batch_downloader.R
@@ -53,7 +53,6 @@ batch_downloader <- function(url,
 
   #Import records in batches
   df <- tibble::tibble()
-  batch_size <- batch_size # number of records to import per iteration
   skip <- 0
   message("****************************")
 

From 7ae103bde3362c3a9ac2a1e197bcf3930e88ed4c Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 13:45:25 +0000
Subject: [PATCH 039/203] linted export_downloader

---
 R/export_downloader.R | 125 ++++++++++++++++++++++++++++++++----------
 1 file changed, 96 insertions(+), 29 deletions(-)

diff --git a/R/export_downloader.R b/R/export_downloader.R
index 8bfa28a..b122c90 100644
--- a/R/export_downloader.R
+++ b/R/export_downloader.R
@@ -2,15 +2,21 @@
 #'
 #' A housekeeping function to do export requests & downloads.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
 #' @param api_call_request The API url to get the number of records.
-#' @param wait The number of seconds to wait in between iterations of checking the status of the export.
-#' @param file.type Whether the resulting data frame should contain nested fields (`file.type="json"`, the default) or an entirely flat data structure (`file.type="csv"`)
-
+#' @param wait The number of seconds to wait in between iterations of checking
+#' the status of the export.
+#' @param file.type Whether the resulting data frame should contain nested
+#' fields (`file.type = "json"`, the default) or an entirely flat data structure
+#' (`file.type = "csv"`)
+#'
 #' @return
-#' Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+#' Returns a data frame. Some fields, such as addresses, hospitalization
+#' history, and questionnaire fields may require further unnesting. See
+#' `\link[tidyr]{nest}` for assitance with unnesting.
 #'
 #' @examples
 #' \dontrun{
@@ -19,10 +25,12 @@
 #' password <- "mypassword"
 #' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 #'
-#' cases <- get_cases(url=url,
-#'                    username=username,
-#'                    password=password,
-#'                    outbreak_id=outbreak_id)
+#' cases <- get_cases(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
 #' }
 #' @importFrom magrittr %>%
 #' @import dplyr
@@ -32,8 +40,6 @@
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
 #' @importFrom utils read.csv
-#'
-#'
 export_downloader <- function(url = url,
                              username = username,
                              password = password,
@@ -41,37 +47,100 @@ export_downloader <- function(url = url,
                              wait = wait,
                              file.type = file.type) {
 
-  request_id <- GET(paste0(api_call_request,
-                           "?filter=%7B%22where%22%3A%7B%22useDbColumns%22%3A%22true%22%2C%20%22dontTranslateValues%22%3A%22true%22%2C%20%22jsonReplaceUndefinedWithNull%22%3A%22true%22%20%7D%7D",
-                           "&type=",file.type,
-                           "&access_token=",get_access_token(url=url, username=username, password=password))) %>%
+  request_id <- GET(
+    paste0(
+      api_call_request,
+      "?filter=%7B%22where%22%3A%7B%22useDbColumns%22%3A%22true%22%2C%20%22",
+      "dontTranslateValues%22%3A%22true%22%2C%20%22",
+      "jsonReplaceUndefinedWithNull%22%3A%22true%22%20%7D%7D",
+      "&type=",
+      file.type,
+      "&access_token=",
+      get_access_token(
+        url = url,
+        username = username,
+        password = password
+      )
+    )
+  ) %>%
     content() %>%
     pluck("exportLogId")
 
 
   #Check status of request periodcially, until finished
-  #function argument 'wait' determines the number of seconds to wait between iterations
-  export.request.status <- get_export_status(url=url, username=username, password=password, request_id=request_id)
+  #function argument 'wait' determines the number of seconds to wait between
+  #iterations
+  export_request_status <- get_export_status(
+    url = url,
+    username = username,
+    password = password,
+    request_id = request_id
+  )
 
-  while(export.request.status$statusStep != "LNG_STATUS_STEP_EXPORT_FINISHED") {
+  status_step <- export_request_status$statusStep
+  while (status_step != "LNG_STATUS_STEP_EXPORT_FINISHED") {
     Sys.sleep(wait)
-    export.request.status <- GET(paste0(url,"api/export-logs/",request_id,"?access_token=",get_access_token(url=url, username=username, password=password))) %>%
+    export_request_status <- GET(
+      paste0(
+        url,
+        "api/export-logs/",
+        request_id,
+        "?access_token=",
+        get_access_token(
+          url = url,
+          username = username,
+          password = password
+        )
+      )
+    ) %>%
       content()
-    message(paste0("...processed ",export.request.status$processedNo, " of ", export.request.status$totalNo, " records"))
+    message(
+      paste0(
+        "...processed ",
+        export_request_status$processedNo,
+        " of ",
+        export_request_status$totalNo,
+        " records"
+      )
+    )
   }
 
   #Download the export
   message("...beginning download")
-  if (file.type=="json") {
-    df <- GET(paste0(url,"api/export-logs/",request_id,"/download?access_token=",get_access_token(url=url, username=username, password=password))) %>%
-      content("text", encoding="UTF-8") %>%
-      fromJSON(flatten=TRUE)
+  if (file.type == "json") {
+    df <- GET(
+      paste0(
+        url,
+        "api/export-logs/",
+        request_id,
+        "/download?access_token=",
+        get_access_token(
+          url = url,
+          username = username,
+          password = password
+        )
+      )
+    ) %>%
+      content("text", encoding = "UTF-8") %>%
+      fromJSON(flatten = TRUE)
 
     # fix one strange variable name
     names(df)[names(df) %in% "_id"] <- "id"
-  } else if (file.type=="csv") {
-    df <- GET(paste0(url,"api/export-logs/",request_id,"/download?access_token=",get_access_token(url=url, username=username, password=password))) %>%
-      content("text", encoding="UTF-8") %>%
+  } else if (file.type == "csv") {
+    df <- GET(
+      paste0(
+        url,
+        "api/export-logs/",
+        request_id,
+        "/download?access_token=",
+        get_access_token(
+          url = url,
+          username = username,
+          password = password
+        )
+      )
+    ) %>%
+      content("text", encoding = "UTF-8") %>%
       textConnection() %>%
       read.csv()
     names(df)[names(df) %in% "X_id"] <- "id"
@@ -80,5 +149,3 @@ export_downloader <- function(url = url,
   message("...download complete!")
   return(df)
 }
-
-

From 2fb3a39cb9515a0ca4584116d2e43ffb37e4a095 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 13:46:01 +0000
Subject: [PATCH 040/203] added tests for export_downloader (skipped by
 default)

---
 tests/testthat/test-export_downloader.R | 96 +++++++++++++++++++++++++
 1 file changed, 96 insertions(+)
 create mode 100644 tests/testthat/test-export_downloader.R

diff --git a/tests/testthat/test-export_downloader.R b/tests/testthat/test-export_downloader.R
new file mode 100644
index 0000000..90b02c4
--- /dev/null
+++ b/tests/testthat/test-export_downloader.R
@@ -0,0 +1,96 @@
+test_that("export_downloader works as expected", {
+  skip("export_downloader requires API call")
+
+  api_call_request <- paste0(
+    url, "api/outbreaks/", outbreak_id, "/cases/export"
+  )
+  res <- export_downloader(
+    url = url,
+    username = username,
+    password = password,
+    api_call_request = api_call_request,
+    wait = 2,
+    file.type = "json"
+  )
+
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(13L, 357L))
+  expect_true(
+    all(c(
+      "id", "visualId", "dateOfReporting", "isDateOfReportingApproximate",
+      "createdAt", "createdBy", "updatedAt", "updatedBy", "deleted",
+      "deletedAt", "createdOn", "firstName", "middleName", "lastName", "gender",
+      "occupation", "dob", "classification", "wasContact", "dateBecomeCase",
+      "wasCase", "dateOfInfection", "dateOfOnset", "riskLevel", "riskReason",
+      "outcomeId", "dateOfOutcome", "documents", "type", "dateRanges",
+      "transferRefused", "addresses", "safeBurial", "dateOfBurial",
+      "isDateOfOnsetApproximate", "numberOfExposures", "numberOfContacts",
+      "burialLocationId", "burialLocationId Identifiers",
+      "burialLocationId Location geographical level",
+      "burialLocationId Parent location", "burialPlaceName",
+      "investigationStatus", "dateInvestigationCompleted", "vaccinesReceived",
+      "pregnancyStatus", "responsibleUserId", "age.years", "age.months"
+    ) %in% colnames(res))
+  )
+
+  expect_true(
+    all(grepl(pattern = "^questionnaireAnswers", x = colnames(res)[50:357]))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "character", "character", "logical", "character",
+      "character", "character", "character", "logical", "logical", "character",
+      "character", "character", "character", "character", "character",
+      "character", "character", "logical", "character", "logical", "character",
+      "character", "character", "character", "character", "character", "list",
+      "character", "list", "logical", "list", "logical", "logical", "logical",
+      "integer", "integer", "logical", "list", "list", "list", "logical",
+      "character", "logical", "list", "character", "character", "integer",
+      "integer", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "list", "list", "list",
+      "list", "list", "list", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "list", "list", "list",
+      "list", "list", "list", "list", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "logical",
+      "list", "list", "list", "list", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "list", "logical", "logical", "list", "logical", "logical",
+      "logical", "list", "logical", "list", "logical", "list", "logical",
+      "list", "logical", "list", "logical", "list", "logical", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "logical", "list", "logical", "list",
+      "logical", "logical", "logical", "logical", "list", "logical", "logical",
+      "logical", "logical", "list", "logical", "list", "logical", "list",
+      "list", "logical", "list", "logical", "list", "logical", "list",
+      "logical", "list", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "list", "list", "list"))
+})

From 4751cc5d21d2fb7f50229bd51635b2f85209c909 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 13:46:19 +0000
Subject: [PATCH 041/203] updated documentation for export_downloader

---
 man/export_downloader.Rd | 24 ++++++++++++++++--------
 1 file changed, 16 insertions(+), 8 deletions(-)

diff --git a/man/export_downloader.Rd b/man/export_downloader.Rd
index 2558cc4..529151c 100644
--- a/man/export_downloader.Rd
+++ b/man/export_downloader.Rd
@@ -14,7 +14,8 @@ export_downloader(
 )
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
@@ -22,12 +23,17 @@ export_downloader(
 
 \item{api_call_request}{The API url to get the number of records.}
 
-\item{wait}{The number of seconds to wait in between iterations of checking the status of the export.}
+\item{wait}{The number of seconds to wait in between iterations of checking
+the status of the export.}
 
-\item{file.type}{Whether the resulting data frame should contain nested fields (\code{file.type="json"}, the default) or an entirely flat data structure (\code{file.type="csv"})}
+\item{file.type}{Whether the resulting data frame should contain nested
+fields (\code{file.type = "json"}, the default) or an entirely flat data structure
+(\code{file.type = "csv"})}
 }
 \value{
-Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+Returns a data frame. Some fields, such as addresses, hospitalization
+history, and questionnaire fields may require further unnesting. See
+\verb{\link[tidyr]\{nest\}} for assitance with unnesting.
 }
 \description{
 A housekeeping function to do export requests & downloads.
@@ -39,9 +45,11 @@ username <- "myemail@email.com"
 password <- "mypassword"
 outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 
-cases <- get_cases(url=url,
-                   username=username,
-                   password=password,
-                   outbreak_id=outbreak_id)
+cases <- get_cases(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
 }
 }

From 45455fbfafdd437a69a43158682cac63a02949b8 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 20 Jan 2023 13:49:06 +0000
Subject: [PATCH 042/203] changes file.type argument to file_type in
 export_downloader

---
 R/export_downloader.R                   | 14 +++++++-------
 man/export_downloader.Rd                |  8 ++++----
 tests/testthat/test-export_downloader.R |  2 +-
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/R/export_downloader.R b/R/export_downloader.R
index b122c90..aaf9fb6 100644
--- a/R/export_downloader.R
+++ b/R/export_downloader.R
@@ -9,9 +9,9 @@
 #' @param api_call_request The API url to get the number of records.
 #' @param wait The number of seconds to wait in between iterations of checking
 #' the status of the export.
-#' @param file.type Whether the resulting data frame should contain nested
-#' fields (`file.type = "json"`, the default) or an entirely flat data structure
-#' (`file.type = "csv"`)
+#' @param file_type Whether the resulting data frame should contain nested
+#' fields (`file_type = "json"`, the default) or an entirely flat data structure
+#' (`file_type = "csv"`)
 #'
 #' @return
 #' Returns a data frame. Some fields, such as addresses, hospitalization
@@ -45,7 +45,7 @@ export_downloader <- function(url = url,
                              password = password,
                              api_call_request = api_call_request,
                              wait = wait,
-                             file.type = file.type) {
+                             file_type = file_type) {
 
   request_id <- GET(
     paste0(
@@ -54,7 +54,7 @@ export_downloader <- function(url = url,
       "dontTranslateValues%22%3A%22true%22%2C%20%22",
       "jsonReplaceUndefinedWithNull%22%3A%22true%22%20%7D%7D",
       "&type=",
-      file.type,
+      file_type,
       "&access_token=",
       get_access_token(
         url = url,
@@ -107,7 +107,7 @@ export_downloader <- function(url = url,
 
   #Download the export
   message("...beginning download")
-  if (file.type == "json") {
+  if (file_type == "json") {
     df <- GET(
       paste0(
         url,
@@ -126,7 +126,7 @@ export_downloader <- function(url = url,
 
     # fix one strange variable name
     names(df)[names(df) %in% "_id"] <- "id"
-  } else if (file.type == "csv") {
+  } else if (file_type == "csv") {
     df <- GET(
       paste0(
         url,
diff --git a/man/export_downloader.Rd b/man/export_downloader.Rd
index 529151c..0724c1d 100644
--- a/man/export_downloader.Rd
+++ b/man/export_downloader.Rd
@@ -10,7 +10,7 @@ export_downloader(
   password = password,
   api_call_request = api_call_request,
   wait = wait,
-  file.type = file.type
+  file_type = file_type
 )
 }
 \arguments{
@@ -26,9 +26,9 @@ forget the forward slash "/" at end!}
 \item{wait}{The number of seconds to wait in between iterations of checking
 the status of the export.}
 
-\item{file.type}{Whether the resulting data frame should contain nested
-fields (\code{file.type = "json"}, the default) or an entirely flat data structure
-(\code{file.type = "csv"})}
+\item{file_type}{Whether the resulting data frame should contain nested
+fields (\code{file_type = "json"}, the default) or an entirely flat data structure
+(\code{file_type = "csv"})}
 }
 \value{
 Returns a data frame. Some fields, such as addresses, hospitalization
diff --git a/tests/testthat/test-export_downloader.R b/tests/testthat/test-export_downloader.R
index 90b02c4..1a94114 100644
--- a/tests/testthat/test-export_downloader.R
+++ b/tests/testthat/test-export_downloader.R
@@ -10,7 +10,7 @@ test_that("export_downloader works as expected", {
     password = password,
     api_call_request = api_call_request,
     wait = 2,
-    file.type = "json"
+    file_type = "json"
   )
 
   expect_s3_class(res, "data.frame")

From 4e5d1c63d933bd278049a1ae4110099043294d6a Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 14:48:01 +0000
Subject: [PATCH 043/203] removed recursive argument defaults from
 export_downloader

---
 R/export_downloader.R    | 12 ++++++------
 man/export_downloader.Rd |  9 +--------
 2 files changed, 7 insertions(+), 14 deletions(-)

diff --git a/R/export_downloader.R b/R/export_downloader.R
index aaf9fb6..d86adf5 100644
--- a/R/export_downloader.R
+++ b/R/export_downloader.R
@@ -40,12 +40,12 @@
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
 #' @importFrom utils read.csv
-export_downloader <- function(url = url,
-                             username = username,
-                             password = password,
-                             api_call_request = api_call_request,
-                             wait = wait,
-                             file_type = file_type) {
+export_downloader <- function(url,
+                             username,
+                             password,
+                             api_call_request,
+                             wait,
+                             file_type) {
 
   request_id <- GET(
     paste0(
diff --git a/man/export_downloader.Rd b/man/export_downloader.Rd
index 0724c1d..8cc492d 100644
--- a/man/export_downloader.Rd
+++ b/man/export_downloader.Rd
@@ -4,14 +4,7 @@
 \alias{export_downloader}
 \title{Function to manage export downloads}
 \usage{
-export_downloader(
-  url = url,
-  username = username,
-  password = password,
-  api_call_request = api_call_request,
-  wait = wait,
-  file_type = file_type
-)
+export_downloader(url, username, password, api_call_request, wait, file_type)
 }
 \arguments{
 \item{url}{Insert the base URL for your instance of Go.Data here. Don't

From 175ec5e9151d84991e62b1d1338ff7487468dc1a Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 14:58:50 +0000
Subject: [PATCH 044/203] removed pipe from export_downloader

---
 R/export_downloader.R | 47 +++++++++++++++++++++++++------------------
 1 file changed, 27 insertions(+), 20 deletions(-)

diff --git a/R/export_downloader.R b/R/export_downloader.R
index d86adf5..56be3bc 100644
--- a/R/export_downloader.R
+++ b/R/export_downloader.R
@@ -41,13 +41,13 @@
 #' @importFrom purrr pluck
 #' @importFrom utils read.csv
 export_downloader <- function(url,
-                             username,
-                             password,
-                             api_call_request,
-                             wait,
-                             file_type) {
+                              username,
+                              password,
+                              api_call_request,
+                              wait,
+                              file_type) {
 
-  request_id <- GET(
+  export_log_id_request <- GET(
     paste0(
       api_call_request,
       "?filter=%7B%22where%22%3A%7B%22useDbColumns%22%3A%22true%22%2C%20%22",
@@ -62,10 +62,11 @@ export_downloader <- function(url,
         password = password
       )
     )
-  ) %>%
-    content() %>%
-    pluck("exportLogId")
+  )
+
+  export_log_id_request_content <- content(export_log_id_request)
 
+  request_id <- pluck(export_log_id_request_content, "exportLogId")
 
   #Check status of request periodcially, until finished
   #function argument 'wait' determines the number of seconds to wait between
@@ -92,8 +93,9 @@ export_downloader <- function(url,
           password = password
         )
       )
-    ) %>%
-      content()
+    )
+
+    export_request_status_content <- content(export_request_status)
     message(
       paste0(
         "...processed ",
@@ -108,7 +110,7 @@ export_downloader <- function(url,
   #Download the export
   message("...beginning download")
   if (file_type == "json") {
-    df <- GET(
+    df_request <- GET(
       paste0(
         url,
         "api/export-logs/",
@@ -120,14 +122,16 @@ export_downloader <- function(url,
           password = password
         )
       )
-    ) %>%
-      content("text", encoding = "UTF-8") %>%
-      fromJSON(flatten = TRUE)
+    )
+
+    df_content <- content(df_request, "text", encoding = "UTF-8")
+
+    df <- fromJSON(df_content, flatten = TRUE)
 
     # fix one strange variable name
     names(df)[names(df) %in% "_id"] <- "id"
   } else if (file_type == "csv") {
-    df <- GET(
+    df_request <- GET(
       paste0(
         url,
         "api/export-logs/",
@@ -139,10 +143,13 @@ export_downloader <- function(url,
           password = password
         )
       )
-    ) %>%
-      content("text", encoding = "UTF-8") %>%
-      textConnection() %>%
-      read.csv()
+    )
+
+    df_content <- content(df_request, "text", encoding = "UTF-8")
+
+    df_content <- textConnection(df_content)
+
+    df <- read.csv(df_content)
     names(df)[names(df) %in% "X_id"] <- "id"
   }
 

From 95349c5f022b72ff73d7138d2038e3295503566e Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 14:59:30 +0000
Subject: [PATCH 045/203] change output type of export_downloader to tibble

---
 R/export_downloader.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/export_downloader.R b/R/export_downloader.R
index 56be3bc..bb8d354 100644
--- a/R/export_downloader.R
+++ b/R/export_downloader.R
@@ -154,5 +154,6 @@ export_downloader <- function(url,
   }
 
   message("...download complete!")
+  df <- tibble::as_tibble(df)
   return(df)
 }

From 957f18969d364f0b3d0cd20d85f62e46705c4c03 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 15:02:53 +0000
Subject: [PATCH 046/203] used explicit namespace instead of import in
 export_downloader

---
 NAMESPACE             |  1 -
 R/export_downloader.R | 30 +++++++++++-------------------
 2 files changed, 11 insertions(+), 20 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 6c64574..efb977e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -42,4 +42,3 @@ import(urltools)
 importFrom(jsonlite,fromJSON)
 importFrom(magrittr,"%>%")
 importFrom(purrr,pluck)
-importFrom(utils,read.csv)
diff --git a/R/export_downloader.R b/R/export_downloader.R
index bb8d354..f96628c 100644
--- a/R/export_downloader.R
+++ b/R/export_downloader.R
@@ -32,14 +32,6 @@
 #'   outbreak_id = outbreak_id
 #' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @import tibble
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
-#' @importFrom utils read.csv
 export_downloader <- function(url,
                               username,
                               password,
@@ -47,7 +39,7 @@ export_downloader <- function(url,
                               wait,
                               file_type) {
 
-  export_log_id_request <- GET(
+  export_log_id_request <- httr::GET(
     paste0(
       api_call_request,
       "?filter=%7B%22where%22%3A%7B%22useDbColumns%22%3A%22true%22%2C%20%22",
@@ -64,9 +56,9 @@ export_downloader <- function(url,
     )
   )
 
-  export_log_id_request_content <- content(export_log_id_request)
+  export_log_id_request_content <- httr::content(export_log_id_request)
 
-  request_id <- pluck(export_log_id_request_content, "exportLogId")
+  request_id <- purrr::pluck(export_log_id_request_content, "exportLogId")
 
   #Check status of request periodcially, until finished
   #function argument 'wait' determines the number of seconds to wait between
@@ -81,7 +73,7 @@ export_downloader <- function(url,
   status_step <- export_request_status$statusStep
   while (status_step != "LNG_STATUS_STEP_EXPORT_FINISHED") {
     Sys.sleep(wait)
-    export_request_status <- GET(
+    export_request_status <- httr::GET(
       paste0(
         url,
         "api/export-logs/",
@@ -95,7 +87,7 @@ export_downloader <- function(url,
       )
     )
 
-    export_request_status_content <- content(export_request_status)
+    export_request_status_content <- httr::content(export_request_status)
     message(
       paste0(
         "...processed ",
@@ -110,7 +102,7 @@ export_downloader <- function(url,
   #Download the export
   message("...beginning download")
   if (file_type == "json") {
-    df_request <- GET(
+    df_request <- httr::GET(
       paste0(
         url,
         "api/export-logs/",
@@ -124,14 +116,14 @@ export_downloader <- function(url,
       )
     )
 
-    df_content <- content(df_request, "text", encoding = "UTF-8")
+    df_content <- httr::content(df_request, "text", encoding = "UTF-8")
 
-    df <- fromJSON(df_content, flatten = TRUE)
+    df <- jsonlite::fromJSON(df_content, flatten = TRUE)
 
     # fix one strange variable name
     names(df)[names(df) %in% "_id"] <- "id"
   } else if (file_type == "csv") {
-    df_request <- GET(
+    df_request <- httr::GET(
       paste0(
         url,
         "api/export-logs/",
@@ -145,11 +137,11 @@ export_downloader <- function(url,
       )
     )
 
-    df_content <- content(df_request, "text", encoding = "UTF-8")
+    df_content <- httr::content(df_request, "text", encoding = "UTF-8")
 
     df_content <- textConnection(df_content)
 
-    df <- read.csv(df_content)
+    df <- utils::read.csv(df_content)
     names(df)[names(df) %in% "X_id"] <- "id"
   }
 

From ecfcab3083be01d9665864dbc3a03946415fcbea Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 15:07:24 +0000
Subject: [PATCH 047/203] fixed variable name in export_downloader

---
 R/export_downloader.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/export_downloader.R b/R/export_downloader.R
index f96628c..2c19c4f 100644
--- a/R/export_downloader.R
+++ b/R/export_downloader.R
@@ -87,7 +87,7 @@ export_downloader <- function(url,
       )
     )
 
-    export_request_status_content <- httr::content(export_request_status)
+    export_request_status <- httr::content(export_request_status)
     message(
       paste0(
         "...processed ",

From 6d0edf14b9a476246b6db14dbecff94aa4f2dd81 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 15:08:36 +0000
Subject: [PATCH 048/203] added expectation for tibble in export_downloader
 tests

---
 tests/testthat/test-export_downloader.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/testthat/test-export_downloader.R b/tests/testthat/test-export_downloader.R
index 1a94114..424ecbb 100644
--- a/tests/testthat/test-export_downloader.R
+++ b/tests/testthat/test-export_downloader.R
@@ -13,6 +13,7 @@ test_that("export_downloader works as expected", {
     file_type = "json"
   )
 
+  expect_s3_class(res, "tbl_df")
   expect_s3_class(res, "data.frame")
   expect_identical(dim(res), c(13L, 357L))
   expect_true(

From ac3865e5707673732b504902c961b57a1a48cd54 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 15:14:41 +0000
Subject: [PATCH 049/203] removed recursive argument defaults for
 get_active_outbreak

---
 R/get_active_outbreak.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/get_active_outbreak.R b/R/get_active_outbreak.R
index b28509f..7cd5420 100644
--- a/R/get_active_outbreak.R
+++ b/R/get_active_outbreak.R
@@ -27,9 +27,9 @@
 #'   password = password
 #' )
 #' }
-get_active_outbreak <- function(url = url,
-                                username = username,
-                                password = password) {
+get_active_outbreak <- function(url,
+                                username,
+                                password) {
 
   # get request to go.data
   godata_url <- httr::GET(

From 4a5801aad341457b5dc32c8753422ef13c15fcce Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 15:17:33 +0000
Subject: [PATCH 050/203] removed recursive argument defaults for
 get_access_token

---
 R/get_access_token.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/get_access_token.R b/R/get_access_token.R
index 73bff56..1260b4a 100644
--- a/R/get_access_token.R
+++ b/R/get_access_token.R
@@ -24,9 +24,9 @@
 #' @importFrom jsonlite fromJSON
 #' @export
 
-get_access_token <- function(url=url,
-                             username=username,
-                             password=password) {
+get_access_token <- function(url,
+                             username,
+                             password) {
 
   response <- POST(url=paste0(url,"api/oauth/token?access_token=123"),
                    body = list(username=username, password=password),

From 7a2b775e6cde09ee1dd05444d5102276d30ebe17 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 15:20:49 +0000
Subject: [PATCH 051/203] linted get_access_token

---
 R/get_access_token.R | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/R/get_access_token.R b/R/get_access_token.R
index 1260b4a..05bc9cd 100644
--- a/R/get_access_token.R
+++ b/R/get_access_token.R
@@ -5,7 +5,8 @@
 #' function used in many of the other
 #' `godataR` functions.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
 #'
@@ -23,21 +24,19 @@
 #' @import httr
 #' @importFrom jsonlite fromJSON
 #' @export
-
 get_access_token <- function(url,
                              username,
                              password) {
 
-  response <- POST(url=paste0(url,"api/oauth/token?access_token=123"),
-                   body = list(username=username, password=password),
+  response <- POST(url = paste0(url, "api/oauth/token?access_token=123"),
+                   body = list(username = username, password = password),
                    encode = "json")
 
-  if (response$status_code==200) {
-    responseJSON <- content(response, as="text")
-    token <- fromJSON(responseJSON, flatten=TRUE)$access_token
+  if (response$status_code == 200) {
+    response_json <- content(response, as = "text")
+    token <- fromJSON(response_json, flatten = TRUE)$access_token
     return(token)
   } else {
-    stop(paste0("Error: ",response$status_code))
+    stop(paste0("Error: ", response$status_code))
   }
-
 }

From 26e9a281d357c17df8095c9b6408e41677bc0ccf Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 15:23:31 +0000
Subject: [PATCH 052/203] use explicit namespace instead of import for
 get_access_token

---
 R/get_access_token.R | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/get_access_token.R b/R/get_access_token.R
index 05bc9cd..2b055cc 100644
--- a/R/get_access_token.R
+++ b/R/get_access_token.R
@@ -21,22 +21,22 @@
 #'                  username = username,
 #'                  password = password)
 #' }
-#' @import httr
-#' @importFrom jsonlite fromJSON
 #' @export
 get_access_token <- function(url,
                              username,
                              password) {
 
-  response <- POST(url = paste0(url, "api/oauth/token?access_token=123"),
-                   body = list(username = username, password = password),
-                   encode = "json")
+  response <- httr::POST(
+    url = paste0(url, "api/oauth/token?access_token=123"),
+    body = list(username = username, password = password),
+    encode = "json"
+  )
 
   if (response$status_code == 200) {
-    response_json <- content(response, as = "text")
-    token <- fromJSON(response_json, flatten = TRUE)$access_token
+    response_json <- httr::content(response, as = "text")
+    token <- jsonlite::fromJSON(response_json, flatten = TRUE)$access_token
     return(token)
   } else {
-    stop(paste0("Error: ", response$status_code))
+    stop("Error: ", response$status_code)
   }
 }

From 960cca8736539bae97d847ca8197ece97cc67547 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 15:27:49 +0000
Subject: [PATCH 053/203] added test for get_access_token (skipped by default)

---
 tests/testthat/test-get_access_token.R | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 tests/testthat/test-get_access_token.R

diff --git a/tests/testthat/test-get_access_token.R b/tests/testthat/test-get_access_token.R
new file mode 100644
index 0000000..d342755
--- /dev/null
+++ b/tests/testthat/test-get_access_token.R
@@ -0,0 +1,18 @@
+test_that("get_access_token works as expected", {
+  skip("get_access_token requires API call")
+
+  res <- get_access_token(
+    url = url,
+    username = username,
+    password = password
+  )
+
+  expect_type(res, "character")
+  # character string can contain alphanumeric characters
+  expect_true(grepl(pattern = "[:alphanum:]", x = res))
+  # character string cannot contain punctuation marks
+  expect_false(grepl(pattern = "[[:punct:]]", x = res))
+  # character string cannot contain spaces
+  expect_false(grepl(pattern = "\\s", x = res))
+})
+

From a4d47a4d6135a4723a979678221508d2fceb81a7 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 15:53:06 +0000
Subject: [PATCH 054/203] linted get_export_status

---
 R/get_export_status.R | 69 ++++++++++++++++++++++++++++++-------------
 1 file changed, 48 insertions(+), 21 deletions(-)

diff --git a/R/get_export_status.R b/R/get_export_status.R
index 2daf647..4d621a9 100644
--- a/R/get_export_status.R
+++ b/R/get_export_status.R
@@ -4,7 +4,8 @@
 #' request. This is a housekeeping function
 #' used in many of the other `godataR` functions.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
 #' @param request_id The id number for the export request.
@@ -18,23 +19,35 @@
 #' username <- "myemail@email.com"
 #' password <- "mypassword"
 #' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
-#' access_token <- get_access_token(url=url,
-#'                                  username=username,
-#'                                  password=password)
+#' access_token <- get_access_token(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
 #'
-#' #Submit an export request
-#' export.request <- GET(paste0(url,"api/outbreaks/",outbreak_id,"/cases/export",
-#'                                "&access_token=",access_token))
+#' # Submit an export request
+#' export.request <- GET(
+#'   paste0(
+#'     url,
+#'     "api/outbreaks/",
+#'     outbreak_id,
+#'     "/cases/export",
+#'     "&access_token=",
+#'     access_token
+#'   )
+#' )
 #' request_id <- export.request %>%
-#'      content() %>%
-#'      pluck("exportLogId")
+#'   content() %>%
+#'   pluck("exportLogId")
 #'
-#' #Check the status of the export request
+#' # Check the status of the export request
 #'
-#' export.request.status <- get_export_status(url=url,
-#'                                            username=username,
-#'                                            password=password,
-#'                                            request_id=request_id)
+#' export_request_status <- get_export_status(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   request_id = request_id
+#' )
 #' }
 #' @importFrom magrittr %>%
 #' @import dplyr
@@ -43,16 +56,30 @@
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
 
-get_export_status <- function(url=url,
-                              username=username,
-                              password=password,
-                              request_id=request_id) {
+get_export_status <- function(url = url,
+                              username = username,
+                              password = password,
+                              request_id = request_id) {
 
-  export.request.status <- GET(paste0(url,"api/export-logs/",request_id,"?access_token=",get_access_token(url=url, username=username, password=password))) %>%
+  export_request_status <- GET(
+    paste0(
+      url,
+      "api/export-logs/",
+      request_id,
+      "?access_token=",
+      get_access_token(
+        url = url,
+        username = username,
+        password = password
+      )
+    )
+  ) %>%
     content()
 
-  export.request.status <- export.request.status[c("statusStep","totalNo","processedNo")]
+  export_request_status <- export_request_status[
+    c("statusStep", "totalNo", "processedNo")
+  ]
 
-  return(export.request.status)
+  return(export_request_status)
 
 }

From 3c7ff143befb889313dc5fbda6dade56eeb82341 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 15:53:45 +0000
Subject: [PATCH 055/203] removed recursive argument defaults for
 get_export_status

---
 R/get_export_status.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/get_export_status.R b/R/get_export_status.R
index 4d621a9..cec9564 100644
--- a/R/get_export_status.R
+++ b/R/get_export_status.R
@@ -56,10 +56,10 @@
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
 
-get_export_status <- function(url = url,
-                              username = username,
-                              password = password,
-                              request_id = request_id) {
+get_export_status <- function(url,
+                              username,
+                              password,
+                              request_id) {
 
   export_request_status <- GET(
     paste0(

From 4cc6abf1a752bc44966ebca385eaa2af50c3d0c3 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 15:57:00 +0000
Subject: [PATCH 056/203] removed pipe from get_export_status

---
 R/get_export_status.R | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/R/get_export_status.R b/R/get_export_status.R
index cec9564..7b1e5ba 100644
--- a/R/get_export_status.R
+++ b/R/get_export_status.R
@@ -26,7 +26,7 @@
 #' )
 #'
 #' # Submit an export request
-#' export.request <- GET(
+#' export_request <- GET(
 #'   paste0(
 #'     url,
 #'     "api/outbreaks/",
@@ -36,9 +36,8 @@
 #'     access_token
 #'   )
 #' )
-#' request_id <- export.request %>%
-#'   content() %>%
-#'   pluck("exportLogId")
+#' request_id <- content(export_request)
+#' request_id <- pluck(request_id, "exportLogId")
 #'
 #' # Check the status of the export request
 #'
@@ -73,8 +72,8 @@ get_export_status <- function(url,
         password = password
       )
     )
-  ) %>%
-    content()
+  )
+  export_request_status <- content(export_request_status)
 
   export_request_status <- export_request_status[
     c("statusStep", "totalNo", "processedNo")

From 7c6500d1f13d61c34abc6ccadfe549ea2455c099 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 15:59:15 +0000
Subject: [PATCH 057/203] used explicit namespace instead of import for
 get_export_status

---
 R/get_export_status.R      | 12 ++--------
 man/get_access_token.Rd    |  5 ++--
 man/get_active_outbreak.Rd |  2 +-
 man/get_export_status.Rd   | 49 ++++++++++++++++++++++----------------
 4 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/R/get_export_status.R b/R/get_export_status.R
index 7b1e5ba..a400b0c 100644
--- a/R/get_export_status.R
+++ b/R/get_export_status.R
@@ -48,19 +48,12 @@
 #'   request_id = request_id
 #' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
-
 get_export_status <- function(url,
                               username,
                               password,
                               request_id) {
 
-  export_request_status <- GET(
+  export_request_status <- httr::GET(
     paste0(
       url,
       "api/export-logs/",
@@ -73,12 +66,11 @@ get_export_status <- function(url,
       )
     )
   )
-  export_request_status <- content(export_request_status)
+  export_request_status <- httr::content(export_request_status)
 
   export_request_status <- export_request_status[
     c("statusStep", "totalNo", "processedNo")
   ]
 
   return(export_request_status)
-
 }
diff --git a/man/get_access_token.Rd b/man/get_access_token.Rd
index d7df5a4..f504a36 100644
--- a/man/get_access_token.Rd
+++ b/man/get_access_token.Rd
@@ -4,10 +4,11 @@
 \alias{get_access_token}
 \title{Get an access oauth access token for Go.Data}
 \usage{
-get_access_token(url = url, username = username, password = password)
+get_access_token(url, username, password)
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
diff --git a/man/get_active_outbreak.Rd b/man/get_active_outbreak.Rd
index 185500c..20d79e8 100644
--- a/man/get_active_outbreak.Rd
+++ b/man/get_active_outbreak.Rd
@@ -4,7 +4,7 @@
 \alias{get_active_outbreak}
 \title{Get the currently active outbreak id number}
 \usage{
-get_active_outbreak(url = url, username = username, password = password)
+get_active_outbreak(url, username, password)
 }
 \arguments{
 \item{url}{Insert the base URL for your instance of Go.Data here. Don't
diff --git a/man/get_export_status.Rd b/man/get_export_status.Rd
index 47e7a51..b891e7d 100644
--- a/man/get_export_status.Rd
+++ b/man/get_export_status.Rd
@@ -4,15 +4,11 @@
 \alias{get_export_status}
 \title{Check the status of an export request from Go.Data (version 2.38.1 or later)}
 \usage{
-get_export_status(
-  url = url,
-  username = username,
-  password = password,
-  request_id = request_id
-)
+get_export_status(url, username, password, request_id)
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
@@ -34,22 +30,33 @@ url <- "https://MyGoDataServer.com/"
 username <- "myemail@email.com"
 password <- "mypassword"
 outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
-access_token <- get_access_token(url=url,
-                                 username=username,
-                                 password=password)
+access_token <- get_access_token(
+  url = url,
+  username = username,
+  password = password
+)
 
-#Submit an export request
-export.request <- GET(paste0(url,"api/outbreaks/",outbreak_id,"/cases/export",
-                               "&access_token=",access_token))
-request_id <- export.request \%>\%
-     content() \%>\%
-     pluck("exportLogId")
+# Submit an export request
+export_request <- GET(
+  paste0(
+    url,
+    "api/outbreaks/",
+    outbreak_id,
+    "/cases/export",
+    "&access_token=",
+    access_token
+  )
+)
+request_id <- content(export_request)
+request_id <- pluck(request_id, "exportLogId")
 
-#Check the status of the export request
+# Check the status of the export request
 
-export.request.status <- get_export_status(url=url,
-                                           username=username,
-                                           password=password,
-                                           request_id=request_id)
+export_request_status <- get_export_status(
+  url = url,
+  username = username,
+  password = password,
+  request_id = request_id
+)
 }
 }

From dcae444105da4f8eaec17488b41fd33235e9b7d2 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 16:17:10 +0000
Subject: [PATCH 058/203] added test for get_export_status (skipped by default)

---
 tests/testthat/test-get_export_status.R | 42 +++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 tests/testthat/test-get_export_status.R

diff --git a/tests/testthat/test-get_export_status.R b/tests/testthat/test-get_export_status.R
new file mode 100644
index 0000000..e27c1db
--- /dev/null
+++ b/tests/testthat/test-get_export_status.R
@@ -0,0 +1,42 @@
+test_that("get_export_status works as expected", {
+  skip("get_export_status requires API call")
+
+  api_call_request <- paste0(
+    url, "api/outbreaks/", outbreak_id, "/cases/export"
+  )
+
+  export_log_id_request <- httr::GET(
+    paste0(
+      api_call_request,
+      "?filter=%7B%22where%22%3A%7B%22useDbColumns%22%3A%22true%22%2C%20%22",
+      "dontTranslateValues%22%3A%22true%22%2C%20%22",
+      "jsonReplaceUndefinedWithNull%22%3A%22true%22%20%7D%7D",
+      "&type=",
+      "json",
+      "&access_token=",
+      get_access_token(
+        url = url,
+        username = username,
+        password = password
+      )
+    )
+  )
+
+  export_log_id_request_content <- httr::content(export_log_id_request)
+
+  request_id <- purrr::pluck(export_log_id_request_content, "exportLogId")
+
+  res <- get_export_status(
+    url = url,
+    username = username,
+    password = password,
+    request_id = request_id
+  )
+
+  expect_type(res, "list")
+  expect_length(res, 3)
+  expect_named(res, c("statusStep", "totalNo", "processedNo"))
+  expect_type(res$statusStep, "character")
+  expect_type(res$totalNo, "integer")
+  expect_type(res$processedNo, "integer")
+})

From 1b5ccc966539b91886b6a61a2a615dcc086deeee Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 16:31:45 +0000
Subject: [PATCH 059/203] linted get_all_outbreaks

---
 R/get_all_outbreaks.R | 37 ++++++++++++++++++++++++-------------
 1 file changed, 24 insertions(+), 13 deletions(-)

diff --git a/R/get_all_outbreaks.R b/R/get_all_outbreaks.R
index ca98809..25b8faf 100644
--- a/R/get_all_outbreaks.R
+++ b/R/get_all_outbreaks.R
@@ -5,12 +5,15 @@
 #' housekeeping function used in many of the
 #' other `godataR` functions.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
 #'
 #' @return
-#' Returns data frame of outbreaks. The resulting list is filtered by the user's permissions: only outbreaks for which the user has access will be returned.
+#' Returns data frame of outbreaks. The resulting list is filtered by the
+#' user's permissions: only outbreaks for which the user has access will be
+#' returned.
 #' @export
 #' @examples
 #' \dontrun{
@@ -29,18 +32,26 @@
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
 #' @export
+get_all_outbreaks <- function(url = url,
+                              username = username,
+                              password = password) {
 
-get_all_outbreaks <- function(url=url,
-                              username=username,
-                              password=password) {
-
-  outbreaks <- GET(paste0(url,"api/outbreaks",
-                                 "?access_token=",get_access_token(url=url, username=username, password=password))) %>%
-    content(as="text") %>%
-    fromJSON(flatten=TRUE) %>%
-    filter(deleted!=TRUE) %>%
-    select(any_of(c("id", "name", "description","createdBy","createdAt")))
+  outbreaks <- GET(
+    paste0(
+      url,
+      "api/outbreaks",
+      "?access_token=",
+      get_access_token(
+        url = url,
+        username = username,
+        password = password
+      )
+    )
+  ) %>%
+    content(as = "text") %>%
+    fromJSON(flatten = TRUE) %>%
+    filter(.data$deleted != TRUE) %>%
+    select(any_of(c("id", "name", "description", "createdBy", "createdAt")))
 
   return(outbreaks)
-
 }

From 19fc4ddeafd8eb7703bcffc34734ade1e71d4b06 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 16:39:33 +0000
Subject: [PATCH 060/203] removed pipe from get_all_outbreaks

---
 R/get_all_outbreaks.R | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/R/get_all_outbreaks.R b/R/get_all_outbreaks.R
index 25b8faf..2d64972 100644
--- a/R/get_all_outbreaks.R
+++ b/R/get_all_outbreaks.R
@@ -36,7 +36,7 @@ get_all_outbreaks <- function(url = url,
                               username = username,
                               password = password) {
 
-  outbreaks <- GET(
+  outbreaks_request <- GET(
     paste0(
       url,
       "api/outbreaks",
@@ -47,11 +47,18 @@ get_all_outbreaks <- function(url = url,
         password = password
       )
     )
-  ) %>%
-    content(as = "text") %>%
-    fromJSON(flatten = TRUE) %>%
-    filter(.data$deleted != TRUE) %>%
-    select(any_of(c("id", "name", "description", "createdBy", "createdAt")))
+  )
+
+  outbreaks_content <- content(outbreaks_request, as = "text")
+
+  outbreaks <- fromJSON(outbreaks_content, flatten = TRUE)
+
+  outbreaks <- filter(outbreaks, .data$deleted != TRUE)
+
+  outbreaks <- select(
+    outbreaks,
+    any_of(c("id", "name", "description", "createdBy", "createdAt"))
+  )
 
   return(outbreaks)
 }

From 2b95a8a17981100a8cf5053d25858153a8f28109 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 16:40:26 +0000
Subject: [PATCH 061/203] removed recursive argument defaults for
 get_all_outbreaks

---
 R/get_all_outbreaks.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/get_all_outbreaks.R b/R/get_all_outbreaks.R
index 2d64972..b8253f8 100644
--- a/R/get_all_outbreaks.R
+++ b/R/get_all_outbreaks.R
@@ -32,9 +32,9 @@
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
 #' @export
-get_all_outbreaks <- function(url = url,
-                              username = username,
-                              password = password) {
+get_all_outbreaks <- function(url,
+                              username,
+                              password) {
 
   outbreaks_request <- GET(
     paste0(

From 64a7f12d9d3d8f31c017a97d20c52a0e72dd4e25 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 16:42:18 +0000
Subject: [PATCH 062/203] used explicit namespace instead of import for
 get_all_outbreaks

---
 R/get_all_outbreaks.R | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

diff --git a/R/get_all_outbreaks.R b/R/get_all_outbreaks.R
index b8253f8..9062f3e 100644
--- a/R/get_all_outbreaks.R
+++ b/R/get_all_outbreaks.R
@@ -25,18 +25,12 @@
 #'                                username=username,
 #'                                password=password)
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
 #' @export
 get_all_outbreaks <- function(url,
                               username,
                               password) {
 
-  outbreaks_request <- GET(
+  outbreaks_request <- httr::GET(
     paste0(
       url,
       "api/outbreaks",
@@ -49,15 +43,15 @@ get_all_outbreaks <- function(url,
     )
   )
 
-  outbreaks_content <- content(outbreaks_request, as = "text")
+  outbreaks_content <- httr::content(outbreaks_request, as = "text")
 
-  outbreaks <- fromJSON(outbreaks_content, flatten = TRUE)
+  outbreaks <- jsonlite::fromJSON(outbreaks_content, flatten = TRUE)
 
-  outbreaks <- filter(outbreaks, .data$deleted != TRUE)
+  outbreaks <- dplyr::filter(outbreaks, .data$deleted != TRUE)
 
-  outbreaks <- select(
+  outbreaks <- dplyr::select(
     outbreaks,
-    any_of(c("id", "name", "description", "createdBy", "createdAt"))
+    dplyr::any_of(c("id", "name", "description", "createdBy", "createdAt"))
   )
 
   return(outbreaks)

From 552d11ddc18a541eab6ad2167f3a6cc59813df51 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 16:45:25 +0000
Subject: [PATCH 063/203] updated get_all_outbreaks documentation and made
 return type a tibble

---
 R/get_all_outbreaks.R    | 10 +++++++---
 man/get_all_outbreaks.Rd | 17 +++++++++++------
 2 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/R/get_all_outbreaks.R b/R/get_all_outbreaks.R
index 9062f3e..18c9639 100644
--- a/R/get_all_outbreaks.R
+++ b/R/get_all_outbreaks.R
@@ -21,9 +21,11 @@
 #' username <- "myemail@email.com"
 #' password <- "mypassword"
 #'
-#' outbreaks <- get_all_outbreaks(url=url,
-#'                                username=username,
-#'                                password=password)
+#' outbreaks <- get_all_outbreaks(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
 #' }
 #' @export
 get_all_outbreaks <- function(url,
@@ -54,5 +56,7 @@ get_all_outbreaks <- function(url,
     dplyr::any_of(c("id", "name", "description", "createdBy", "createdAt"))
   )
 
+  outbreaks <- tibble::as_tibble(outbreaks)
+
   return(outbreaks)
 }
diff --git a/man/get_all_outbreaks.Rd b/man/get_all_outbreaks.Rd
index 16e9ce3..3e0f6c6 100644
--- a/man/get_all_outbreaks.Rd
+++ b/man/get_all_outbreaks.Rd
@@ -4,17 +4,20 @@
 \alias{get_all_outbreaks}
 \title{Get a list of all outbreaks and their attributes}
 \usage{
-get_all_outbreaks(url = url, username = username, password = password)
+get_all_outbreaks(url, username, password)
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
 \item{password}{The password for your Go.Data login}
 }
 \value{
-Returns data frame of outbreaks. The resulting list is filtered by the user's permissions: only outbreaks for which the user has access will be returned.
+Returns data frame of outbreaks. The resulting list is filtered by the
+user's permissions: only outbreaks for which the user has access will be
+returned.
 }
 \description{
 A function to retrieve all outbreaks assigned
@@ -28,8 +31,10 @@ url <- "https://MyGoDataServer.com/"
 username <- "myemail@email.com"
 password <- "mypassword"
 
-outbreaks <- get_all_outbreaks(url=url,
-                               username=username,
-                               password=password)
+outbreaks <- get_all_outbreaks(
+  url = url,
+  username = username,
+  password = password
+)
 }
 }

From 475cd2f17c626d36efabc833926ee63cab5ec5f3 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 1 Feb 2023 17:01:43 +0000
Subject: [PATCH 064/203] added test for get_all_outbreaks (skipped by default)

---
 tests/testthat/test-get_all_outbreaks.R | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 tests/testthat/test-get_all_outbreaks.R

diff --git a/tests/testthat/test-get_all_outbreaks.R b/tests/testthat/test-get_all_outbreaks.R
new file mode 100644
index 0000000..af05858
--- /dev/null
+++ b/tests/testthat/test-get_all_outbreaks.R
@@ -0,0 +1,21 @@
+test_that("get_all_outbreaks works as expected", {
+  skip("get_all_outbreaks requires API call")
+
+  res <- get_all_outbreaks(
+    url = url,
+    username = username,
+    password = password
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(10L, 5L))
+  expect_identical(
+    colnames(res),
+    c("id", "name", "description", "createdBy", "createdAt" )
+  )
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    rep("character", 5)
+  )
+})

From bc0cc8576790aa84a0555302c3181b3e78243f90 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 10:34:25 +0000
Subject: [PATCH 065/203] linted check_godata_url

---
 R/check_godata_url.R    | 9 +++++----
 man/check_godata_url.Rd | 3 ++-
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/R/check_godata_url.R b/R/check_godata_url.R
index 8a87f79..71d5ee8 100644
--- a/R/check_godata_url.R
+++ b/R/check_godata_url.R
@@ -4,7 +4,8 @@
 #' is valid. This is a housekeeping function
 #' used in many of the other `godataR` functions.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #'
 #' @return
 #' Boolean, where `TRUE` indicates a valid URL.
@@ -17,14 +18,14 @@
 #' @import httr
 #' @importFrom purrr pluck
 #' @export
-check_godata_url <- function(url=url) {
+check_godata_url <- function(url = url) {
 
   # Get status code for version check
-  status_code <- GET(paste0(url,"api/system-settings/version")) %>%
+  status_code <- GET(paste0(url, "api/system-settings/version")) %>%
     pluck("status_code")
 
   # create boolean based on status code being 200 (success)
-  check <- (status_code==200)
+  check <- (status_code == 200)
 
   return(check)
 
diff --git a/man/check_godata_url.Rd b/man/check_godata_url.Rd
index 08c91e2..71e126c 100644
--- a/man/check_godata_url.Rd
+++ b/man/check_godata_url.Rd
@@ -7,7 +7,8 @@
 check_godata_url(url = url)
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 }
 \value{
 Boolean, where \code{TRUE} indicates a valid URL.

From ecb17e0b3750cf66099dd2eb03801db2ec3bf1f2 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 10:34:56 +0000
Subject: [PATCH 066/203] removed recursive argument default for
 check_godata_url

---
 R/check_godata_url.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/check_godata_url.R b/R/check_godata_url.R
index 71d5ee8..21a4354 100644
--- a/R/check_godata_url.R
+++ b/R/check_godata_url.R
@@ -18,7 +18,7 @@
 #' @import httr
 #' @importFrom purrr pluck
 #' @export
-check_godata_url <- function(url = url) {
+check_godata_url <- function(url) {
 
   # Get status code for version check
   status_code <- GET(paste0(url, "api/system-settings/version")) %>%

From cf14b9096cd586dfc71efbd18190f9af97c1b5d3 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 10:35:55 +0000
Subject: [PATCH 067/203] removed pipe from check_godata_url

---
 R/check_godata_url.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/check_godata_url.R b/R/check_godata_url.R
index 21a4354..74afc0a 100644
--- a/R/check_godata_url.R
+++ b/R/check_godata_url.R
@@ -21,8 +21,9 @@
 check_godata_url <- function(url) {
 
   # Get status code for version check
-  status_code <- GET(paste0(url, "api/system-settings/version")) %>%
-    pluck("status_code")
+  status_code <- GET(paste0(url, "api/system-settings/version"))
+
+  status_code <- pluck(status_code, "status_code")
 
   # create boolean based on status code being 200 (success)
   check <- (status_code == 200)

From 99fdf298e4dbaa186623f9ea310ae313c1ed445f Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 10:37:17 +0000
Subject: [PATCH 068/203] used explicit namespace instead of import for
 check_godata_url

---
 R/check_godata_url.R    | 9 +++------
 man/check_godata_url.Rd | 2 +-
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/R/check_godata_url.R b/R/check_godata_url.R
index 74afc0a..e81bc8e 100644
--- a/R/check_godata_url.R
+++ b/R/check_godata_url.R
@@ -14,19 +14,16 @@
 #' url <- "https://MyGoDataServer.com/"
 #' check_godata_url(url=url)
 #' }
-#' @importFrom magrittr %>%
-#' @import httr
-#' @importFrom purrr pluck
 #' @export
 check_godata_url <- function(url) {
 
   # Get status code for version check
-  status_code <- GET(paste0(url, "api/system-settings/version"))
+  status_code <- httr::GET(paste0(url, "api/system-settings/version"))
 
-  status_code <- pluck(status_code, "status_code")
+  status_code <- purrr::pluck(status_code, "status_code")
 
   # create boolean based on status code being 200 (success)
-  check <- (status_code == 200)
+  check <- status_code == 200
 
   return(check)
 
diff --git a/man/check_godata_url.Rd b/man/check_godata_url.Rd
index 71e126c..71e02b5 100644
--- a/man/check_godata_url.Rd
+++ b/man/check_godata_url.Rd
@@ -4,7 +4,7 @@
 \alias{check_godata_url}
 \title{Check if the provided Go.Data URL is valid}
 \usage{
-check_godata_url(url = url)
+check_godata_url(url)
 }
 \arguments{
 \item{url}{Insert the base URL for your instance of Go.Data here. Don't

From c6c3cedccb219daac3f55a37741c4406317cca3c Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 10:40:20 +0000
Subject: [PATCH 069/203] added test for check_godata_url (skipped by default)

---
 tests/testthat/test-check_godata_url.R | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 tests/testthat/test-check_godata_url.R

diff --git a/tests/testthat/test-check_godata_url.R b/tests/testthat/test-check_godata_url.R
new file mode 100644
index 0000000..80177f8
--- /dev/null
+++ b/tests/testthat/test-check_godata_url.R
@@ -0,0 +1,8 @@
+test_that("check_godata_url works as expected", {
+  skip("check_godata_url requires API call")
+
+  res <- check_godata_url(url = url)
+
+  expect_type(res, "logical")
+  expect_length(res, 1)
+})

From b5934e320453e622c5d339a203fae702c48d9654 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 10:41:03 +0000
Subject: [PATCH 070/203] updated check_godata_url documentation

---
 R/check_godata_url.R    | 2 +-
 man/check_godata_url.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/check_godata_url.R b/R/check_godata_url.R
index e81bc8e..f395640 100644
--- a/R/check_godata_url.R
+++ b/R/check_godata_url.R
@@ -12,7 +12,7 @@
 #' @examples
 #' \dontrun{
 #' url <- "https://MyGoDataServer.com/"
-#' check_godata_url(url=url)
+#' check_godata_url(url = url)
 #' }
 #' @export
 check_godata_url <- function(url) {
diff --git a/man/check_godata_url.Rd b/man/check_godata_url.Rd
index 71e02b5..f64d9ce 100644
--- a/man/check_godata_url.Rd
+++ b/man/check_godata_url.Rd
@@ -21,6 +21,6 @@ used in many of the other \code{godataR} functions.
 \examples{
 \dontrun{
 url <- "https://MyGoDataServer.com/"
-check_godata_url(url=url)
+check_godata_url(url = url)
 }
 }

From 7cea7eb2c7b5b845722ce124211e8f6f03f001c2 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 10:43:42 +0000
Subject: [PATCH 071/203] removed recursive default arguments for get_cases

---
 R/get_cases.R    | 8 ++++----
 man/get_cases.Rd | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/get_cases.R b/R/get_cases.R
index d04f0c6..b6bbbd9 100644
--- a/R/get_cases.R
+++ b/R/get_cases.R
@@ -59,10 +59,10 @@
 #'   outbreak_id = outbreak_id
 #' )
 #' }
-get_cases <- function(url = url,
-                      username = username,
-                      password = password,
-                      outbreak_id = outbreak_id,
+get_cases <- function(url,
+                      username,
+                      password,
+                      outbreak_id,
                       method = c("export", "batch"),
                       batch_size = 50000,
                       wait = 2,
diff --git a/man/get_cases.Rd b/man/get_cases.Rd
index aa28bbd..f207f72 100644
--- a/man/get_cases.Rd
+++ b/man/get_cases.Rd
@@ -5,10 +5,10 @@
 \title{Download cases from Go.Data}
 \usage{
 get_cases(
-  url = url,
-  username = username,
-  password = password,
-  outbreak_id = outbreak_id,
+  url,
+  username,
+  password,
+  outbreak_id,
   method = c("export", "batch"),
   batch_size = 50000,
   wait = 2,

From 588ad2c4bf8c3dfb96d012a40a59e32c6fb9742a Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 10:55:43 +0000
Subject: [PATCH 072/203] linted get_clusters

---
 R/get_clusters.R    | 99 ++++++++++++++++++++++++++++++++-------------
 man/get_clusters.Rd | 19 +++++----
 2 files changed, 83 insertions(+), 35 deletions(-)

diff --git a/R/get_clusters.R b/R/get_clusters.R
index fecc251..d7c9517 100644
--- a/R/get_clusters.R
+++ b/R/get_clusters.R
@@ -9,11 +9,14 @@
 #'
 #' This function works on all versions of Go.Data.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
-#' @param outbreak_id The id number for the outbreak for which you want to download clusters.
-#' @param batch_size For large datasets, specify the number of records to retrieve in each iteration.
+#' @param outbreak_id The id number for the outbreak for which you want to
+#' download clusters.
+#' @param batch_size For large datasets, specify the number of records to
+#' retrieve in each iteration.
 #'
 #' @return
 #' Returns data frame.
@@ -26,10 +29,12 @@
 #' password <- "mypassword"
 #' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 #'
-#' clusters <- get_clusters(url=url,
-#'                          username=username,
-#'                          password=password,
-#'                          outbreak_id=outbreak_id)
+#' clusters <- get_clusters(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
 #' }
 #' @importFrom magrittr %>%
 #' @import dplyr
@@ -39,55 +44,93 @@
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
 
-get_clusters <- function(url=url,
-                         username=username,
-                         password=password,
-                         outbreak_id=outbreak_id,
-                         batch_size=50000) {
+get_clusters <- function(url = url,
+                         username = username,
+                         password = password,
+                         outbreak_id = outbreak_id,
+                         batch_size = 50000) {
 
 # no /export endpoint for clusters so no need to check version
 
+  outbreak_id_api <- get_active_outbreak(
+    url = url,
+    username = username,
+    password = password
+  )
   #Check that outbreak_id is active
-  if (outbreak_id != get_active_outbreak(url=url, username=username, password=password)) {
-    set_active_outbreak(url=url, username=username, password=password, outbreak_id=outbreak_id)
+  if (outbreak_id != outbreak_id_api) {
+    set_active_outbreak(
+      url = url,
+      username = username,
+      password = password,
+      outbreak_id = outbreak_id
+    )
   }
 
   #get total number of records
-  df_n <- GET(paste0(url,"api/outbreaks/",outbreak_id,"/clusters/count"),
-              add_headers(Authorization = paste("Bearer", get_access_token(url=url, username=username, password=password), sep = " "))) %>%
-    content(as="text") %>%
-    fromJSON(flatten=TRUE) %>%
+  df_n <- GET(
+    paste0(url, "api/outbreaks/", outbreak_id, "/clusters/count"),
+    add_headers(Authorization = paste("Bearer", get_access_token(
+      url = url,
+      username = username,
+      password = password
+    ), sep = " "))) %>%
+    content(as = "text") %>%
+    fromJSON(flatten = TRUE) %>%
     unlist() %>%
     unname()
 
   #Import records in batches
   df <- tibble()
   batch_size <- batch_size # number of records to import per iteration
-  skip <-0
+  skip <- 0
   message("****************************")
 
   #Download records in batches, and then append them into a single dataset
   while (skip < df_n) {
 
     #Progress message
-    if (df_n <= batch_size) message(paste0("...downloading records 1 to ",df_n))
-    if (df_n > batch_size)     message(paste0("...downloading records ", as.character(skip+1, scientific = FALSE), " to ", format(skip+batch_size, scientific = FALSE)))
+    if (df_n <= batch_size) {
+      message(paste0("...downloading records 1 to ", df_n))
+    }
+    if (df_n > batch_size) {
+      message(paste0(
+        "...downloading records ",
+        as.character(skip + 1, scientific = FALSE),
+        " to ",
+        format(skip + batch_size, scientific = FALSE)
+      ))
+    }
 
     #fetch the batch of records
-    df.i <- GET(paste0(url,"api/outbreaks/",outbreak_id,"/clusters",
-                       "/?filter={%22limit%22:",format(batch_size, scientific = FALSE),",%22skip%22:",format(skip, scientific = FALSE),"}"),
-                add_headers(Authorization = paste("Bearer", get_access_token(url=url, username=username, password=password), sep = " "))) %>%
-      content(as='text') %>%
-      fromJSON( flatten=TRUE) %>%
+    df_i <- GET(
+      paste0(
+        url,
+        "api/outbreaks/",
+        outbreak_id,
+        "/clusters",
+        "/?filter={%22limit%22:",
+        format(batch_size, scientific = FALSE),
+        ",%22skip%22:",
+        format(skip, scientific = FALSE),
+        "}"
+      ),
+      add_headers(Authorization = paste("Bearer", get_access_token(
+        url = url,
+        username = username,
+        password = password
+      ), sep = " "))) %>%
+      content(as = "text") %>%
+      fromJSON(flatten = TRUE) %>%
       as_tibble()
 
     #append the new batch of records to the existing data frame
     df <- df %>%
-      bind_rows(df.i)
+      bind_rows(df_i)
 
     #update numbers for the next iteration
     skip <- skip + batch_size
-    rm(df.i)
+    rm(df_i)
   }
   rm(batch_size, skip, df_n)
 
diff --git a/man/get_clusters.Rd b/man/get_clusters.Rd
index a629ae9..1f743c6 100644
--- a/man/get_clusters.Rd
+++ b/man/get_clusters.Rd
@@ -13,15 +13,18 @@ get_clusters(
 )
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
 \item{password}{The password for your Go.Data login}
 
-\item{outbreak_id}{The id number for the outbreak for which you want to download clusters.}
+\item{outbreak_id}{The id number for the outbreak for which you want to
+download clusters.}
 
-\item{batch_size}{For large datasets, specify the number of records to retrieve in each iteration.}
+\item{batch_size}{For large datasets, specify the number of records to
+retrieve in each iteration.}
 }
 \value{
 Returns data frame.
@@ -44,9 +47,11 @@ username <- "myemail@email.com"
 password <- "mypassword"
 outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 
-clusters <- get_clusters(url=url,
-                         username=username,
-                         password=password,
-                         outbreak_id=outbreak_id)
+clusters <- get_clusters(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
 }
 }

From 45a7beaf0ff6a43f9d256f85fdec5e30d7f69a44 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 10:56:19 +0000
Subject: [PATCH 073/203] removed recursive argument defaults for get_clusters

---
 R/get_clusters.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/get_clusters.R b/R/get_clusters.R
index d7c9517..6c5bd4c 100644
--- a/R/get_clusters.R
+++ b/R/get_clusters.R
@@ -44,10 +44,10 @@
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
 
-get_clusters <- function(url = url,
-                         username = username,
-                         password = password,
-                         outbreak_id = outbreak_id,
+get_clusters <- function(url,
+                         username,
+                         password,
+                         outbreak_id,
                          batch_size = 50000) {
 
 # no /export endpoint for clusters so no need to check version

From 996633810ea027079a9e92928ae6f927fa46584f Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 11:00:56 +0000
Subject: [PATCH 074/203] removed pipe from get_clusters

---
 R/get_clusters.R | 30 +++++++++++++++++-------------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/R/get_clusters.R b/R/get_clusters.R
index 6c5bd4c..0a74339 100644
--- a/R/get_clusters.R
+++ b/R/get_clusters.R
@@ -68,17 +68,18 @@ get_clusters <- function(url,
   }
 
   #get total number of records
-  df_n <- GET(
+  df_n_request <- GET(
     paste0(url, "api/outbreaks/", outbreak_id, "/clusters/count"),
     add_headers(Authorization = paste("Bearer", get_access_token(
       url = url,
       username = username,
       password = password
-    ), sep = " "))) %>%
-    content(as = "text") %>%
-    fromJSON(flatten = TRUE) %>%
-    unlist() %>%
-    unname()
+    ), sep = " ")))
+
+  df_n_content <- content(df_n_request, as = "text")
+
+  df_n <- fromJSON(df_n_content, flatten = TRUE)
+  df_n <- unname(unlist(df_n))
 
   #Import records in batches
   df <- tibble()
@@ -103,7 +104,7 @@ get_clusters <- function(url,
     }
 
     #fetch the batch of records
-    df_i <- GET(
+    df_i_request <- GET(
       paste0(
         url,
         "api/outbreaks/",
@@ -119,14 +120,17 @@ get_clusters <- function(url,
         url = url,
         username = username,
         password = password
-      ), sep = " "))) %>%
-      content(as = "text") %>%
-      fromJSON(flatten = TRUE) %>%
-      as_tibble()
+      ), sep = " "))
+    )
+
+    df_i_content <- content(df_i_request, as = "text")
+
+    df_i <- fromJSON(df_i_content, flatten = TRUE)
+
+    df_i <- as_tibble(df_i)
 
     #append the new batch of records to the existing data frame
-    df <- df %>%
-      bind_rows(df_i)
+    df <- bind_rows(df, df_i)
 
     #update numbers for the next iteration
     skip <- skip + batch_size

From 0d4f3ca520618f77b3c0bd3beb70b768d3e117bf Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 11:04:15 +0000
Subject: [PATCH 075/203] used explicit namespace instead of import for
 get_clusters

---
 R/get_clusters.R    | 30 +++++++++++-------------------
 man/get_clusters.Rd |  8 +-------
 2 files changed, 12 insertions(+), 26 deletions(-)

diff --git a/R/get_clusters.R b/R/get_clusters.R
index 0a74339..dbbd548 100644
--- a/R/get_clusters.R
+++ b/R/get_clusters.R
@@ -36,14 +36,6 @@
 #'   outbreak_id = outbreak_id
 #' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @import tibble
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
-
 get_clusters <- function(url,
                          username,
                          password,
@@ -68,21 +60,21 @@ get_clusters <- function(url,
   }
 
   #get total number of records
-  df_n_request <- GET(
+  df_n_request <- httr::GET(
     paste0(url, "api/outbreaks/", outbreak_id, "/clusters/count"),
-    add_headers(Authorization = paste("Bearer", get_access_token(
+    httr::add_headers(Authorization = paste("Bearer", get_access_token(
       url = url,
       username = username,
       password = password
     ), sep = " ")))
 
-  df_n_content <- content(df_n_request, as = "text")
+  df_n_content <- httr::content(df_n_request, as = "text")
 
-  df_n <- fromJSON(df_n_content, flatten = TRUE)
+  df_n <- jsonlite::fromJSON(df_n_content, flatten = TRUE)
   df_n <- unname(unlist(df_n))
 
   #Import records in batches
-  df <- tibble()
+  df <- tibble::tibble()
   batch_size <- batch_size # number of records to import per iteration
   skip <- 0
   message("****************************")
@@ -104,7 +96,7 @@ get_clusters <- function(url,
     }
 
     #fetch the batch of records
-    df_i_request <- GET(
+    df_i_request <- httr::GET(
       paste0(
         url,
         "api/outbreaks/",
@@ -116,21 +108,21 @@ get_clusters <- function(url,
         format(skip, scientific = FALSE),
         "}"
       ),
-      add_headers(Authorization = paste("Bearer", get_access_token(
+      httr::add_headers(Authorization = paste("Bearer", get_access_token(
         url = url,
         username = username,
         password = password
       ), sep = " "))
     )
 
-    df_i_content <- content(df_i_request, as = "text")
+    df_i_content <- httr::content(df_i_request, as = "text")
 
-    df_i <- fromJSON(df_i_content, flatten = TRUE)
+    df_i <- jsonlite::fromJSON(df_i_content, flatten = TRUE)
 
-    df_i <- as_tibble(df_i)
+    df_i <- tibble::as_tibble(df_i)
 
     #append the new batch of records to the existing data frame
-    df <- bind_rows(df, df_i)
+    df <- dplyr::bind_rows(df, df_i)
 
     #update numbers for the next iteration
     skip <- skip + batch_size
diff --git a/man/get_clusters.Rd b/man/get_clusters.Rd
index 1f743c6..550a938 100644
--- a/man/get_clusters.Rd
+++ b/man/get_clusters.Rd
@@ -4,13 +4,7 @@
 \alias{get_clusters}
 \title{Download clusters from Go.Data (version agnostic)}
 \usage{
-get_clusters(
-  url = url,
-  username = username,
-  password = password,
-  outbreak_id = outbreak_id,
-  batch_size = 50000
-)
+get_clusters(url, username, password, outbreak_id, batch_size = 50000)
 }
 \arguments{
 \item{url}{Insert the base URL for your instance of Go.Data here. Don't

From 0c9cb7b5088b9bfde8b2a115a6fcf67ad4476ffb Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 11:42:07 +0000
Subject: [PATCH 076/203] added test for get_clusters

---
 tests/testthat/test-get_clusters.R | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 tests/testthat/test-get_clusters.R

diff --git a/tests/testthat/test-get_clusters.R b/tests/testthat/test-get_clusters.R
new file mode 100644
index 0000000..3155a80
--- /dev/null
+++ b/tests/testthat/test-get_clusters.R
@@ -0,0 +1,23 @@
+test_that("get_clusters works as expected", {
+  skip("get_clusters requires API call")
+
+  res <- get_clusters(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(1L, 11L))
+  expect_identical(
+    colnames(res),
+    c("name", "description", "icon", "colorCode", "id", "createdAt",
+      "createdBy", "updatedAt", "updatedBy", "createdOn", "deleted")
+  )
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c(rep("character", 10), "logical")
+  )
+})

From a8fe768d61e551c981a11532587e6f490b129216 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 11:56:16 +0000
Subject: [PATCH 077/203] linted set_active_outbreak

---
 R/set_active_outbreak.R    | 87 ++++++++++++++++++++++++++++----------
 man/set_active_outbreak.Rd |  3 +-
 2 files changed, 66 insertions(+), 24 deletions(-)

diff --git a/R/set_active_outbreak.R b/R/set_active_outbreak.R
index 530dcd7..960067c 100644
--- a/R/set_active_outbreak.R
+++ b/R/set_active_outbreak.R
@@ -8,7 +8,8 @@
 #' Each Go.Data user can have 1 and only 1 active
 #' outbreak at a given time.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
 #' @param outbreak_id The id number for the outbreak to set to active.
@@ -34,37 +35,77 @@
 #' @import httr
 #' @importFrom jsonlite fromJSON
 
-set_active_outbreak <- function(url=url,
-                                username=username,
-                                password=password,
-                                outbreak_id=outbreak_id) {
+set_active_outbreak <- function(url = url,
+                                username = username,
+                                password = password,
+                                outbreak_id = outbreak_id) {
 
 
   #Get User ID & Active Outbreak ID
-  user.details <- GET(paste0(url,"api/users",
-                      "?access_token=",get_access_token(url=url, username=username, password=password))) %>%
-    content(as="text") %>%
-    fromJSON(flatten=TRUE) %>%
-    filter(email==username)
+  user_details <- GET(
+    paste0(
+      url,
+      "api/users",
+      "?access_token=",
+      get_access_token(
+        url = url,
+        username = username,
+        password = password
+      )
+    )
+  ) %>%
+    content(as = "text") %>%
+    fromJSON(flatten = TRUE) %>%
+    filter(.data$email == username)
 
-  current.active.outbreak <- user.details$activeOutbreakId
-  user.id <- user.details$id
+  current_active_outbreak <- user_details$activeOutbreakId
+  user_id <- user_details$id
 
   #Get List of Available Outbreak IDs
-  available.outbreaks <- get_all_outbreaks(url=url, username=username, password=password) %>%
-    select(id) %>% unlist()
+  available_outbreaks <- get_all_outbreaks(
+    url = url,
+    username = username,
+    password = password
+  ) %>%
+    select(id) %>%
+    unlist()
 
-  if (current.active.outbreak == outbreak_id) {   #Is outbreak_id already active?
-    text <- paste0("Active outbreak not changed. ", outbreak_id, " is already active.")
-  } else if (!(outbreak_id %in% available.outbreaks)) {
-    stop(paste0("Active outbreak not changed. ",outbreak_id, " not in list of user's available outbreaks. Make sure the id number is correct & that the user has proper access."))
+  if (current_active_outbreak == outbreak_id) { # Is outbreak_id already active?
+    text <- paste0(
+      "Active outbreak not changed. ",
+      outbreak_id,
+      " is already active."
+    )
+  } else if (!(outbreak_id %in% available_outbreaks)) {
+    stop(paste0(
+      "Active outbreak not changed. ",
+      outbreak_id,
+      " not in list of user's available outbreaks. Make sure the id number is",
+      " correct & that the user has proper access."
+    ))
   } else {
 
-    new.data <- list("activeOutbreakId"=outbreak_id)
-    patch.active.outbreak <- PATCH(paste0(url,"api/users/",user.id),
-                                   add_headers(Authorization = paste("Bearer", get_access_token(url=url, username=username, password=password), sep = " ")),
-                                   body=new.data,
-                                   encode="json")
+    new_data <- list("activeOutbreakId" = outbreak_id)
+    patch_active_outbreak <- PATCH(
+      paste0(
+        url,
+        "api/users/",
+        user_id
+      ),
+      add_headers(
+        Authorization = paste(
+          "Bearer",
+          get_access_token(
+            url = url,
+            username = username,
+            password = password
+          ),
+          sep = " "
+        )
+      ),
+      body = new_data,
+      encode = "json"
+    )
     text <- paste0("Active outbreak changed! ", outbreak_id, " is now active.")
   }
 
diff --git a/man/set_active_outbreak.Rd b/man/set_active_outbreak.Rd
index 8ffbc8a..9bc8d0f 100644
--- a/man/set_active_outbreak.Rd
+++ b/man/set_active_outbreak.Rd
@@ -12,7 +12,8 @@ set_active_outbreak(
 )
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 

From 270e43061ee6f7354e0e4d5433032fe7429176fb Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 11:56:59 +0000
Subject: [PATCH 078/203] removed recursive argument defaults from
 set_active_outbreak

---
 R/set_active_outbreak.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/set_active_outbreak.R b/R/set_active_outbreak.R
index 960067c..52bbbe9 100644
--- a/R/set_active_outbreak.R
+++ b/R/set_active_outbreak.R
@@ -35,10 +35,10 @@
 #' @import httr
 #' @importFrom jsonlite fromJSON
 
-set_active_outbreak <- function(url = url,
-                                username = username,
-                                password = password,
-                                outbreak_id = outbreak_id) {
+set_active_outbreak <- function(url,
+                                username,
+                                password,
+                                outbreak_id) {
 
 
   #Get User ID & Active Outbreak ID

From a52f48f7931fee08537941113e0bfd72c3c50f68 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 12:00:02 +0000
Subject: [PATCH 079/203] removed pipe from set_active_outbreak

---
 R/set_active_outbreak.R | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/R/set_active_outbreak.R b/R/set_active_outbreak.R
index 52bbbe9..56187bd 100644
--- a/R/set_active_outbreak.R
+++ b/R/set_active_outbreak.R
@@ -42,7 +42,7 @@ set_active_outbreak <- function(url,
 
 
   #Get User ID & Active Outbreak ID
-  user_details <- GET(
+  user_details_request <- GET(
     paste0(
       url,
       "api/users",
@@ -53,10 +53,13 @@ set_active_outbreak <- function(url,
         password = password
       )
     )
-  ) %>%
-    content(as = "text") %>%
-    fromJSON(flatten = TRUE) %>%
-    filter(.data$email == username)
+  )
+
+  user_details_content <-  content(user_details_request, as = "text")
+
+  user_details <- fromJSON(user_details_content, flatten = TRUE)
+
+  user_details <- filter(user_details, .data$email == username)
 
   current_active_outbreak <- user_details$activeOutbreakId
   user_id <- user_details$id
@@ -66,9 +69,10 @@ set_active_outbreak <- function(url,
     url = url,
     username = username,
     password = password
-  ) %>%
-    select(id) %>%
-    unlist()
+  )
+
+  available_outbreaks <- unlist(select(available_outbreaks, id))
+
 
   if (current_active_outbreak == outbreak_id) { # Is outbreak_id already active?
     text <- paste0(

From 77d87db72b1225653a990809d39c68c1ee96f0ae Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 12:03:33 +0000
Subject: [PATCH 080/203] used explicit namespace instead of import for
 set_active_outbreak

---
 R/set_active_outbreak.R    | 30 +++++++++++++-----------------
 man/set_active_outbreak.Rd | 17 +++++++----------
 2 files changed, 20 insertions(+), 27 deletions(-)

diff --git a/R/set_active_outbreak.R b/R/set_active_outbreak.R
index 56187bd..9a602f7 100644
--- a/R/set_active_outbreak.R
+++ b/R/set_active_outbreak.R
@@ -24,17 +24,13 @@
 #' password <- "mypassword"
 #' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 #'
-#' set_active_outbreak(url=url,
-#'                     username=username,
-#'                     password=password,
-#'                     outbreak_id=outbreak_id)
+#' set_active_outbreak(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @importFrom jsonlite fromJSON
-
 set_active_outbreak <- function(url,
                                 username,
                                 password,
@@ -42,7 +38,7 @@ set_active_outbreak <- function(url,
 
 
   #Get User ID & Active Outbreak ID
-  user_details_request <- GET(
+  user_details_request <- httr::GET(
     paste0(
       url,
       "api/users",
@@ -55,11 +51,11 @@ set_active_outbreak <- function(url,
     )
   )
 
-  user_details_content <-  content(user_details_request, as = "text")
+  user_details_content <- httr::content(user_details_request, as = "text")
 
-  user_details <- fromJSON(user_details_content, flatten = TRUE)
+  user_details <- jsonlite::fromJSON(user_details_content, flatten = TRUE)
 
-  user_details <- filter(user_details, .data$email == username)
+  user_details <- dplyr::filter(user_details, .data$email == username)
 
   current_active_outbreak <- user_details$activeOutbreakId
   user_id <- user_details$id
@@ -71,7 +67,7 @@ set_active_outbreak <- function(url,
     password = password
   )
 
-  available_outbreaks <- unlist(select(available_outbreaks, id))
+  available_outbreaks <- unlist(dplyr::select(available_outbreaks, id))
 
 
   if (current_active_outbreak == outbreak_id) { # Is outbreak_id already active?
@@ -90,13 +86,13 @@ set_active_outbreak <- function(url,
   } else {
 
     new_data <- list("activeOutbreakId" = outbreak_id)
-    patch_active_outbreak <- PATCH(
+    patch_active_outbreak <- httr::PATCH(
       paste0(
         url,
         "api/users/",
         user_id
       ),
-      add_headers(
+      httr::add_headers(
         Authorization = paste(
           "Bearer",
           get_access_token(
diff --git a/man/set_active_outbreak.Rd b/man/set_active_outbreak.Rd
index 9bc8d0f..549b038 100644
--- a/man/set_active_outbreak.Rd
+++ b/man/set_active_outbreak.Rd
@@ -4,12 +4,7 @@
 \alias{set_active_outbreak}
 \title{Change the currently active outbreak}
 \usage{
-set_active_outbreak(
-  url = url,
-  username = username,
-  password = password,
-  outbreak_id = outbreak_id
-)
+set_active_outbreak(url, username, password, outbreak_id)
 }
 \arguments{
 \item{url}{Insert the base URL for your instance of Go.Data here. Don't
@@ -41,9 +36,11 @@ username <- "myemail@email.com"
 password <- "mypassword"
 outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 
-set_active_outbreak(url=url,
-                    username=username,
-                    password=password,
-                    outbreak_id=outbreak_id)
+set_active_outbreak(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
 }
 }

From 5f56dcfd4b4ceadfcf9063734c0cb08c5b9dc016 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 13:38:25 +0000
Subject: [PATCH 081/203] set_active_outbreak now returns outbreak_id invisibly

---
 R/set_active_outbreak.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/set_active_outbreak.R b/R/set_active_outbreak.R
index 9a602f7..1b112d2 100644
--- a/R/set_active_outbreak.R
+++ b/R/set_active_outbreak.R
@@ -36,7 +36,6 @@ set_active_outbreak <- function(url,
                                 password,
                                 outbreak_id) {
 
-
   #Get User ID & Active Outbreak ID
   user_details_request <- httr::GET(
     paste0(
@@ -111,6 +110,6 @@ set_active_outbreak <- function(url,
 
   message(text)
 
-
+  invisible(outbreak_id)
 
 }

From 2eaec65d9a92c724e79b2ebc193781e36006db64 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 13:43:04 +0000
Subject: [PATCH 082/203] added tests for set_active_outbreak

---
 tests/testthat/test-set_active_outbreak.R | 32 +++++++++++++++++++++++
 1 file changed, 32 insertions(+)
 create mode 100644 tests/testthat/test-set_active_outbreak.R

diff --git a/tests/testthat/test-set_active_outbreak.R b/tests/testthat/test-set_active_outbreak.R
new file mode 100644
index 0000000..8a3ec4c
--- /dev/null
+++ b/tests/testthat/test-set_active_outbreak.R
@@ -0,0 +1,32 @@
+test_that("set_active_outbreak works as expected", {
+  skip("set_active_outbreak requires API call")
+
+  expect_message(
+    res <- set_active_outbreak(
+      url = url,
+      username = username,
+      password = password,
+      outbreak_id = outbreak_id
+    ),
+    regexp = "Active outbreak not changed."
+  )
+
+  expect_type(res, "character")
+})
+
+test_that("set_active_outbreak works as expected with non-valid outbreak id", {
+  skip("set_active_outbreak requires API call")
+
+  expect_error(
+    set_active_outbreak(
+      url = url,
+      username = username,
+      password = password,
+      outbreak_id = "123"
+    ),
+    regexp = paste0(
+      "Active outbreak not changed. 123 not in list of user's ",
+      "available outbreaks"
+    )
+  )
+})

From 7abe81faae1fef291e4d425223112468e880872e Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 14:07:51 +0000
Subject: [PATCH 083/203] linted get_contacts

---
 R/get_contacts.R    | 116 ++++++++++++++++++++++++++++----------------
 man/get_contacts.Rd |  34 ++++++++-----
 2 files changed, 96 insertions(+), 54 deletions(-)

diff --git a/R/get_contacts.R b/R/get_contacts.R
index c79b1e3..1a686e2 100644
--- a/R/get_contacts.R
+++ b/R/get_contacts.R
@@ -6,33 +6,43 @@
 #' This function works on all versions of Go.Data. There
 #' are two methods for downloading the data:
 #'
-#' `method="batches"` will work on all versions of
+#' `method = "batches"` will work on all versions of
 #'    Go.Data. This method relies on the GET outbreak/{id}/contacts
 #'    API endpoint. Records are then retrieved in batches
 #'    based on `batch_size` and appended together into
-#'    a final dataset. `method="batches"` will be the default and
+#'    a final dataset. `method = "batches"` will be the default and
 #'    only available method for Go.Data version 2.38.0 or older.
 #'
-#' `method="export"` will only work on Go.Data versions
+#' `method = "export"` will only work on Go.Data versions
 #'    2.38.1 or newer. This method relies on the GET
 #'    outbreak/{id}/contacts/export API endpoint. An export
 #'    request is submitted to the server, and then when the
 #'    export is ready, it will be downloaded. Due to better
-#'    performance and more options, `method="export"` will
+#'    performance and more options, `method = "export"` will
 #'    be the default if you are using Go.Data version 2.38.1
 #'    or newer.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
-#' @param outbreak_id The id number for the outbreak for which you want to download data.
-#' @param method The method to download data. `method="export"` is the preferred and default method for Go.Data version 2.38.1 or later. See Details.
-#' @param batch_size If `method="batches"`, then `batch_size` specifies the number of records to retrieve in each iteration.
-#' @param wait If `method="export"`, then `wait` is the number of seconds to wait in between iterations of checking the status of the export.
-#' @param file.type If `method="export"`, then `file.type` determines Whether the resulting data frame should contain nested fields (`file.type="json"`, the default) or an entirely flat data structure (`file.type="csv"`)
+#' @param outbreak_id The id number for the outbreak for which you want to
+#' download data.
+#' @param method The method to download data. `method="export"` is the
+#' preferred and default method for Go.Data version 2.38.1 or later. See
+#' Details.
+#' @param batch_size If `method = "batches"`, then `batch_size` specifies the
+#' number of records to retrieve in each iteration.
+#' @param wait If `method = "export"`, then `wait` is the number of seconds to
+#' wait in between iterations of checking the status of the export.
+#' @param file_type If `method="export"`, then `file_type` determines Whether
+#' the resulting data frame should contain nested fields (`file_type = "json"`,
+#' the default) or an entirely flat data structure (`file_type = "csv"`)
 #'
 #' @return
-#' Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+#' Returns a data frame. Some fields, such as addresses, hospitalization
+#' history, and questionnaire fields may require further unnesting. See
+#' \code{\link[tidyr]{nest}} for assitance with unnesting.
 #' @export
 #'
 #' @examples
@@ -56,23 +66,33 @@
 #' @importFrom purrr pluck
 
 
-get_contacts <- function(url=url,
-                      username=username,
-                      password=password,
-                      outbreak_id=outbreak_id,
-                      method=c("export","batch"),
-                      batch_size=50000,
-                      wait=2,
-                      file.type=c("json","csv")) {
+get_contacts <- function(url = url,
+                         username = username,
+                         password = password,
+                         outbreak_id = outbreak_id,
+                         method = c("export", "batch"),
+                         batch_size = 50000,
+                         wait = 2,
+                         file_type = c("json", "csv")) {
 
+  active_outbreak <- get_active_outbreak(
+    url = url,
+    username = username,
+    password = password
+  )
   #Check that outbreak_id is active
-  if (outbreak_id != get_active_outbreak(url=url, username=username, password=password)) {
-    set_active_outbreak(url=url, username=username, password=password, outbreak_id=outbreak_id)
+  if (outbreak_id != active_outbreak) {
+    set_active_outbreak(
+      url = url,
+      username = username,
+      password = password,
+      outbreak_id = outbreak_id
+    )
   }
 
   #Set default method based on current version of Go.Data
-  version.check <- check_godata_version(url=url)
-  if (!version.check) {
+  version_check <- check_godata_version(url = url)
+  if (!version_check) {
     method <- "batches" #Older version of Go.Data can only use the batch method
   } else if (missing(method)) {
     method <- "export" # For new versions of Go.Data, default to export method
@@ -81,30 +101,42 @@ get_contacts <- function(url=url,
 
   if (method == "batches") {
 
-    api_call_n <- paste0(url, "api/outbreaks/",outbreak_id,"/contacts/filtered-count")
-    api_call_get <- paste0(url, "api/outbreaks/",outbreak_id,"/contacts")
-    df <- batch_downloader(url=url,
-                           username=username,
-                           password=password,
-                           api_call_n=api_call_n,
-                           api_call_get=api_call_get,
-                           batch_size=batch_size)
+    api_call_n <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/contacts/filtered-count"
+    )
+    api_call_get <- paste0(url, "api/outbreaks/", outbreak_id, "/contacts")
+    df <- batch_downloader(
+      url = url,
+      username = username,
+      password = password,
+      api_call_n = api_call_n,
+      api_call_get = api_call_get,
+      batch_size = batch_size
+    )
 
   } else if (method == "export") {
 
-    #Default value of file.type is "json"
-    if (missing(file.type)) file.type <- "json"
+    #Default value of file_type is "json"
+    if (missing(file_type)) file_type <- "json"
 
     #Submit an export request to the system
-    api_call_request <- paste0(url,"api/outbreaks/",outbreak_id,"/contacts/export")
-    df <- export_downloader(url=url,
-                            username=username,
-                            password=password,
-                            api_call_request=api_call_request,
-                            file.type = file.type,
-                            wait = wait)
-
-
+    api_call_request <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/contacts/export"
+    )
+    df <- export_downloader(
+      url = url,
+      username = username,
+      password = password,
+      api_call_request = api_call_request,
+      file_type = file_type,
+      wait = wait
+    )
   }
 
   return(df)
diff --git a/man/get_contacts.Rd b/man/get_contacts.Rd
index 68817ca..6bc714a 100644
--- a/man/get_contacts.Rd
+++ b/man/get_contacts.Rd
@@ -12,28 +12,38 @@ get_contacts(
   method = c("export", "batch"),
   batch_size = 50000,
   wait = 2,
-  file.type = c("json", "csv")
+  file_type = c("json", "csv")
 )
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
 \item{password}{The password for your Go.Data login}
 
-\item{outbreak_id}{The id number for the outbreak for which you want to download data.}
+\item{outbreak_id}{The id number for the outbreak for which you want to
+download data.}
 
-\item{method}{The method to download data. \code{method="export"} is the preferred and default method for Go.Data version 2.38.1 or later. See Details.}
+\item{method}{The method to download data. \code{method="export"} is the
+preferred and default method for Go.Data version 2.38.1 or later. See
+Details.}
 
-\item{batch_size}{If \code{method="batches"}, then \code{batch_size} specifies the number of records to retrieve in each iteration.}
+\item{batch_size}{If \code{method = "batches"}, then \code{batch_size} specifies the
+number of records to retrieve in each iteration.}
 
-\item{wait}{If \code{method="export"}, then \code{wait} is the number of seconds to wait in between iterations of checking the status of the export.}
+\item{wait}{If \code{method = "export"}, then \code{wait} is the number of seconds to
+wait in between iterations of checking the status of the export.}
 
-\item{file.type}{If \code{method="export"}, then \code{file.type} determines Whether the resulting data frame should contain nested fields (\code{file.type="json"}, the default) or an entirely flat data structure (\code{file.type="csv"})}
+\item{file_type}{If \code{method="export"}, then \code{file_type} determines Whether
+the resulting data frame should contain nested fields (\code{file_type = "json"},
+the default) or an entirely flat data structure (\code{file_type = "csv"})}
 }
 \value{
-Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+Returns a data frame. Some fields, such as addresses, hospitalization
+history, and questionnaire fields may require further unnesting. See
+\code{\link[tidyr]{nest}} for assitance with unnesting.
 }
 \description{
 A function to retrieve the contact data for a
@@ -43,19 +53,19 @@ specific \code{outbreak_id}.
 This function works on all versions of Go.Data. There
 are two methods for downloading the data:
 
-\code{method="batches"} will work on all versions of
+\code{method = "batches"} will work on all versions of
 Go.Data. This method relies on the GET outbreak/{id}/contacts
 API endpoint. Records are then retrieved in batches
 based on \code{batch_size} and appended together into
-a final dataset. \code{method="batches"} will be the default and
+a final dataset. \code{method = "batches"} will be the default and
 only available method for Go.Data version 2.38.0 or older.
 
-\code{method="export"} will only work on Go.Data versions
+\code{method = "export"} will only work on Go.Data versions
 2.38.1 or newer. This method relies on the GET
 outbreak/{id}/contacts/export API endpoint. An export
 request is submitted to the server, and then when the
 export is ready, it will be downloaded. Due to better
-performance and more options, \code{method="export"} will
+performance and more options, \code{method = "export"} will
 be the default if you are using Go.Data version 2.38.1
 or newer.
 }

From cf5c17b2909a0c5641efded05a961a02743e81e2 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 14:09:31 +0000
Subject: [PATCH 084/203] removed recursive argument defaults for get_contacts

---
 R/get_contacts.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/get_contacts.R b/R/get_contacts.R
index 1a686e2..e5d6a91 100644
--- a/R/get_contacts.R
+++ b/R/get_contacts.R
@@ -66,10 +66,10 @@
 #' @importFrom purrr pluck
 
 
-get_contacts <- function(url = url,
-                         username = username,
-                         password = password,
-                         outbreak_id = outbreak_id,
+get_contacts <- function(url,
+                         username,
+                         password,
+                         outbreak_id,
                          method = c("export", "batch"),
                          batch_size = 50000,
                          wait = 2,

From dadff767b1001e421e681b7c60b2a22e8cdba49a Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 14:13:14 +0000
Subject: [PATCH 085/203] removed imports from get_contacts

---
 R/get_contacts.R    | 19 ++++++-------------
 man/get_contacts.Rd | 18 ++++++++++--------
 2 files changed, 16 insertions(+), 21 deletions(-)

diff --git a/R/get_contacts.R b/R/get_contacts.R
index e5d6a91..1ae54bb 100644
--- a/R/get_contacts.R
+++ b/R/get_contacts.R
@@ -52,20 +52,13 @@
 #' password <- "mypassword"
 #' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 #'
-#' contacts <- get_contacts(url=url,
-#'                          username=username,
-#'                          password=password,
-#'                          outbreak_id=outbreak_id)
+#' contacts <- get_contacts(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id=outbreak_id
+#' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @import tibble
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
-
-
 get_contacts <- function(url,
                          username,
                          password,
diff --git a/man/get_contacts.Rd b/man/get_contacts.Rd
index 6bc714a..3e9389e 100644
--- a/man/get_contacts.Rd
+++ b/man/get_contacts.Rd
@@ -5,10 +5,10 @@
 \title{Download contacts from Go.Data}
 \usage{
 get_contacts(
-  url = url,
-  username = username,
-  password = password,
-  outbreak_id = outbreak_id,
+  url,
+  username,
+  password,
+  outbreak_id,
   method = c("export", "batch"),
   batch_size = 50000,
   wait = 2,
@@ -76,9 +76,11 @@ username <- "myemail@email.com"
 password <- "mypassword"
 outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 
-contacts <- get_contacts(url=url,
-                         username=username,
-                         password=password,
-                         outbreak_id=outbreak_id)
+contacts <- get_contacts(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id=outbreak_id
+)
 }
 }

From 28e64bdea5f52f1dd4f50a77a6dac04bad29b061 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 14:29:35 +0000
Subject: [PATCH 086/203] added test for get_contacts

---
 tests/testthat/test-get_contacts.R | 55 ++++++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 tests/testthat/test-get_contacts.R

diff --git a/tests/testthat/test-get_contacts.R b/tests/testthat/test-get_contacts.R
new file mode 100644
index 0000000..0df14a6
--- /dev/null
+++ b/tests/testthat/test-get_contacts.R
@@ -0,0 +1,55 @@
+test_that("get_contacts works as expected", {
+  skip("get_contacts requires API call")
+
+  res <- get_contacts(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(14L, 64L))
+  expect_identical(
+    colnames(res),
+    c("id", "visualId", "dateOfReporting", "isDateOfReportingApproximate",
+      "createdAt", "createdBy", "updatedAt", "updatedBy", "deleted",
+      "deletedAt", "createdOn", "firstName", "middleName", "lastName", "gender",
+      "occupation", "dob", "classification", "wasContact", "wasCase",
+      "dateBecomeContact", "riskLevel", "riskReason", "outcomeId",
+      "dateOfOutcome", "documents", "type", "transferRefused", "addresses",
+      "safeBurial", "dateOfBurial", "followUpTeamId", "dateOfLastContact",
+      "numberOfExposures", "numberOfContacts", "vaccinesReceived",
+      "pregnancyStatus", "responsibleUserId", "age.years", "age.months",
+      "followUp.originalStartDate", "followUp.startDate", "followUp.endDate",
+      "followUp.status", "relationship.contactDate",
+      "relationship.contactDateEstimated", "relationship.certaintyLevelId",
+      "relationship.createdAt", "relationship.createdBy",
+      "relationship.updatedAt", "relationship.updatedBy",
+      "relationship.createdOn", "relationship.deleted",
+      "relationship.relatedId", "relationship.id",
+      "relationship.exposureTypeId", "relationship.exposureFrequencyId",
+      "relationship.exposureDurationId",
+      "relationship.socialRelationshipTypeId",
+      "relationship.socialRelationshipDetail", "relationship.clusterId",
+      "relationship.comment", "relationship.deletedAt",
+      "questionnaireAnswers.test")
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "character", "character", "logical", "character",
+      "character", "character", "character", "logical", "logical", "character",
+      "character", "logical", "character", "character", "character", "logical",
+      "character", "logical", "logical", "character", "character", "character",
+      "logical", "logical", "list", "character", "logical", "list", "logical",
+      "logical", "character", "character", "integer", "integer", "list",
+      "logical", "character", "integer", "integer", "character", "character",
+      "character", "character", "character", "logical", "character",
+      "character", "character", "character", "character", "character",
+      "logical", "character", "character", "character", "character",
+      "character", "character", "character", "logical", "logical", "logical",
+      "list")
+  )
+})

From 58d4309bd6d0683f26c937d22b6930824c9461ad Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 14:30:44 +0000
Subject: [PATCH 087/203] ensure contacts are returned as tibble in
 get_contacts

---
 R/get_contacts.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/get_contacts.R b/R/get_contacts.R
index 1ae54bb..3095f00 100644
--- a/R/get_contacts.R
+++ b/R/get_contacts.R
@@ -132,5 +132,7 @@ get_contacts <- function(url,
     )
   }
 
+  df <- tibble::as_tibble(df)
+
   return(df)
 }

From 98796a17648340390f188b2135e80e62fcbea482 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 14:43:46 +0000
Subject: [PATCH 088/203] linted get_contacts_of_contacts

---
 R/get_contacts_of_contacts.R    | 131 +++++++++++++++++++++-----------
 man/get_contacts_of_contacts.Rd |  44 +++++++----
 2 files changed, 113 insertions(+), 62 deletions(-)

diff --git a/R/get_contacts_of_contacts.R b/R/get_contacts_of_contacts.R
index 7459ffb..c97a513 100644
--- a/R/get_contacts_of_contacts.R
+++ b/R/get_contacts_of_contacts.R
@@ -6,34 +6,44 @@
 #' This function works on all versions of Go.Data. There
 #' are two methods for downloading the data:
 #'
-#' `method="batches"` will work on all versions of
+#' `method = "batches"` will work on all versions of
 #'    Go.Data. This method relies on the GET
 #'    outbreak/{id}/contacts-of-contacts API endpoint.
 #'    Records are then retrieved in batches based on
 #'    `batch_size` and appended together into a final
-#'    dataset. `method="batches"` will be the default and
+#'    dataset. `method = "batches"` will be the default and
 #'    only available method for Go.Data version 2.38.0 or older.
 #'
-#' `method="export"` will only work on Go.Data versions
+#' `method = "export"` will only work on Go.Data versions
 #'    2.38.1 or newer. This method relies on the GET
 #'    outbreak/{id}/contacts-of-contacts/export API endpoint.
 #'    An export request is submitted to the server, and then
 #'    when the export is ready, it will be downloaded. Due to
-#'    better performance and more options, `method="export"` will
+#'    better performance and more options, `method = "export"` will
 #'    be the default if you are using Go.Data version 2.38.1
 #'    or newer.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
-#' @param outbreak_id The id number for the outbreak for which you want to download data.
-#' @param method The method to download data. `method="export"` is the preferred and default method for Go.Data version 2.38.1 or later. See Details.
-#' @param batch_size If `method="batches"`, then `batch_size` specifies the number of records to retrieve in each iteration.
-#' @param wait If `method="export"`, then `wait` is the number of seconds to wait in between iterations of checking the status of the export.
-#' @param file.type If `method="export"`, then `file.type` determines Whether the resulting data frame should contain nested fields (`file.type="json"`, the default) or an entirely flat data structure (`file.type="csv"`)
+#' @param outbreak_id The id number for the outbreak for which you want to
+#' download data.
+#' @param method The method to download data. `method = "export"` is the
+#' preferred and default method for Go.Data version 2.38.1 or later. See
+#' Details.
+#' @param batch_size If `method = "batches"`, then `batch_size` specifies the
+#' number of records to retrieve in each iteration.
+#' @param wait If `method = "export"`, then `wait` is the number of seconds to
+#' wait in between iterations of checking the status of the export.
+#' @param file_type If `method = "export"`, then `file_type` determines Whether
+#' the resulting data frame should contain nested fields (`file_type = "json"`,
+#' the default) or an entirely flat data structure (`file_type = "csv"`)
 #'
 #' @return
-#' Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+#' Returns a data frame. Some fields, such as addresses, hospitalization
+#' history, and questionnaire fields may require further unnesting. See
+#' \code{\link[tidyr]{nest}} for assitance with unnesting.
 #' @export
 #'
 #' @examples
@@ -43,10 +53,12 @@
 #' password <- "mypassword"
 #' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 #'
-#' contacts_of_contacts <- get_contacts_of_contacts(url=url,
-#'                                                  username=username,
-#'                                                  password=password,
-#'                                                  outbreak_id=outbreak_id)
+#' contacts_of_contacts <- get_contacts_of_contacts(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
 #' }
 #' @importFrom magrittr %>%
 #' @import dplyr
@@ -57,23 +69,33 @@
 #' @importFrom purrr pluck
 
 
-get_contacts_of_contacts <- function(url=url,
-                                     username=username,
-                                     password=password,
-                                     outbreak_id=outbreak_id,
-                                     method=c("export","batch"),
-                                     batch_size=50000,
-                                     wait=2,
-                                     file.type=c("json","csv")) {
+get_contacts_of_contacts <- function(url = url,
+                                     username = username,
+                                     password = password,
+                                     outbreak_id = outbreak_id,
+                                     method = c("export", "batch"),
+                                     batch_size = 50000,
+                                     wait = 2,
+                                     file_type = c("json", "csv")) {
 
   #Check that outbreak_id is active
-  if (outbreak_id != get_active_outbreak(url=url, username=username, password=password)) {
-    set_active_outbreak(url=url, username=username, password=password, outbreak_id=outbreak_id)
+  active_outbreak <- get_active_outbreak(
+    url = url,
+    username = username,
+    password = password
+  )
+  if (outbreak_id != active_outbreak) {
+    set_active_outbreak(
+      url = url,
+      username = username,
+      password = password,
+      outbreak_id = outbreak_id
+    )
   }
 
   #Set default method based on current version of Go.Data
-  version.check <- check_godata_version(url=url)
-  if (!version.check) {
+  version_check <- check_godata_version(url = url)
+  if (!version_check) {
     method <- "batches" #Older version of Go.Data can only use the batch method
   } else if (missing(method)) {
     method <- "export" # For new versions of Go.Data, default to export method
@@ -82,30 +104,47 @@ get_contacts_of_contacts <- function(url=url,
 
   if (method == "batches") {
 
-    api_call_n <- paste0(url, "api/outbreaks/",outbreak_id,"/contacts-of-contacts/filtered-count")
-    api_call_get <- paste0(url, "api/outbreaks/",outbreak_id,"/contacts-of-contacts")
-    df <- batch_downloader(url=url,
-                           username=username,
-                           password=password,
-                           api_call_n=api_call_n,
-                           api_call_get=api_call_get,
-                           batch_size=batch_size)
+    api_call_n <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/contacts-of-contacts/filtered-count"
+    )
+    api_call_get <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/contacts-of-contacts"
+    )
+    df <- batch_downloader(
+      url = url,
+      username = username,
+      password = password,
+      api_call_n = api_call_n,
+      api_call_get = api_call_get,
+      batch_size = batch_size
+    )
 
   } else if (method == "export") {
 
-    #Default value of file.type is "json"
-    if (missing(file.type)) file.type <- "json"
+    #Default value of file_type is "json"
+    if (missing(file_type)) file_type <- "json"
 
     #Submit an export request to the system
-    api_call_request <- paste0(url,"api/outbreaks/",outbreak_id,"/contacts-of-contacts/export")
-    df <- export_downloader(url=url,
-                            username=username,
-                            password=password,
-                            api_call_request=api_call_request,
-                            file.type = file.type,
-                            wait = wait)
-
-
+    api_call_request <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/contacts-of-contacts/export"
+    )
+    df <- export_downloader(
+      url = url,
+      username = username,
+      password = password,
+      api_call_request = api_call_request,
+      file_type = file_type,
+      wait = wait
+    )
   }
 
   return(df)
diff --git a/man/get_contacts_of_contacts.Rd b/man/get_contacts_of_contacts.Rd
index 66bc41f..0c5de92 100644
--- a/man/get_contacts_of_contacts.Rd
+++ b/man/get_contacts_of_contacts.Rd
@@ -12,28 +12,38 @@ get_contacts_of_contacts(
   method = c("export", "batch"),
   batch_size = 50000,
   wait = 2,
-  file.type = c("json", "csv")
+  file_type = c("json", "csv")
 )
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
 \item{password}{The password for your Go.Data login}
 
-\item{outbreak_id}{The id number for the outbreak for which you want to download data.}
+\item{outbreak_id}{The id number for the outbreak for which you want to
+download data.}
 
-\item{method}{The method to download data. \code{method="export"} is the preferred and default method for Go.Data version 2.38.1 or later. See Details.}
+\item{method}{The method to download data. \code{method = "export"} is the
+preferred and default method for Go.Data version 2.38.1 or later. See
+Details.}
 
-\item{batch_size}{If \code{method="batches"}, then \code{batch_size} specifies the number of records to retrieve in each iteration.}
+\item{batch_size}{If \code{method = "batches"}, then \code{batch_size} specifies the
+number of records to retrieve in each iteration.}
 
-\item{wait}{If \code{method="export"}, then \code{wait} is the number of seconds to wait in between iterations of checking the status of the export.}
+\item{wait}{If \code{method = "export"}, then \code{wait} is the number of seconds to
+wait in between iterations of checking the status of the export.}
 
-\item{file.type}{If \code{method="export"}, then \code{file.type} determines Whether the resulting data frame should contain nested fields (\code{file.type="json"}, the default) or an entirely flat data structure (\code{file.type="csv"})}
+\item{file_type}{If \code{method = "export"}, then \code{file_type} determines Whether
+the resulting data frame should contain nested fields (\code{file_type = "json"},
+the default) or an entirely flat data structure (\code{file_type = "csv"})}
 }
 \value{
-Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+Returns a data frame. Some fields, such as addresses, hospitalization
+history, and questionnaire fields may require further unnesting. See
+\code{\link[tidyr]{nest}} for assitance with unnesting.
 }
 \description{
 A function to retrieve the contact-of-contact
@@ -43,20 +53,20 @@ data for a specific \code{outbreak_id}.
 This function works on all versions of Go.Data. There
 are two methods for downloading the data:
 
-\code{method="batches"} will work on all versions of
+\code{method = "batches"} will work on all versions of
 Go.Data. This method relies on the GET
 outbreak/{id}/contacts-of-contacts API endpoint.
 Records are then retrieved in batches based on
 \code{batch_size} and appended together into a final
-dataset. \code{method="batches"} will be the default and
+dataset. \code{method = "batches"} will be the default and
 only available method for Go.Data version 2.38.0 or older.
 
-\code{method="export"} will only work on Go.Data versions
+\code{method = "export"} will only work on Go.Data versions
 2.38.1 or newer. This method relies on the GET
 outbreak/{id}/contacts-of-contacts/export API endpoint.
 An export request is submitted to the server, and then
 when the export is ready, it will be downloaded. Due to
-better performance and more options, \code{method="export"} will
+better performance and more options, \code{method = "export"} will
 be the default if you are using Go.Data version 2.38.1
 or newer.
 }
@@ -67,9 +77,11 @@ username <- "myemail@email.com"
 password <- "mypassword"
 outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 
-contacts_of_contacts <- get_contacts_of_contacts(url=url,
-                                                 username=username,
-                                                 password=password,
-                                                 outbreak_id=outbreak_id)
+contacts_of_contacts <- get_contacts_of_contacts(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
 }
 }

From e9fddf36523080374e81c5df1d1684fe78b5815f Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 14:44:28 +0000
Subject: [PATCH 089/203] removed recursive default arguments from
 get_contacts_of_contacts

---
 R/get_contacts_of_contacts.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/get_contacts_of_contacts.R b/R/get_contacts_of_contacts.R
index c97a513..8b25612 100644
--- a/R/get_contacts_of_contacts.R
+++ b/R/get_contacts_of_contacts.R
@@ -69,10 +69,10 @@
 #' @importFrom purrr pluck
 
 
-get_contacts_of_contacts <- function(url = url,
-                                     username = username,
-                                     password = password,
-                                     outbreak_id = outbreak_id,
+get_contacts_of_contacts <- function(url,
+                                     username,
+                                     password,
+                                     outbreak_id,
                                      method = c("export", "batch"),
                                      batch_size = 50000,
                                      wait = 2,

From b298b01e91fa565ac47531dd0f2abe87fa0cbb2a Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 14:45:33 +0000
Subject: [PATCH 090/203] removed imports from get_contacts_of_contacts

---
 R/get_contacts_of_contacts.R    | 9 ---------
 man/get_contacts_of_contacts.Rd | 8 ++++----
 2 files changed, 4 insertions(+), 13 deletions(-)

diff --git a/R/get_contacts_of_contacts.R b/R/get_contacts_of_contacts.R
index 8b25612..cd98bdf 100644
--- a/R/get_contacts_of_contacts.R
+++ b/R/get_contacts_of_contacts.R
@@ -60,15 +60,6 @@
 #'   outbreak_id = outbreak_id
 #' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @import tibble
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
-
-
 get_contacts_of_contacts <- function(url,
                                      username,
                                      password,
diff --git a/man/get_contacts_of_contacts.Rd b/man/get_contacts_of_contacts.Rd
index 0c5de92..33d8205 100644
--- a/man/get_contacts_of_contacts.Rd
+++ b/man/get_contacts_of_contacts.Rd
@@ -5,10 +5,10 @@
 \title{Download contacts-of-contacts from Go.Data}
 \usage{
 get_contacts_of_contacts(
-  url = url,
-  username = username,
-  password = password,
-  outbreak_id = outbreak_id,
+  url,
+  username,
+  password,
+  outbreak_id,
   method = c("export", "batch"),
   batch_size = 50000,
   wait = 2,

From 9f10f0c5cbcd4236719627c0f5842dccc4831717 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 14:46:11 +0000
Subject: [PATCH 091/203] ensure get_contact_of_contacts is returned as a
 tibble

---
 R/get_contacts_of_contacts.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/get_contacts_of_contacts.R b/R/get_contacts_of_contacts.R
index cd98bdf..a18baae 100644
--- a/R/get_contacts_of_contacts.R
+++ b/R/get_contacts_of_contacts.R
@@ -138,5 +138,7 @@ get_contacts_of_contacts <- function(url,
     )
   }
 
+  df <- tibble::as_tibble(df)
+
   return(df)
 }

From d771daa3f6c13231cfee2eff5b4d3b325f93ce5f Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 2 Feb 2023 14:55:22 +0000
Subject: [PATCH 092/203] added test for get_contacts_of_contacts

---
 .../testthat/test-get_contacts_of_contacts.R  | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 tests/testthat/test-get_contacts_of_contacts.R

diff --git a/tests/testthat/test-get_contacts_of_contacts.R b/tests/testthat/test-get_contacts_of_contacts.R
new file mode 100644
index 0000000..170436f
--- /dev/null
+++ b/tests/testthat/test-get_contacts_of_contacts.R
@@ -0,0 +1,37 @@
+test_that("get_contacts_of_contacts works as expected", {
+  skip("get_contacts_of_contacts requires API call")
+
+  res <- get_contacts_of_contacts(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(1L, 39L))
+  expect_identical(
+    colnames(res),
+    c("id", "visualId", "dateOfReporting", "isDateOfReportingApproximate",
+      "createdAt", "createdBy", "updatedAt", "updatedBy", "deleted",
+      "deletedAt", "createdOn", "firstName", "middleName", "lastName",
+      "gender", "occupation", "dob", "classification", "wasContact", "wasCase",
+      "dateBecomeContact", "riskLevel", "riskReason", "outcomeId",
+      "dateOfOutcome", "documents", "type", "transferRefused", "addresses",
+      "safeBurial", "dateOfBurial", "dateOfLastContact", "numberOfExposures",
+      "vaccinesReceived", "pregnancyStatus", "responsibleUserId",
+      "relationship", "age.years", "age.months")
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "character", "character", "logical", "character",
+      "character", "character", "character", "logical", "logical", "character",
+      "character", "logical", "character", "character", "logical", "logical",
+      "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "logical", "list", "character", "logical", "list", "logical",
+      "logical", "character", "integer", "list", "character", "logical",
+      "logical", "integer", "logical")
+  )
+})

From e23a8897b18e930ee97b0b40020fe391003ea8e1 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 3 Feb 2023 10:04:10 +0000
Subject: [PATCH 093/203] linted get_languages

---
 R/get_languages.R    | 36 ++++++++++++++++++++++++------------
 man/get_languages.Rd | 11 +++++++----
 2 files changed, 31 insertions(+), 16 deletions(-)

diff --git a/R/get_languages.R b/R/get_languages.R
index 6777c3e..96969ec 100644
--- a/R/get_languages.R
+++ b/R/get_languages.R
@@ -1,7 +1,8 @@
 #' Get lanuages in Go.Data
 #'
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
 #'
@@ -15,9 +16,11 @@
 #' password <- "mypassword"
 #' language <- "english_us"
 #'
-#' languages <- get_languages(url=url,
-#'                            username=username,
-#'                            password=password)
+#' languages <- get_languages(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
 #' }
 #' @importFrom magrittr %>%
 #' @import dplyr
@@ -27,16 +30,25 @@
 #' @importFrom purrr pluck
 
 
-get_languages <- function(url=url,
-                          username=username,
-                          password=password) {
+get_languages <- function(url = url,
+                          username = username,
+                          password = password) {
 
-  df <- GET(paste0(url,"api/languages/",
-                   "?access_token=",get_access_token(url=url, username=username, password=password))) %>%
-    content(as="text") %>%
-    fromJSON(flatten=TRUE) %>%
+  df <- GET(
+    paste0(
+      url,
+      "api/languages/",
+      "?access_token=",
+      get_access_token(
+        url = url,
+        username = username,
+        password = password
+      )
+    )
+  ) %>%
+    content(as = "text") %>%
+    fromJSON(flatten = TRUE) %>%
     as_tibble()
 
   return(df)
-
 }
diff --git a/man/get_languages.Rd b/man/get_languages.Rd
index 2790301..6ad8a3a 100644
--- a/man/get_languages.Rd
+++ b/man/get_languages.Rd
@@ -7,7 +7,8 @@
 get_languages(url = url, username = username, password = password)
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
@@ -26,8 +27,10 @@ username <- "myemail@email.com"
 password <- "mypassword"
 language <- "english_us"
 
-languages <- get_languages(url=url,
-                           username=username,
-                           password=password)
+languages <- get_languages(
+  url = url,
+  username = username,
+  password = password
+)
 }
 }

From 4e44181c746978f722b6e442333c69eaf957db4b Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 3 Feb 2023 10:05:08 +0000
Subject: [PATCH 094/203] removed pipe from get_languages

---
 R/get_languages.R | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/R/get_languages.R b/R/get_languages.R
index 96969ec..8e46b9c 100644
--- a/R/get_languages.R
+++ b/R/get_languages.R
@@ -34,7 +34,7 @@ get_languages <- function(url = url,
                           username = username,
                           password = password) {
 
-  df <- GET(
+  df_request <- GET(
     paste0(
       url,
       "api/languages/",
@@ -45,10 +45,13 @@ get_languages <- function(url = url,
         password = password
       )
     )
-  ) %>%
-    content(as = "text") %>%
-    fromJSON(flatten = TRUE) %>%
-    as_tibble()
+  )
+
+  df_content <- content(df_request, as = "text")
+
+  df <- fromJSON(df_content, flatten = TRUE)
+
+  df <- as_tibble(df)
 
   return(df)
 }

From 2ec3a5f2a46f609d3894d0251bc87843d5e88bf9 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 3 Feb 2023 10:05:35 +0000
Subject: [PATCH 095/203] removed recursive default arugments from
 get_languages

---
 R/get_languages.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/get_languages.R b/R/get_languages.R
index 8e46b9c..0d084db 100644
--- a/R/get_languages.R
+++ b/R/get_languages.R
@@ -30,9 +30,9 @@
 #' @importFrom purrr pluck
 
 
-get_languages <- function(url = url,
-                          username = username,
-                          password = password) {
+get_languages <- function(url,
+                          username,
+                          password) {
 
   df_request <- GET(
     paste0(

From 668c3a8d678a68b007a003cb1b4e661f02ebfe5c Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 3 Feb 2023 10:07:29 +0000
Subject: [PATCH 096/203] used explicit namespace instead of import for
 get_languages

---
 R/get_languages.R    | 16 ++++------------
 man/get_languages.Rd |  2 +-
 2 files changed, 5 insertions(+), 13 deletions(-)

diff --git a/R/get_languages.R b/R/get_languages.R
index 0d084db..c227830 100644
--- a/R/get_languages.R
+++ b/R/get_languages.R
@@ -22,19 +22,11 @@
 #'   password = password
 #' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
-
-
 get_languages <- function(url,
                           username,
                           password) {
 
-  df_request <- GET(
+  df_request <- httr::GET(
     paste0(
       url,
       "api/languages/",
@@ -47,11 +39,11 @@ get_languages <- function(url,
     )
   )
 
-  df_content <- content(df_request, as = "text")
+  df_content <- httr::content(df_request, as = "text")
 
-  df <- fromJSON(df_content, flatten = TRUE)
+  df <- jsonlite::fromJSON(df_content, flatten = TRUE)
 
-  df <- as_tibble(df)
+  df <- tibble::as_tibble(df)
 
   return(df)
 }
diff --git a/man/get_languages.Rd b/man/get_languages.Rd
index 6ad8a3a..003e55d 100644
--- a/man/get_languages.Rd
+++ b/man/get_languages.Rd
@@ -4,7 +4,7 @@
 \alias{get_languages}
 \title{Get lanuages in Go.Data}
 \usage{
-get_languages(url = url, username = username, password = password)
+get_languages(url, username, password)
 }
 \arguments{
 \item{url}{Insert the base URL for your instance of Go.Data here. Don't

From 31389c7a20f23b2d1c103c25ee3e1e483b9a837a Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 3 Feb 2023 10:12:13 +0000
Subject: [PATCH 097/203] added test for get_languages

---
 tests/testthat/test-get_languages.R | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 tests/testthat/test-get_languages.R

diff --git a/tests/testthat/test-get_languages.R b/tests/testthat/test-get_languages.R
new file mode 100644
index 0000000..16cc933
--- /dev/null
+++ b/tests/testthat/test-get_languages.R
@@ -0,0 +1,23 @@
+test_that("get_languages works as expected", {
+  skip("get_languages requires API call")
+
+  res <- get_languages(
+    url = url,
+    username = username,
+    password = password
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(6L, 9L))
+  expect_identical(
+    colnames(res),
+    c("name", "readOnly", "id", "createdAt", "createdBy", "updatedAt",
+      "updatedBy", "createdOn", "deleted")
+  )
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "logical", "character", "character", "character",
+      "character", "character", "character", "logical")
+  )
+})

From 52e1d831036f3457c0acb11becf1fdb53194c7f6 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 3 Feb 2023 10:16:20 +0000
Subject: [PATCH 098/203] linted get_language_tokens

---
 R/get_language_tokens.R    | 50 ++++++++++++++++++++++++++------------
 man/get_language_tokens.Rd | 25 ++++++++++++-------
 2 files changed, 50 insertions(+), 25 deletions(-)

diff --git a/R/get_language_tokens.R b/R/get_language_tokens.R
index 28c365e..0fe61c1 100644
--- a/R/get_language_tokens.R
+++ b/R/get_language_tokens.R
@@ -1,13 +1,17 @@
-#' Get a list of variable tokens and their labels for the language you specify, in order to re-code variables in R.
+#' Get a list of variable tokens and their labels for the language you specify,
+#' in order to re-code variables in R.
 #'
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
-#' @param language The language ID you are retrieving translation file for, for instance "english_us"
+#' @param language The language ID you are retrieving translation file for,
+#' for instance "english_us"
 #'
 #' @return
-#' Returns data frame of language tokens for your language. You will only be able to execute this function if you have access to the language tokens.
+#' Returns data frame of language tokens for your language. You will only be
+#' able to execute this function if you have access to the language tokens.
 #' @export
 #' @examples
 #' \dontrun{
@@ -16,10 +20,12 @@
 #' password <- "mypassword"
 #' language <- "english_us"
 #'
-#' language_tokens <- get_language_tokens(url=url,
-#'                                        username=username,
-#'                                        password=password,
-#'                                        language=language)
+#' language_tokens <- get_language_tokens(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   language = language
+#' )
 #' }
 #' @importFrom magrittr %>%
 #' @import dplyr
@@ -29,15 +35,27 @@
 #' @importFrom purrr pluck
 
 
-get_language_tokens <- function(url=url,
-                                username=username,
-                                password=password,
-                                language=language) {
+get_language_tokens <- function(url = url,
+                                username = username,
+                                password = password,
+                                language = language) {
 
-  df <- GET(paste0(url,"api/languages/",language,"/language-tokens",
-                          "?access_token=",get_access_token(url=url, username=username, password=password))) %>%
-    content(as="text") %>%
-    fromJSON(flatten=TRUE) %>%
+  df <- GET(
+    paste0(
+      url,
+      "api/languages/",
+      language,
+      "/language-tokens",
+      "?access_token=",
+      get_access_token(
+        url = url,
+        username = username,
+        password = password
+      )
+    )
+  ) %>%
+    content(as = "text") %>%
+    fromJSON(flatten = TRUE) %>%
     as_tibble()
 
   return(df)
diff --git a/man/get_language_tokens.Rd b/man/get_language_tokens.Rd
index f40f3f3..5c40d4c 100644
--- a/man/get_language_tokens.Rd
+++ b/man/get_language_tokens.Rd
@@ -2,7 +2,8 @@
 % Please edit documentation in R/get_language_tokens.R
 \name{get_language_tokens}
 \alias{get_language_tokens}
-\title{Get a list of variable tokens and their labels for the language you specify, in order to re-code variables in R.}
+\title{Get a list of variable tokens and their labels for the language you specify,
+in order to re-code variables in R.}
 \usage{
 get_language_tokens(
   url = url,
@@ -12,19 +13,23 @@ get_language_tokens(
 )
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
 \item{password}{The password for your Go.Data login}
 
-\item{language}{The language ID you are retrieving translation file for, for instance "english_us"}
+\item{language}{The language ID you are retrieving translation file for,
+for instance "english_us"}
 }
 \value{
-Returns data frame of language tokens for your language. You will only be able to execute this function if you have access to the language tokens.
+Returns data frame of language tokens for your language. You will only be
+able to execute this function if you have access to the language tokens.
 }
 \description{
-Get a list of variable tokens and their labels for the language you specify, in order to re-code variables in R.
+Get a list of variable tokens and their labels for the language you specify,
+in order to re-code variables in R.
 }
 \examples{
 \dontrun{
@@ -33,9 +38,11 @@ username <- "myemail@email.com"
 password <- "mypassword"
 language <- "english_us"
 
-language_tokens <- get_language_tokens(url=url,
-                                       username=username,
-                                       password=password,
-                                       language=language)
+language_tokens <- get_language_tokens(
+  url = url,
+  username = username,
+  password = password,
+  language = language
+)
 }
 }

From 72b47a0687a278e83447802c33f1d644b4d21724 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 3 Feb 2023 10:20:52 +0000
Subject: [PATCH 099/203] removed recursive argument defaults for
 get_language_tokens

---
 R/get_language_tokens.R    | 8 ++++----
 man/get_language_tokens.Rd | 7 +------
 2 files changed, 5 insertions(+), 10 deletions(-)

diff --git a/R/get_language_tokens.R b/R/get_language_tokens.R
index 0fe61c1..773a541 100644
--- a/R/get_language_tokens.R
+++ b/R/get_language_tokens.R
@@ -35,10 +35,10 @@
 #' @importFrom purrr pluck
 
 
-get_language_tokens <- function(url = url,
-                                username = username,
-                                password = password,
-                                language = language) {
+get_language_tokens <- function(url,
+                                username,
+                                password,
+                                language) {
 
   df <- GET(
     paste0(
diff --git a/man/get_language_tokens.Rd b/man/get_language_tokens.Rd
index 5c40d4c..d6ab57c 100644
--- a/man/get_language_tokens.Rd
+++ b/man/get_language_tokens.Rd
@@ -5,12 +5,7 @@
 \title{Get a list of variable tokens and their labels for the language you specify,
 in order to re-code variables in R.}
 \usage{
-get_language_tokens(
-  url = url,
-  username = username,
-  password = password,
-  language = language
-)
+get_language_tokens(url, username, password, language)
 }
 \arguments{
 \item{url}{Insert the base URL for your instance of Go.Data here. Don't

From 339ef2d532795c68c24668abf6f74b635df86297 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 3 Feb 2023 10:22:01 +0000
Subject: [PATCH 100/203] removed pipe from get_language_tokens

---
 R/get_language_tokens.R | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/R/get_language_tokens.R b/R/get_language_tokens.R
index 773a541..742cea2 100644
--- a/R/get_language_tokens.R
+++ b/R/get_language_tokens.R
@@ -40,7 +40,7 @@ get_language_tokens <- function(url,
                                 password,
                                 language) {
 
-  df <- GET(
+  df_request <- GET(
     paste0(
       url,
       "api/languages/",
@@ -53,10 +53,13 @@ get_language_tokens <- function(url,
         password = password
       )
     )
-  ) %>%
-    content(as = "text") %>%
-    fromJSON(flatten = TRUE) %>%
-    as_tibble()
+  )
+
+  df_content <-  content(df_request, as = "text")
+
+  df <- fromJSON(df_content, flatten = TRUE)
+
+  df <- as_tibble(df)
 
   return(df)
 

From 79a1801bb6e507e2c690dd3adb91e054040fd8de Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 3 Feb 2023 10:26:38 +0000
Subject: [PATCH 101/203] used explicit namespace instead of import for
 get_language_tokens

---
 R/get_language_tokens.R | 17 ++++-------------
 1 file changed, 4 insertions(+), 13 deletions(-)

diff --git a/R/get_language_tokens.R b/R/get_language_tokens.R
index 742cea2..2f0a5af 100644
--- a/R/get_language_tokens.R
+++ b/R/get_language_tokens.R
@@ -27,20 +27,12 @@
 #'   language = language
 #' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
-
-
 get_language_tokens <- function(url,
                                 username,
                                 password,
                                 language) {
 
-  df_request <- GET(
+  df_request <- httr::GET(
     paste0(
       url,
       "api/languages/",
@@ -55,12 +47,11 @@ get_language_tokens <- function(url,
     )
   )
 
-  df_content <-  content(df_request, as = "text")
+  df_content <- httr::content(df_request, as = "text")
 
-  df <- fromJSON(df_content, flatten = TRUE)
+  df <- jsonlite::fromJSON(df_content, flatten = TRUE)
 
-  df <- as_tibble(df)
+  df <- tibble::as_tibble(df)
 
   return(df)
-
 }

From 73cf55919d57562be5ddd8d17d79b4a30cee811e Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 3 Feb 2023 10:34:45 +0000
Subject: [PATCH 102/203] added test for get_language_tokens

---
 tests/testthat/test-get_language_tokens.R | 24 +++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 tests/testthat/test-get_language_tokens.R

diff --git a/tests/testthat/test-get_language_tokens.R b/tests/testthat/test-get_language_tokens.R
new file mode 100644
index 0000000..23e975d
--- /dev/null
+++ b/tests/testthat/test-get_language_tokens.R
@@ -0,0 +1,24 @@
+test_that("get_language_tokens works as expected", {
+  skip("get_language_tokens requires API call")
+
+  res <- get_language_tokens(
+    url = url,
+    username = username,
+    password = password,
+    language = "english_us"
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(13641L, 3L))
+  expect_identical(
+    colnames(res),
+    c("languageId", "lastUpdateDate", "tokens")
+  )
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "character", "data.frame")
+  )
+  expect_identical(colnames(res$tokens),c("token", "translation"))
+  expect_identical(dim(res$tokens), c(13641L, 2L))
+})

From af77bd75b37ec74d72a76eaa4f470485d737aa00 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Sun, 5 Feb 2023 20:07:32 +0000
Subject: [PATCH 103/203] added translate_categories function and helper
 functions

---
 NAMESPACE                   |  1 +
 R/translate_categories.R    | 95 +++++++++++++++++++++++++++++++++++++
 man/any_tokens.Rd           | 21 ++++++++
 man/translate_categories.Rd | 44 +++++++++++++++++
 man/translate_token.Rd      | 22 +++++++++
 5 files changed, 183 insertions(+)
 create mode 100644 R/translate_categories.R
 create mode 100644 man/any_tokens.Rd
 create mode 100644 man/translate_categories.Rd
 create mode 100644 man/translate_token.Rd

diff --git a/NAMESPACE b/NAMESPACE
index efb977e..4ce71b1 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -29,6 +29,7 @@ export(get_users)
 export(mongify_date)
 export(null2na)
 export(set_active_outbreak)
+export(translate_categories)
 import(data.table)
 import(dplyr)
 import(httr)
diff --git a/R/translate_categories.R b/R/translate_categories.R
new file mode 100644
index 0000000..a10a81d
--- /dev/null
+++ b/R/translate_categories.R
@@ -0,0 +1,95 @@
+#' Translates cateogories with API labels to more readable forms using the
+#' translation specified in the output of `get_language_tokens()`.
+#'
+#' @param data A data frame (or data frame extension)
+#' @param language_tokens A data frame (or data frame extension) containing
+#' the translations. Output from `get_language_tokens()`
+#'
+#' @return A tibble
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' cases <- get_cases(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' language_tokens <- get_language_tokens(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   language = "english_us"
+#' )
+#'
+#' translate_categories(
+#'   data = cases,
+#'   language_tokens = language_tokens
+#' )
+#' }
+translate_categories <- function(data, language_tokens) {
+
+  stopifnot(
+    "data must be tabular data" =
+      is.data.frame(data),
+    "language_tokens must be tabular data" =
+      is.data.frame(language_tokens)
+  )
+
+  if (isFALSE(any_tokens(data, language_tokens))) {
+    return(data)
+  }
+
+  data <- translate_token(data = data, language_tokens = language_tokens)
+
+  data <- tibble::as_tibble(data)
+
+  return(data)
+}
+
+#' Translates tokens given a specified translation.
+#'
+#' @description This function does all the translation for
+#' `translate_categories`.
+#'
+#' @inheritParams translate_categories
+#'
+#' @return A tibble
+#' @keywords internal
+translate_token <- function(data, language_tokens) {
+  if (is.list(data)) {
+    for (i in seq_along(data)) {
+      if (any_tokens(data[[i]], language_tokens)) {
+        data[[i]] <- translate_token(
+          data = data[[i]],
+          language_tokens = language_tokens
+        )
+      }
+    }
+  } else {
+    token_index <- lapply(
+      data,
+      function(x) which(language_tokens$tokens$token %in% x)
+    )
+    token_index <- unlist(
+      lapply(
+        token_index,
+        function(x) if (length(x) == 0) NA else x
+      )
+    )
+    data <- language_tokens$tokens$translation[token_index]
+  }
+  return(data)
+}
+
+#' Checks if there are any recognized tokens in the data provided
+#'
+#' @inheritParams translate_categories
+#'
+#' @return Boolean logical (TRUE or FALSE)
+#' @keywords internal
+any_tokens <- function(data, language_tokens) {
+  any(unname(unlist(data)) %in% language_tokens$tokens$token)
+}
diff --git a/man/any_tokens.Rd b/man/any_tokens.Rd
new file mode 100644
index 0000000..31a91ef
--- /dev/null
+++ b/man/any_tokens.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/translate_categories.R
+\name{any_tokens}
+\alias{any_tokens}
+\title{Checks if there are any recognized tokens in the data provided}
+\usage{
+any_tokens(data, language_tokens)
+}
+\arguments{
+\item{data}{A data frame (or data frame extension)}
+
+\item{language_tokens}{A data frame (or data frame extension) containing
+the translations. Output from \code{get_language_tokens()}}
+}
+\value{
+Boolean logical (TRUE or FALSE)
+}
+\description{
+Checks if there are any recognized tokens in the data provided
+}
+\keyword{internal}
diff --git a/man/translate_categories.Rd b/man/translate_categories.Rd
new file mode 100644
index 0000000..d6fdc1b
--- /dev/null
+++ b/man/translate_categories.Rd
@@ -0,0 +1,44 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/translate_categories.R
+\name{translate_categories}
+\alias{translate_categories}
+\title{Translates cateogories with API labels to more readable forms using the
+translation specified in the output of \code{get_language_tokens()}.}
+\usage{
+translate_categories(data, language_tokens)
+}
+\arguments{
+\item{data}{A data frame (or data frame extension)}
+
+\item{language_tokens}{A data frame (or data frame extension) containing
+the translations. Output from \code{get_language_tokens()}}
+}
+\value{
+A tibble
+}
+\description{
+Translates cateogories with API labels to more readable forms using the
+translation specified in the output of \code{get_language_tokens()}.
+}
+\examples{
+\dontrun{
+cases <- get_cases(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+language_tokens <- get_language_tokens(
+  url = url,
+  username = username,
+  password = password,
+  language = "english_us"
+)
+
+translate_categories(
+  data = cases,
+  language_tokens = language_tokens
+)
+}
+}
diff --git a/man/translate_token.Rd b/man/translate_token.Rd
new file mode 100644
index 0000000..4be70c6
--- /dev/null
+++ b/man/translate_token.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/translate_categories.R
+\name{translate_token}
+\alias{translate_token}
+\title{Translates tokens given a specified translation.}
+\usage{
+translate_token(data, language_tokens)
+}
+\arguments{
+\item{data}{A data frame (or data frame extension)}
+
+\item{language_tokens}{A data frame (or data frame extension) containing
+the translations. Output from \code{get_language_tokens()}}
+}
+\value{
+A tibble
+}
+\description{
+This function does all the translation for
+\code{translate_categories}.
+}
+\keyword{internal}

From 998c2c76cac58842626bf5b3718bdb55985994ff Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 09:06:27 +0000
Subject: [PATCH 104/203] linted get_labresults

---
 R/get_labresults.R | 125 +++++++++++++++++++++++++++++----------------
 1 file changed, 81 insertions(+), 44 deletions(-)

diff --git a/R/get_labresults.R b/R/get_labresults.R
index fa5af62..d9e5ac9 100644
--- a/R/get_labresults.R
+++ b/R/get_labresults.R
@@ -22,17 +22,27 @@
 #'    be the default if you are using Go.Data version 2.38.1
 #'    or newer.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
-#' @param outbreak_id The id number for the outbreak for which you want to download data.
-#' @param method The method to download data. `method="export"` is the preferred and default method for Go.Data version 2.38.1 or later. See Details.
-#' @param batch_size If `method="batches"`, then `batch_size` specifies the number of records to retrieve in each iteration.
-#' @param wait If `method="export"`, then `wait` is the number of seconds to wait in between iterations of checking the status of the export.
-#' @param file.type If `method="export"`, then `file.type` determines Whether the resulting data frame should contain nested fields (`file.type="json"`, the default) or an entirely flat data structure (`file.type="csv"`)
+#' @param outbreak_id The id number for the outbreak for which you want to
+#' download data.
+#' @param method The method to download data. `method="export"` is the
+#' preferred and default method for Go.Data version 2.38.1 or later. See
+#' Details.
+#' @param batch_size If `method = "batches"`, then `batch_size` specifies the
+#' number of records to retrieve in each iteration.
+#' @param wait If `method = "export"`, then `wait` is the number of seconds to
+#' wait in between iterations of checking the status of the export.
+#' @param file_type If `method = "export"`, then `file_type` determines Whether
+#' the resulting data frame should contain nested fields (`file_type = "json"`,
+#' the default) or an entirely flat data structure (`file_type = "csv"`)
 #'
 #' @return
-#' Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+#' Returns a data frame. Some fields, such as addresses, hospitalization
+#' history, and questionnaire fields may require further unnesting. See
+#' \code{\link[tidyr]{nest}} for assitance with unnesting.
 #' @export
 #'
 #' @examples
@@ -42,10 +52,12 @@
 #' password <- "mypassword"
 #' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 #'
-#' labresults <- get_labresults(url=url,
-#'                              username=username,
-#'                              password=password,
-#'                              outbreak_id=outbreak_id)
+#' labresults <- get_labresults(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
 #' }
 #' @importFrom magrittr %>%
 #' @import dplyr
@@ -54,25 +66,33 @@
 #' @import tibble
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
-
-
-get_labresults <- function(url=url,
-                       username=username,
-                       password=password,
-                       outbreak_id=outbreak_id,
-                       method=c("export","batch"),
-                       batch_size=50000,
-                       wait=2,
-                       file.type=c("json","csv")) {
+get_labresults <- function(url = url,
+                           username = username,
+                           password = password,
+                           outbreak_id = outbreak_id,
+                           method = c("export", "batch"),
+                           batch_size = 50000,
+                           wait = 2,
+                           file_type = c("json", "csv")) {
 
   #Check that outbreak_id is active
-  if (outbreak_id != get_active_outbreak(url=url, username=username, password=password)) {
-    set_active_outbreak(url=url, username=username, password=password, outbreak_id=outbreak_id)
+  active_outbreak <- get_active_outbreak(
+    url = url,
+    username = username,
+    password = password
+  )
+  if (outbreak_id != active_outbreak) {
+    set_active_outbreak(
+      url = url,
+      username = username,
+      password = password,
+      outbreak_id = outbreak_id
+    )
   }
 
   #Set default method based on current version of Go.Data
-  version.check <- check_godata_version(url=url)
-  if (!version.check) {
+  version_check <- check_godata_version(url = url)
+  if (!version_check) {
     method <- "batches" #Older version of Go.Data can only use the batch method
   } else if (missing(method)) {
     method <- "export" # For new versions of Go.Data, default to export method
@@ -81,30 +101,47 @@ get_labresults <- function(url=url,
 
   if (method == "batches") {
 
-    api_call_n <- paste0(url, "api/outbreaks/",outbreak_id,"/lab-results/aggregate-filtered-count")
-    api_call_get <- paste0(url, "api/outbreaks/",outbreak_id,"/lab-results/aggregate")
-    df <- batch_downloader(url=url,
-                           username=username,
-                           password=password,
-                           api_call_n=api_call_n,
-                           api_call_get=api_call_get,
-                           batch_size=batch_size)
+    api_call_n <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/lab-results/aggregate-filtered-count"
+    )
+    api_call_get <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/lab-results/aggregate"
+    )
+    df <- batch_downloader(
+      url = url,
+      username = username,
+      password = password,
+      api_call_n = api_call_n,
+      api_call_get = api_call_get,
+      batch_size = batch_size
+    )
 
   } else if (method == "export") {
 
-    #Default value of file.type is "json"
-    if (missing(file.type)) file.type <- "json"
+    #Default value of file_type is "json"
+    if (missing(file_type)) file_type <- "json"
 
     #Submit an export request to the system
-    api_call_request <- paste0(url,"api/outbreaks/",outbreak_id,"/lab-results/export")
-    df <- export_downloader(url=url,
-                            username=username,
-                            password=password,
-                            api_call_request=api_call_request,
-                            file.type = file.type,
-                            wait = wait)
-
-
+    api_call_request <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/lab-results/export"
+    )
+    df <- export_downloader(
+      url = url,
+      username = username,
+      password = password,
+      api_call_request = api_call_request,
+      file_type = file_type,
+      wait = wait
+    )
   }
 
   return(df)

From 69a0167b6cbb0913381b2b4279c33bbec9c74537 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 09:07:06 +0000
Subject: [PATCH 105/203] removed recursive arugment defaults for
 get_labresults

---
 R/get_labresults.R    |  8 ++++----
 man/get_labresults.Rd | 44 +++++++++++++++++++++++++++----------------
 2 files changed, 32 insertions(+), 20 deletions(-)

diff --git a/R/get_labresults.R b/R/get_labresults.R
index d9e5ac9..24c98f6 100644
--- a/R/get_labresults.R
+++ b/R/get_labresults.R
@@ -66,10 +66,10 @@
 #' @import tibble
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
-get_labresults <- function(url = url,
-                           username = username,
-                           password = password,
-                           outbreak_id = outbreak_id,
+get_labresults <- function(url,
+                           username,
+                           password,
+                           outbreak_id,
                            method = c("export", "batch"),
                            batch_size = 50000,
                            wait = 2,
diff --git a/man/get_labresults.Rd b/man/get_labresults.Rd
index 4dbac8d..3fc40cc 100644
--- a/man/get_labresults.Rd
+++ b/man/get_labresults.Rd
@@ -5,35 +5,45 @@
 \title{Download lab results from Go.Data}
 \usage{
 get_labresults(
-  url = url,
-  username = username,
-  password = password,
-  outbreak_id = outbreak_id,
+  url,
+  username,
+  password,
+  outbreak_id,
   method = c("export", "batch"),
   batch_size = 50000,
   wait = 2,
-  file.type = c("json", "csv")
+  file_type = c("json", "csv")
 )
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
 \item{password}{The password for your Go.Data login}
 
-\item{outbreak_id}{The id number for the outbreak for which you want to download data.}
+\item{outbreak_id}{The id number for the outbreak for which you want to
+download data.}
 
-\item{method}{The method to download data. \code{method="export"} is the preferred and default method for Go.Data version 2.38.1 or later. See Details.}
+\item{method}{The method to download data. \code{method="export"} is the
+preferred and default method for Go.Data version 2.38.1 or later. See
+Details.}
 
-\item{batch_size}{If \code{method="batches"}, then \code{batch_size} specifies the number of records to retrieve in each iteration.}
+\item{batch_size}{If \code{method = "batches"}, then \code{batch_size} specifies the
+number of records to retrieve in each iteration.}
 
-\item{wait}{If \code{method="export"}, then \code{wait} is the number of seconds to wait in between iterations of checking the status of the export.}
+\item{wait}{If \code{method = "export"}, then \code{wait} is the number of seconds to
+wait in between iterations of checking the status of the export.}
 
-\item{file.type}{If \code{method="export"}, then \code{file.type} determines Whether the resulting data frame should contain nested fields (\code{file.type="json"}, the default) or an entirely flat data structure (\code{file.type="csv"})}
+\item{file_type}{If \code{method = "export"}, then \code{file_type} determines Whether
+the resulting data frame should contain nested fields (\code{file_type = "json"},
+the default) or an entirely flat data structure (\code{file_type = "csv"})}
 }
 \value{
-Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+Returns a data frame. Some fields, such as addresses, hospitalization
+history, and questionnaire fields may require further unnesting. See
+\code{\link[tidyr]{nest}} for assitance with unnesting.
 }
 \description{
 A function to retrieve the lab result data for a
@@ -66,9 +76,11 @@ username <- "myemail@email.com"
 password <- "mypassword"
 outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 
-labresults <- get_labresults(url=url,
-                             username=username,
-                             password=password,
-                             outbreak_id=outbreak_id)
+labresults <- get_labresults(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
 }
 }

From 13a9f09bd77325bd575a9b8f9dbb8a77f7679fe1 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 09:09:24 +0000
Subject: [PATCH 106/203] used explicit namespace instead of import in
 get_labresults

---
 R/get_labresults.R | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/R/get_labresults.R b/R/get_labresults.R
index 24c98f6..9ed02fa 100644
--- a/R/get_labresults.R
+++ b/R/get_labresults.R
@@ -59,13 +59,6 @@
 #'   outbreak_id = outbreak_id
 #' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @import tibble
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
 get_labresults <- function(url,
                            username,
                            password,
@@ -143,6 +136,5 @@ get_labresults <- function(url,
       wait = wait
     )
   }
-
-  return(df)
+  return(tibble::as_tibble(df))
 }

From 56ab9a6cb6d2924033419f3bbf2dfb47b3fe2077 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 09:23:28 +0000
Subject: [PATCH 107/203] added test for get_labresults

---
 tests/testthat/test-get_labresults.R | 58 ++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 tests/testthat/test-get_labresults.R

diff --git a/tests/testthat/test-get_labresults.R b/tests/testthat/test-get_labresults.R
new file mode 100644
index 0000000..3f0b7c5
--- /dev/null
+++ b/tests/testthat/test-get_labresults.R
@@ -0,0 +1,58 @@
+test_that("get_labresults works as expected", {
+  skip("get_labresults requires API call")
+
+  res <- get_labresults(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id,
+    method = "export",
+    batch_size = 50000,
+    wait = 2,
+    file_type = "json"
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(9L, 55L))
+  expect_true(
+    all(c(
+      "id", "createdAt", "createdBy", "updatedAt", "updatedBy", "deleted",
+      "deletedAt", "createdOn", "personId", "dateSampleTaken",
+      "dateSampleDelivered", "dateTesting", "dateOfResult", "labName",
+      "sampleIdentifier", "sampleType", "testType", "testedFor", "result",
+      "quantitativeResult", "notes", "status", "sequence.hasSequence",
+      "sequence.dateSampleSent", "sequence.labId", "sequence.dateResult",
+      "sequence.resultId", "sequence.noSequenceReason", "person.visualId",
+      "person.type", "person.lastName", "person.firstName",
+      "person.dateOfOnset", "person.dateOfReporting", "person.middleName",
+      "person.address.typeId", "person.address.city",
+      "person.address.locationId", "person.address.Identifiers",
+      "person.address.Location geographical level",
+      "person.address.Parent location", "person.address.geoLocationAccurate",
+      "person.address.date", "person.address.country",
+      "person.address.addressLine1", "person.address.postalCode",
+      "person.address.phoneNumber", "person.address.emailAddress",
+      "person.address.geoLocation.lat", "person.address.geoLocation.lng",
+      "questionnaireAnswers.Lab_SpecimenCollection_Symptoms",
+      "questionnaireAnswers.Lab_SpecimenShippedAnotherLaboratory",
+      "questionnaireAnswers.test",
+      "questionnaireAnswers.Lab_specimenshipped_laboratoryname",
+      "questionnaireAnswers.Lab_specimenshipped_dateofshipping"
+    ) %in% colnames(res))
+  )
+
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "character", "character", "character", "character",
+      "logical", "logical", "character", "character", "character", "character",
+      "character", "character", "logical", "character", "character",
+      "character", "logical", "character", "logical", "logical", "character",
+      "logical", "character", "character", "character", "character", "logical",
+      "character", "character", "character", "character", "character",
+      "character", "character", "character", "character", "character", "list",
+      "list", "list", "logical", "character", "logical", "logical", "logical",
+      "logical", "logical", "numeric", "numeric", "list", "list", "list",
+      "list", "list"))
+})

From aac21b5937a878342978b727759c53fed172a2f1 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 09:34:48 +0000
Subject: [PATCH 108/203] linted get_relationships

---
 R/get_relationships.R    | 131 +++++++++++++++++++++++++--------------
 man/get_relationships.Rd |  42 ++++++++-----
 2 files changed, 112 insertions(+), 61 deletions(-)

diff --git a/R/get_relationships.R b/R/get_relationships.R
index cef852a..6b22300 100644
--- a/R/get_relationships.R
+++ b/R/get_relationships.R
@@ -6,33 +6,43 @@
 #' This function works on all versions of Go.Data. There
 #' are two methods for downloading the data:
 #'
-#' `method="batches"` will work on all versions of
+#' `method = "batches"` will work on all versions of
 #'    Go.Data. This method relies on the GET outbreak/{id}/relationships
 #'    API endpoint. Records are then retrieved in batches
 #'    based on `batch_size` and appended together into
-#'    a final dataset. `method="batches"` will be the default and
+#'    a final dataset. `method = "batches"` will be the default and
 #'    only available method for Go.Data version 2.38.0 or older.
 #'
-#' `method="export"` will only work on Go.Data versions
+#' `method = "export"` will only work on Go.Data versions
 #'    2.38.1 or newer. This method relies on the GET
 #'    outbreak/{id}/relationships/export API endpoint. An export
 #'    request is submitted to the server, and then when the
 #'    export is ready, it will be downloaded. Due to better
-#'    performance and more options, `method="export"` will
+#'    performance and more options, `method = "export"` will
 #'    be the default if you are using Go.Data version 2.38.1
 #'    or newer.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
-#' @param outbreak_id The id number for the outbreak for which you want to download data.
-#' @param method The method to download data. `method="export"` is the preferred and default method for Go.Data version 2.38.1 or later. See Details.
-#' @param batch_size If `method="batches"`, then `batch_size` specifies the number of records to retrieve in each iteration.
-#' @param wait If `method="export"`, then `wait` is the number of seconds to wait in between iterations of checking the status of the export.
-#' @param file.type If `method="export"`, then `file.type` determines Whether the resulting data frame should contain nested fields (`file.type="json"`, the default) or an entirely flat data structure (`file.type="csv"`)
+#' @param outbreak_id The id number for the outbreak for which you want to
+#' download data.
+#' @param method The method to download data. `method = "export"` is the
+#' preferred and default method for Go.Data version 2.38.1 or later. See
+#' Details.
+#' @param batch_size If `method = "batches"`, then `batch_size` specifies the
+#' number of records to retrieve in each iteration.
+#' @param wait If `method = "export"`, then `wait` is the number of seconds to
+#' wait in between iterations of checking the status of the export.
+#' @param file_type If `method = "export"`, then `file_type` determines Whether
+#' the resulting data frame should contain nested fields (`file_type = "json"`,
+#' the default) or an entirely flat data structure (`file_type = "csv"`)
 #'
 #' @return
-#' Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+#' Returns a data frame. Some fields, such as addresses, hospitalization
+#' history, and questionnaire fields may require further unnesting. See
+#' \code{\link[tidyr]{nest}} for assitance with unnesting.
 #' @export
 #'
 #' @examples
@@ -42,10 +52,12 @@
 #' password <- "mypassword"
 #' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 #'
-#' relationships <- get_relationships(url=url,
-#'                                    username=username,
-#'                                    password=password,
-#'                                    outbreak_id=outbreak_id)
+#' relationships <- get_relationships(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
 #' }
 #' @importFrom magrittr %>%
 #' @import dplyr
@@ -54,25 +66,33 @@
 #' @import tibble
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
-
-
-get_relationships <- function(url=url,
-                      username=username,
-                      password=password,
-                      outbreak_id=outbreak_id,
-                      method=c("export","batch"),
-                      batch_size=50000,
-                      wait=2,
-                      file.type=c("json","csv")) {
+get_relationships <- function(url = url,
+                              username = username,
+                              password = password,
+                              outbreak_id = outbreak_id,
+                              method = c("export", "batch"),
+                              batch_size = 50000,
+                              wait = 2,
+                              file_type = c("json", "csv")) {
 
   #Check that outbreak_id is active
-  if (outbreak_id != get_active_outbreak(url=url, username=username, password=password)) {
-    set_active_outbreak(url=url, username=username, password=password, outbreak_id=outbreak_id)
+  active_outbreak <- get_active_outbreak(
+    url = url,
+    username = username,
+    password = password
+  )
+  if (outbreak_id != active_outbreak) {
+    set_active_outbreak(
+      url = url,
+      username = username,
+      password = password,
+      outbreak_id = outbreak_id
+    )
   }
 
   #Set default method based on current version of Go.Data
-  version.check <- check_godata_version(url=url)
-  if (!version.check) {
+  version_check <- check_godata_version(url = url)
+  if (!version_check) {
     method <- "batches" #Older version of Go.Data can only use the batch method
   } else if (missing(method)) {
     method <- "export" # For new versions of Go.Data, default to export method
@@ -81,28 +101,47 @@ get_relationships <- function(url=url,
 
   if (method == "batches") {
 
-    api_call_n <- paste0(url, "api/outbreaks/",outbreak_id,"/relationships/count")
-    api_call_get <- paste0(url, "api/outbreaks/",outbreak_id,"/relationships")
-    df <- batch_downloader(url=url,
-                           username=username,
-                           password=password,
-                           api_call_n=api_call_n,
-                           api_call_get=api_call_get,
-                           batch_size=batch_size)
+    api_call_n <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/relationships/count"
+    )
+    api_call_get <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/relationships"
+    )
+    df <- batch_downloader(
+      url = url,
+      username = username,
+      password = password,
+      api_call_n = api_call_n,
+      api_call_get = api_call_get,
+      batch_size = batch_size
+    )
 
   } else if (method == "export") {
 
-    #Default value of file.type is "json"
-    if (missing(file.type)) file.type <- "json"
+    #Default value of file_type is "json"
+    if (missing(file_type)) file_type <- "json"
 
     #Submit an export request to the system
-    api_call_request <- paste0(url,"api/outbreaks/",outbreak_id,"/relationships/export")
-    df <- export_downloader(url=url,
-                            username=username,
-                            password=password,
-                            api_call_request=api_call_request,
-                            file.type = file.type,
-                            wait = wait)
+    api_call_request <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/relationships/export"
+    )
+    df <- export_downloader(
+      url = url,
+      username = username,
+      password = password,
+      api_call_request = api_call_request,
+      file_type = file_type,
+      wait = wait
+    )
 
 
   }
diff --git a/man/get_relationships.Rd b/man/get_relationships.Rd
index f485fe8..5d87b4b 100644
--- a/man/get_relationships.Rd
+++ b/man/get_relationships.Rd
@@ -16,24 +16,34 @@ get_relationships(
 )
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
 \item{password}{The password for your Go.Data login}
 
-\item{outbreak_id}{The id number for the outbreak for which you want to download data.}
+\item{outbreak_id}{The id number for the outbreak for which you want to
+download data.}
 
-\item{method}{The method to download data. \code{method="export"} is the preferred and default method for Go.Data version 2.38.1 or later. See Details.}
+\item{method}{The method to download data. \code{method = "export"} is the
+preferred and default method for Go.Data version 2.38.1 or later. See
+Details.}
 
-\item{batch_size}{If \code{method="batches"}, then \code{batch_size} specifies the number of records to retrieve in each iteration.}
+\item{batch_size}{If \code{method = "batches"}, then \code{batch_size} specifies the
+number of records to retrieve in each iteration.}
 
-\item{wait}{If \code{method="export"}, then \code{wait} is the number of seconds to wait in between iterations of checking the status of the export.}
+\item{wait}{If \code{method = "export"}, then \code{wait} is the number of seconds to
+wait in between iterations of checking the status of the export.}
 
-\item{file.type}{If \code{method="export"}, then \code{file.type} determines Whether the resulting data frame should contain nested fields (\code{file.type="json"}, the default) or an entirely flat data structure (\code{file.type="csv"})}
+\item{file.type}{If \code{method = "export"}, then \code{file.type} determines Whether
+the resulting data frame should contain nested fields (\code{file.type = "json"},
+the default) or an entirely flat data structure (\code{file.type = "csv"})}
 }
 \value{
-Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+Returns a data frame. Some fields, such as addresses, hospitalization
+history, and questionnaire fields may require further unnesting. See
+\code{\link[tidyr]{nest}} for assitance with unnesting.
 }
 \description{
 A function to retrieve the relationship data for a
@@ -43,19 +53,19 @@ specific \code{outbreak_id}.
 This function works on all versions of Go.Data. There
 are two methods for downloading the data:
 
-\code{method="batches"} will work on all versions of
+\code{method = "batches"} will work on all versions of
 Go.Data. This method relies on the GET outbreak/{id}/relationships
 API endpoint. Records are then retrieved in batches
 based on \code{batch_size} and appended together into
-a final dataset. \code{method="batches"} will be the default and
+a final dataset. \code{method = "batches"} will be the default and
 only available method for Go.Data version 2.38.0 or older.
 
-\code{method="export"} will only work on Go.Data versions
+\code{method = "export"} will only work on Go.Data versions
 2.38.1 or newer. This method relies on the GET
 outbreak/{id}/relationships/export API endpoint. An export
 request is submitted to the server, and then when the
 export is ready, it will be downloaded. Due to better
-performance and more options, \code{method="export"} will
+performance and more options, \code{method = "export"} will
 be the default if you are using Go.Data version 2.38.1
 or newer.
 }
@@ -66,9 +76,11 @@ username <- "myemail@email.com"
 password <- "mypassword"
 outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 
-relationships <- get_relationships(url=url,
-                                   username=username,
-                                   password=password,
-                                   outbreak_id=outbreak_id)
+relationships <- get_relationships(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
 }
 }

From eab74905ce9e29f4f6a5fb284dd8e380f0b97245 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 09:35:51 +0000
Subject: [PATCH 109/203] removed recursive argument defaults from
 get_relationships

---
 R/get_relationships.R    |  8 ++++----
 man/get_relationships.Rd | 16 ++++++++--------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/R/get_relationships.R b/R/get_relationships.R
index 6b22300..32c6752 100644
--- a/R/get_relationships.R
+++ b/R/get_relationships.R
@@ -66,10 +66,10 @@
 #' @import tibble
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
-get_relationships <- function(url = url,
-                              username = username,
-                              password = password,
-                              outbreak_id = outbreak_id,
+get_relationships <- function(url,
+                              username,
+                              password,
+                              outbreak_id,
                               method = c("export", "batch"),
                               batch_size = 50000,
                               wait = 2,
diff --git a/man/get_relationships.Rd b/man/get_relationships.Rd
index 5d87b4b..f6f3a6b 100644
--- a/man/get_relationships.Rd
+++ b/man/get_relationships.Rd
@@ -5,14 +5,14 @@
 \title{Download relationships from Go.Data}
 \usage{
 get_relationships(
-  url = url,
-  username = username,
-  password = password,
-  outbreak_id = outbreak_id,
+  url,
+  username,
+  password,
+  outbreak_id,
   method = c("export", "batch"),
   batch_size = 50000,
   wait = 2,
-  file.type = c("json", "csv")
+  file_type = c("json", "csv")
 )
 }
 \arguments{
@@ -36,9 +36,9 @@ number of records to retrieve in each iteration.}
 \item{wait}{If \code{method = "export"}, then \code{wait} is the number of seconds to
 wait in between iterations of checking the status of the export.}
 
-\item{file.type}{If \code{method = "export"}, then \code{file.type} determines Whether
-the resulting data frame should contain nested fields (\code{file.type = "json"},
-the default) or an entirely flat data structure (\code{file.type = "csv"})}
+\item{file_type}{If \code{method = "export"}, then \code{file_type} determines Whether
+the resulting data frame should contain nested fields (\code{file_type = "json"},
+the default) or an entirely flat data structure (\code{file_type = "csv"})}
 }
 \value{
 Returns a data frame. Some fields, such as addresses, hospitalization

From a31aa7573f58924a0c6e3986299d877a125c2d6d Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 09:37:22 +0000
Subject: [PATCH 110/203] used explicit namespace instead of import in
 get_relationships

---
 R/get_relationships.R | 12 +-----------
 1 file changed, 1 insertion(+), 11 deletions(-)

diff --git a/R/get_relationships.R b/R/get_relationships.R
index 32c6752..5c859fc 100644
--- a/R/get_relationships.R
+++ b/R/get_relationships.R
@@ -59,13 +59,6 @@
 #'   outbreak_id = outbreak_id
 #' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @import tibble
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
 get_relationships <- function(url,
                               username,
                               password,
@@ -142,9 +135,6 @@ get_relationships <- function(url,
       file_type = file_type,
       wait = wait
     )
-
-
   }
-
-  return(df)
+  return(tibble::as_tibble(df))
 }

From ab55e6a50d6a1c6e100ce9e124e50687c7a26dc9 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 09:46:07 +0000
Subject: [PATCH 111/203] added test for get_relationships

---
 tests/testthat/test-get_relationships.R | 47 +++++++++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 tests/testthat/test-get_relationships.R

diff --git a/tests/testthat/test-get_relationships.R b/tests/testthat/test-get_relationships.R
new file mode 100644
index 0000000..3b534e3
--- /dev/null
+++ b/tests/testthat/test-get_relationships.R
@@ -0,0 +1,47 @@
+test_that("get_relationships works as expected", {
+  skip("get_relationships requires API call")
+
+  res <- get_relationships(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id,
+    method = "export",
+    batch_size = 50000,
+    wait = 2,
+    file_type = "json"
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(29L, 43L))
+  expect_true(
+    all(c(
+      "id", "createdAt", "createdBy", "updatedAt", "updatedBy", "deleted",
+      "deletedAt", "createdOn", "dateOfFirstContact", "contactDate",
+      "contactDateEstimated", "certaintyLevelId", "exposureTypeId",
+      "exposureFrequencyId", "exposureDurationId", "socialRelationshipTypeId",
+      "socialRelationshipDetail", "clusterId", "comment", "sourcePerson.type",
+      "sourcePerson.firstName", "sourcePerson.gender", "sourcePerson.visualId",
+      "sourcePerson.lastName", "sourcePerson.dob", "sourcePerson.id",
+      "sourcePerson.source", "sourcePerson.name", "sourcePerson.middleName",
+      "sourcePerson.age.years", "sourcePerson.age.months", "targetPerson.type",
+      "targetPerson.firstName", "targetPerson.gender", "targetPerson.visualId",
+      "targetPerson.lastName", "targetPerson.id", "targetPerson.target",
+      "targetPerson.name", "targetPerson.middleName", "targetPerson.dob",
+      "targetPerson.age.years", "targetPerson.age.months"
+    ) %in% colnames(res))
+  )
+
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "character", "character", "character", "character",
+      "logical", "logical", "character", "character", "character", "logical",
+      "character", "character", "character", "character", "character",
+      "character", "character", "character", "character", "character",
+      "character", "character", "character", "logical", "character", "logical",
+      "logical", "character", "integer", "integer", "character", "character",
+      "character", "character", "character", "character", "logical",
+      "character", "character", "character", "integer", "integer"))
+})

From a0da8ea751f99ad722b315d832806972f5bece58 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 09:55:52 +0000
Subject: [PATCH 112/203] linted get_followups

---
 R/get_followups.R    | 134 +++++++++++++++++++++++++++----------------
 man/get_followups.Rd |  44 ++++++++------
 2 files changed, 113 insertions(+), 65 deletions(-)

diff --git a/R/get_followups.R b/R/get_followups.R
index 731a860..5ab10b4 100644
--- a/R/get_followups.R
+++ b/R/get_followups.R
@@ -6,33 +6,43 @@
 #' This function works on all versions of Go.Data. There
 #' are two methods for downloading the data:
 #'
-#' `method="batches"` will work on all versions of
+#' `method = "batches"` will work on all versions of
 #'    Go.Data. This method relies on the GET outbreak/{id}/follow-ups
 #'    API endpoint. Records are then retrieved in batches
 #'    based on `batch_size` and appended together into
-#'    a final dataset. `method="batches"` will be the default and
+#'    a final dataset. `method = "batches"` will be the default and
 #'    only available method for Go.Data version 2.38.0 or older.
 #'
-#' `method="export"` will only work on Go.Data versions
+#' `method = "export"` will only work on Go.Data versions
 #'    2.38.1 or newer. This method relies on the GET
 #'    outbreak/{id}/follow-ups/export API endpoint. An export
 #'    request is submitted to the server, and then when the
 #'    export is ready, it will be downloaded. Due to better
-#'    performance and more options, `method="export"` will
+#'    performance and more options, `method = "export"` will
 #'    be the default if you are using Go.Data version 2.38.1
 #'    or newer.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
-#' @param outbreak_id The id number for the outbreak for which you want to download data.
-#' @param method The method to download data. `method="export"` is the preferred and default method for Go.Data version 2.38.1 or later. See Details.
-#' @param batch_size If `method="batches"`, then `batch_size` specifies the number of records to retrieve in each iteration.
-#' @param wait If `method="export"`, then `wait` is the number of seconds to wait in between iterations of checking the status of the export.
-#' @param file.type If `method="export"`, then `file.type` determines Whether the resulting data frame should contain nested fields (`file.type="json"`, the default) or an entirely flat data structure (`file.type="csv"`)
+#' @param outbreak_id The id number for the outbreak for which you want to
+#' download data.
+#' @param method The method to download data. `method = "export"` is the
+#' preferred and default method for Go.Data version 2.38.1 or later. See
+#' Details.
+#' @param batch_size If `method = "batches"`, then `batch_size` specifies the
+#' number of records to retrieve in each iteration.
+#' @param wait If `method = "export"`, then `wait` is the number of seconds to
+#' wait in between iterations of checking the status of the export.
+#' @param file_type If `method = "export"`, then `file_type` determines Whether
+#' the resulting data frame should contain nested fields (`file_type = "json"`,
+#' the default) or an entirely flat data structure (`file_type = "csv"`)
 #'
 #' @return
-#' Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+#' Returns a data frame. Some fields, such as addresses, hospitalization
+#' history, and questionnaire fields may require further unnesting. See
+#' \code{\link[tidyr]{nest}} for assitance with unnesting.
 #' @export
 #'
 #' @examples
@@ -42,10 +52,12 @@
 #' password <- "mypassword"
 #' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 #'
-#' followups <- get_followups(url=url,
-#'                            username=username,
-#'                            password=password,
-#'                            outbreak_id=outbreak_id)
+#' followups <- get_followups(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
 #' }
 #' @importFrom magrittr %>%
 #' @import dplyr
@@ -54,25 +66,33 @@
 #' @import tibble
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
-
-
-get_followups <- function(url=url,
-                       username=username,
-                       password=password,
-                       outbreak_id=outbreak_id,
-                       method=c("export","batch"),
-                       batch_size=50000,
-                       wait=2,
-                       file.type=c("json","csv")) {
+get_followups <- function(url = url,
+                          username = username,
+                          password = password,
+                          outbreak_id = outbreak_id,
+                          method = c("export", "batch"),
+                          batch_size = 50000,
+                          wait = 2,
+                          file_type = c("json", "csv")) {
 
   #Check that outbreak_id is active
-  if (outbreak_id != get_active_outbreak(url=url, username=username, password=password)) {
-    set_active_outbreak(url=url, username=username, password=password, outbreak_id=outbreak_id)
+  active_outbreak <- get_active_outbreak(
+    url = url,
+    username = username,
+    password = password
+  )
+  if (outbreak_id != active_outbreak) {
+    set_active_outbreak(
+      url = url,
+      username = username,
+      password = password,
+      outbreak_id = outbreak_id
+    )
   }
 
   #Set default method based on current version of Go.Data
-  version.check <- check_godata_version(url=url)
-  if (!version.check) {
+  version_check <- check_godata_version(url = url)
+  if (!version_check) {
     method <- "batches" #Older version of Go.Data can only use the batch method
   } else if (missing(method)) {
     method <- "export" # For new versions of Go.Data, default to export method
@@ -81,31 +101,47 @@ get_followups <- function(url=url,
 
   if (method == "batches") {
 
-    api_call_n <- paste0(url, "api/outbreaks/",outbreak_id,"/follow-ups/filtered-count")
-    api_call_get <- paste0(url, "api/outbreaks/",outbreak_id,"/follow-ups")
-    df <- batch_downloader(url=url,
-                           username=username,
-                           password=password,
-                           api_call_n=api_call_n,
-                           api_call_get=api_call_get,
-                           batch_size=batch_size)
+    api_call_n <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/follow-ups/filtered-count"
+    )
+    api_call_get <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/follow-ups"
+    )
+    df <- batch_downloader(
+      url = url,
+      username = username,
+      password = password,
+      api_call_n = api_call_n,
+      api_call_get = api_call_get,
+      batch_size = batch_size
+    )
 
   } else if (method == "export") {
 
-    #Default value of file.type is "json"
-    if (missing(file.type)) file.type <- "json"
+    #Default value of file_type is "json"
+    if (missing(file_type)) file_type <- "json"
 
     #Submit an export request to the system
-    api_call_request <- paste0(url,"api/outbreaks/",outbreak_id,"/follow-ups/export")
-    df <- export_downloader(url=url,
-                            username=username,
-                            password=password,
-                            api_call_request=api_call_request,
-                            file.type = file.type,
-                            wait = wait)
-
-
+    api_call_request <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/follow-ups/export"
+    )
+    df <- export_downloader(
+      url = url,
+      username = username,
+      password = password,
+      api_call_request = api_call_request,
+      file_type = file_type,
+      wait = wait
+    )
   }
-
   return(df)
 }
diff --git a/man/get_followups.Rd b/man/get_followups.Rd
index 82b6fcc..82e92e9 100644
--- a/man/get_followups.Rd
+++ b/man/get_followups.Rd
@@ -12,28 +12,38 @@ get_followups(
   method = c("export", "batch"),
   batch_size = 50000,
   wait = 2,
-  file.type = c("json", "csv")
+  file_type = c("json", "csv")
 )
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
 \item{password}{The password for your Go.Data login}
 
-\item{outbreak_id}{The id number for the outbreak for which you want to download data.}
+\item{outbreak_id}{The id number for the outbreak for which you want to
+download data.}
 
-\item{method}{The method to download data. \code{method="export"} is the preferred and default method for Go.Data version 2.38.1 or later. See Details.}
+\item{method}{The method to download data. \code{method = "export"} is the
+preferred and default method for Go.Data version 2.38.1 or later. See
+Details.}
 
-\item{batch_size}{If \code{method="batches"}, then \code{batch_size} specifies the number of records to retrieve in each iteration.}
+\item{batch_size}{If \code{method = "batches"}, then \code{batch_size} specifies the
+number of records to retrieve in each iteration.}
 
-\item{wait}{If \code{method="export"}, then \code{wait} is the number of seconds to wait in between iterations of checking the status of the export.}
+\item{wait}{If \code{method = "export"}, then \code{wait} is the number of seconds to
+wait in between iterations of checking the status of the export.}
 
-\item{file.type}{If \code{method="export"}, then \code{file.type} determines Whether the resulting data frame should contain nested fields (\code{file.type="json"}, the default) or an entirely flat data structure (\code{file.type="csv"})}
+\item{file_type}{If \code{method = "export"}, then \code{file_type} determines Whether
+the resulting data frame should contain nested fields (\code{file_type = "json"},
+the default) or an entirely flat data structure (\code{file_type = "csv"})}
 }
 \value{
-Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+Returns a data frame. Some fields, such as addresses, hospitalization
+history, and questionnaire fields may require further unnesting. See
+\code{\link[tidyr]{nest}} for assitance with unnesting.
 }
 \description{
 A function to retrieve the follow-up data for a
@@ -43,19 +53,19 @@ specific \code{outbreak_id}.
 This function works on all versions of Go.Data. There
 are two methods for downloading the data:
 
-\code{method="batches"} will work on all versions of
+\code{method = "batches"} will work on all versions of
 Go.Data. This method relies on the GET outbreak/{id}/follow-ups
 API endpoint. Records are then retrieved in batches
 based on \code{batch_size} and appended together into
-a final dataset. \code{method="batches"} will be the default and
+a final dataset. \code{method = "batches"} will be the default and
 only available method for Go.Data version 2.38.0 or older.
 
-\code{method="export"} will only work on Go.Data versions
+\code{method = "export"} will only work on Go.Data versions
 2.38.1 or newer. This method relies on the GET
 outbreak/{id}/follow-ups/export API endpoint. An export
 request is submitted to the server, and then when the
 export is ready, it will be downloaded. Due to better
-performance and more options, \code{method="export"} will
+performance and more options, \code{method = "export"} will
 be the default if you are using Go.Data version 2.38.1
 or newer.
 }
@@ -66,9 +76,11 @@ username <- "myemail@email.com"
 password <- "mypassword"
 outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 
-followups <- get_followups(url=url,
-                           username=username,
-                           password=password,
-                           outbreak_id=outbreak_id)
+followups <- get_followups(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
 }
 }

From c78f04e4f7b341a97eded2f0e13fb39364aa98f7 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 09:56:36 +0000
Subject: [PATCH 113/203] removed recursive argument defaults for get_followups

---
 R/get_followups.R    | 8 ++++----
 man/get_followups.Rd | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/get_followups.R b/R/get_followups.R
index 5ab10b4..5f59860 100644
--- a/R/get_followups.R
+++ b/R/get_followups.R
@@ -66,10 +66,10 @@
 #' @import tibble
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
-get_followups <- function(url = url,
-                          username = username,
-                          password = password,
-                          outbreak_id = outbreak_id,
+get_followups <- function(url,
+                          username,
+                          password,
+                          outbreak_id,
                           method = c("export", "batch"),
                           batch_size = 50000,
                           wait = 2,
diff --git a/man/get_followups.Rd b/man/get_followups.Rd
index 82e92e9..75fd1b8 100644
--- a/man/get_followups.Rd
+++ b/man/get_followups.Rd
@@ -5,10 +5,10 @@
 \title{Download contact follow-ups from Go.Data}
 \usage{
 get_followups(
-  url = url,
-  username = username,
-  password = password,
-  outbreak_id = outbreak_id,
+  url,
+  username,
+  password,
+  outbreak_id,
   method = c("export", "batch"),
   batch_size = 50000,
   wait = 2,

From 9fb10413cf8a88f6626fdd8d9585672b48d55335 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 09:57:29 +0000
Subject: [PATCH 114/203] used explicit namespace instead of import for
 get_followups

---
 R/get_followups.R | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/R/get_followups.R b/R/get_followups.R
index 5f59860..6eccdb3 100644
--- a/R/get_followups.R
+++ b/R/get_followups.R
@@ -59,13 +59,6 @@
 #'   outbreak_id = outbreak_id
 #' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @import tibble
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
 get_followups <- function(url,
                           username,
                           password,
@@ -143,5 +136,5 @@ get_followups <- function(url,
       wait = wait
     )
   }
-  return(df)
+  return(tibble::as_tibble(df))
 }

From da9ca87205dc6295d45a5d0bbfc8cef9ea1feca4 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 10:11:42 +0000
Subject: [PATCH 115/203] added test for get_followups

---
 tests/testthat/test-get_followups.R | 48 +++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 tests/testthat/test-get_followups.R

diff --git a/tests/testthat/test-get_followups.R b/tests/testthat/test-get_followups.R
new file mode 100644
index 0000000..345df53
--- /dev/null
+++ b/tests/testthat/test-get_followups.R
@@ -0,0 +1,48 @@
+test_that("get_followups works as expected", {
+  skip("get_followups requires API call")
+
+  res <- get_followups(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id,
+    method = "export",
+    batch_size = 50000,
+    wait = 2,
+    file_type = "json"
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(49L, 201L))
+  expect_true(
+    all(c(
+      "id", "date", "index", "createdAt", "createdBy", "updatedAt", "updatedBy",
+      "deleted", "deletedAt", "createdOn", "fillLocation", "teamId", "statusId",
+      "targeted", "comment", "responsibleUserId", "contact.firstName",
+      "contact.lastName", "contact.visualId", "contact.id", "address.typeId",
+      "address.locationId", "address.Identifiers",
+      "address.Location geographical level", "address.Parent location",
+      "address.geoLocationAccurate", "address.date", "address.country",
+      "address.city", "address.addressLine1", "address.postalCode",
+      "address.phoneNumber", "address.emailAddress", "address.geoLocation.lat",
+      "address.geoLocation.lng"
+    ) %in% colnames(res))
+  )
+
+  expect_true(
+    all(grepl(pattern = "^questionnaireAnswers", x = colnames(res)[36:201]))
+  )
+
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "character", "integer", "character", "character",
+      "character", "character", "logical", "logical", "character", "logical",
+      "character", "character", "logical", "logical", "character", "character",
+      "character", "character", "character", "character", "character", "list",
+      "list", "list", "logical", "character", "logical", "logical", "logical",
+      "logical", "logical", "logical", "numeric", "numeric", "list", "list",
+      "list", "list", "list", "list", "list", "logical", "list", "logical",
+      "list", "list", rep("logical", 152), "list", "list"))
+})

From 8f67af0ea6e25a277f08863460acbf30c702c44b Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 10:46:20 +0000
Subject: [PATCH 116/203] linted get_events

---
 R/get_events.R    | 258 ++++++++++++++++++++++++++--------------------
 man/get_events.Rd |  44 +++++---
 2 files changed, 175 insertions(+), 127 deletions(-)

diff --git a/R/get_events.R b/R/get_events.R
index 88f474f..2959393 100644
--- a/R/get_events.R
+++ b/R/get_events.R
@@ -1,111 +1,147 @@
-#' Download events from Go.Data
-#'
-#' A function to retrieve the event data for a
-#' specific `outbreak_id`.
-#'
-#' This function works on all versions of Go.Data. There
-#' are two methods for downloading the data:
-#'
-#' `method="batches"` will work on all versions of
-#'    Go.Data. This method relies on the GET outbreak/{id}/events
-#'    API endpoint. Records are then retrieved in batches
-#'    based on `batch_size` and appended together into
-#'    a final dataset. `method="batches"` will be the default and
-#'    only available method for Go.Data version 2.38.0 or older.
-#'
-#' `method="export"` will only work on Go.Data versions
-#'    2.38.1 or newer. This method relies on the GET
-#'    outbreak/{id}/events/export API endpoint. An export
-#'    request is submitted to the server, and then when the
-#'    export is ready, it will be downloaded. Due to better
-#'    performance and more options, `method="export"` will
-#'    be the default if you are using Go.Data version 2.38.1
-#'    or newer.
-#'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
-#' @param username The email address for your Go.Data login.
-#' @param password The password for your Go.Data login
-#' @param outbreak_id The id number for the outbreak for which you want to download data.
-#' @param method The method to download data. `method="export"` is the preferred and default method for Go.Data version 2.38.1 or later. See Details.
-#' @param batch_size If `method="batches"`, then `batch_size` specifies the number of records to retrieve in each iteration.
-#' @param wait If `method="export"`, then `wait` is the number of seconds to wait in between iterations of checking the status of the export.
-#' @param file.type If `method="export"`, then `file.type` determines Whether the resulting data frame should contain nested fields (`file.type="json"`, the default) or an entirely flat data structure (`file.type="csv"`)
-#'
-#' @return
-#' Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
-#' @export
-#'
-#' @examples
-#' \dontrun{
-#' url <- "https://MyGoDataServer.com/"
-#' username <- "myemail@email.com"
-#' password <- "mypassword"
-#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
-#'
-#' events <- get_events(url=url,
-#'                      username=username,
-#'                      password=password,
-#'                      outbreak_id=outbreak_id)
-#' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @import tibble
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
-
-
-get_events <- function(url=url,
-                         username=username,
-                         password=password,
-                         outbreak_id=outbreak_id,
-                         method=c("export","batch"),
-                         batch_size=50000,
-                         wait=2,
-                         file.type=c("json","csv")) {
-
-  #Check that outbreak_id is active
-  if (outbreak_id != get_active_outbreak(url=url, username=username, password=password)) {
-    set_active_outbreak(url=url, username=username, password=password, outbreak_id=outbreak_id)
-  }
-
-  #Set default method based on current version of Go.Data
-  version.check <- check_godata_version(url=url)
-  if (!version.check) {
-    method <- "batches" #Older version of Go.Data can only use the batch method
-  } else if (missing(method)) {
-    method <- "export" # For new versions of Go.Data, default to export method
-  }
-
-
-  if (method == "batches") {
-
-    api_call_n <- paste0(url, "api/outbreaks/",outbreak_id,"/events/filtered-count")
-    api_call_get <- paste0(url, "api/outbreaks/",outbreak_id,"/events")
-    df <- batch_downloader(url=url,
-                           username=username,
-                           password=password,
-                           api_call_n=api_call_n,
-                           api_call_get=api_call_get,
-                           batch_size=batch_size)
-
-  } else if (method == "export") {
-
-    #Default value of file.type is "json"
-    if (missing(file.type)) file.type <- "json"
-
-    #Submit an export request to the system
-    api_call_request <- paste0(url,"api/outbreaks/",outbreak_id,"/events/export")
-    df <- export_downloader(url=url,
-                            username=username,
-                            password=password,
-                            api_call_request=api_call_request,
-                            file.type = file.type,
-                            wait = wait)
-
-
-  }
-
-  return(df)
-}
+#' Download events from Go.Data
+#'
+#' A function to retrieve the event data for a
+#' specific `outbreak_id`.
+#'
+#' This function works on all versions of Go.Data. There
+#' are two methods for downloading the data:
+#'
+#' `method = "batches"` will work on all versions of
+#'    Go.Data. This method relies on the GET outbreak/{id}/events
+#'    API endpoint. Records are then retrieved in batches
+#'    based on `batch_size` and appended together into
+#'    a final dataset. `method = "batches"` will be the default and
+#'    only available method for Go.Data version 2.38.0 or older.
+#'
+#' `method = "export"` will only work on Go.Data versions
+#'    2.38.1 or newer. This method relies on the GET
+#'    outbreak/{id}/events/export API endpoint. An export
+#'    request is submitted to the server, and then when the
+#'    export is ready, it will be downloaded. Due to better
+#'    performance and more options, `method = "export"` will
+#'    be the default if you are using Go.Data version 2.38.1
+#'    or newer.
+#'
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
+#' @param username The email address for your Go.Data login.
+#' @param password The password for your Go.Data login
+#' @param outbreak_id The id number for the outbreak for which you want to
+#' download data.
+#' @param method The method to download data. `method = "export"` is the
+#' preferred and default method for Go.Data version 2.38.1 or later. See
+#' Details.
+#' @param batch_size If `method = "batches"`, then `batch_size` specifies the
+#' number of records to retrieve in each iteration.
+#' @param wait If `method = "export"`, then `wait` is the number of seconds to
+#' wait in between iterations of checking the status of the export.
+#' @param file_type If `method = "export"`, then `file_type` determines Whether
+#' the resulting data frame should contain nested fields (`file_type = "json"`,
+#' the default) or an entirely flat data structure (`file_type = "csv"`)
+#'
+#' @return
+#' Returns a data frame. Some fields, such as addresses, hospitalization
+#' history, and questionnaire fields may require further unnesting. See
+#' \code{\link[tidyr]{nest}} for assitance with unnesting.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' events <- get_events(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#' }
+#' @importFrom magrittr %>%
+#' @import dplyr
+#' @import tidyr
+#' @import httr
+#' @import tibble
+#' @importFrom jsonlite fromJSON
+#' @importFrom purrr pluck
+get_events <- function(url = url,
+                       username = username,
+                       password = password,
+                       outbreak_id = outbreak_id,
+                       method = c("export", "batch"),
+                       batch_size = 50000,
+                       wait = 2,
+                       file_type = c("json", "csv")) {
+
+  #Check that outbreak_id is active
+  active_outbreak <- get_active_outbreak(
+    url = url,
+    username = username,
+    password = password
+  )
+  if (outbreak_id != active_outbreak) {
+    set_active_outbreak(
+      url = url,
+      username = username,
+      password = password,
+      outbreak_id = outbreak_id
+    )
+  }
+
+  #Set default method based on current version of Go.Data
+  version_check <- check_godata_version(url = url)
+  if (!version_check) {
+    method <- "batches" #Older version of Go.Data can only use the batch method
+  } else if (missing(method)) {
+    method <- "export" # For new versions of Go.Data, default to export method
+  }
+
+
+  if (method == "batches") {
+
+    api_call_n <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/events/filtered-count"
+    )
+    api_call_get <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/events"
+    )
+    df <- batch_downloader(
+      url = url,
+      username = username,
+      password = password,
+      api_call_n = api_call_n,
+      api_call_get = api_call_get,
+      batch_size = batch_size
+    )
+
+  } else if (method == "export") {
+
+    #Default value of file_type is "json"
+    if (missing(file_type)) file_type <- "json"
+
+    #Submit an export request to the system
+    api_call_request <- paste0(
+      url,
+      "api/outbreaks/",
+      outbreak_id,
+      "/events/export"
+    )
+    df <- export_downloader(
+      url = url,
+      username = username,
+      password = password,
+      api_call_request = api_call_request,
+      file_type = file_type,
+      wait = wait
+    )
+  }
+  return(df)
+}
diff --git a/man/get_events.Rd b/man/get_events.Rd
index 6985f16..ba678f3 100644
--- a/man/get_events.Rd
+++ b/man/get_events.Rd
@@ -12,28 +12,38 @@ get_events(
   method = c("export", "batch"),
   batch_size = 50000,
   wait = 2,
-  file.type = c("json", "csv")
+  file_type = c("json", "csv")
 )
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
 \item{password}{The password for your Go.Data login}
 
-\item{outbreak_id}{The id number for the outbreak for which you want to download data.}
+\item{outbreak_id}{The id number for the outbreak for which you want to
+download data.}
 
-\item{method}{The method to download data. \code{method="export"} is the preferred and default method for Go.Data version 2.38.1 or later. See Details.}
+\item{method}{The method to download data. \code{method = "export"} is the
+preferred and default method for Go.Data version 2.38.1 or later. See
+Details.}
 
-\item{batch_size}{If \code{method="batches"}, then \code{batch_size} specifies the number of records to retrieve in each iteration.}
+\item{batch_size}{If \code{method = "batches"}, then \code{batch_size} specifies the
+number of records to retrieve in each iteration.}
 
-\item{wait}{If \code{method="export"}, then \code{wait} is the number of seconds to wait in between iterations of checking the status of the export.}
+\item{wait}{If \code{method = "export"}, then \code{wait} is the number of seconds to
+wait in between iterations of checking the status of the export.}
 
-\item{file.type}{If \code{method="export"}, then \code{file.type} determines Whether the resulting data frame should contain nested fields (\code{file.type="json"}, the default) or an entirely flat data structure (\code{file.type="csv"})}
+\item{file_type}{If \code{method = "export"}, then \code{file_type} determines Whether
+the resulting data frame should contain nested fields (\code{file_type = "json"},
+the default) or an entirely flat data structure (\code{file_type = "csv"})}
 }
 \value{
-Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+Returns a data frame. Some fields, such as addresses, hospitalization
+history, and questionnaire fields may require further unnesting. See
+\code{\link[tidyr]{nest}} for assitance with unnesting.
 }
 \description{
 A function to retrieve the event data for a
@@ -43,19 +53,19 @@ specific \code{outbreak_id}.
 This function works on all versions of Go.Data. There
 are two methods for downloading the data:
 
-\code{method="batches"} will work on all versions of
+\code{method = "batches"} will work on all versions of
 Go.Data. This method relies on the GET outbreak/{id}/events
 API endpoint. Records are then retrieved in batches
 based on \code{batch_size} and appended together into
-a final dataset. \code{method="batches"} will be the default and
+a final dataset. \code{method = "batches"} will be the default and
 only available method for Go.Data version 2.38.0 or older.
 
-\code{method="export"} will only work on Go.Data versions
+\code{method = "export"} will only work on Go.Data versions
 2.38.1 or newer. This method relies on the GET
 outbreak/{id}/events/export API endpoint. An export
 request is submitted to the server, and then when the
 export is ready, it will be downloaded. Due to better
-performance and more options, \code{method="export"} will
+performance and more options, \code{method = "export"} will
 be the default if you are using Go.Data version 2.38.1
 or newer.
 }
@@ -66,9 +76,11 @@ username <- "myemail@email.com"
 password <- "mypassword"
 outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 
-events <- get_events(url=url,
-                     username=username,
-                     password=password,
-                     outbreak_id=outbreak_id)
+events <- get_events(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
 }
 }

From 25fcab92149da9be64638af82972e0101091ea97 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 10:47:06 +0000
Subject: [PATCH 117/203] removed recurive argument defaults from get_events

---
 R/get_events.R    | 8 ++++----
 man/get_events.Rd | 8 ++++----
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/get_events.R b/R/get_events.R
index 2959393..608e25a 100644
--- a/R/get_events.R
+++ b/R/get_events.R
@@ -66,10 +66,10 @@
 #' @import tibble
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
-get_events <- function(url = url,
-                       username = username,
-                       password = password,
-                       outbreak_id = outbreak_id,
+get_events <- function(url,
+                       username,
+                       password,
+                       outbreak_id,
                        method = c("export", "batch"),
                        batch_size = 50000,
                        wait = 2,
diff --git a/man/get_events.Rd b/man/get_events.Rd
index ba678f3..f7ad66f 100644
--- a/man/get_events.Rd
+++ b/man/get_events.Rd
@@ -5,10 +5,10 @@
 \title{Download events from Go.Data}
 \usage{
 get_events(
-  url = url,
-  username = username,
-  password = password,
-  outbreak_id = outbreak_id,
+  url,
+  username,
+  password,
+  outbreak_id,
   method = c("export", "batch"),
   batch_size = 50000,
   wait = 2,

From 6736ff184b5c9594e80eadae3f573a26945e2cd9 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 10:48:53 +0000
Subject: [PATCH 118/203] used explicit namespace instead of import for
 get_events

---
 R/get_events.R | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/R/get_events.R b/R/get_events.R
index 608e25a..cbb2a29 100644
--- a/R/get_events.R
+++ b/R/get_events.R
@@ -59,13 +59,6 @@
 #'   outbreak_id = outbreak_id
 #' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @import tibble
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
 get_events <- function(url,
                        username,
                        password,
@@ -143,5 +136,5 @@ get_events <- function(url,
       wait = wait
     )
   }
-  return(df)
+  return(tibble::as_tibble(df))
 }

From e54a4b32598153155f4fb9b68d024b6cc265d77d Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 10:59:15 +0000
Subject: [PATCH 119/203] added test for get_events

---
 tests/testthat/test-get_events.R | 43 ++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 tests/testthat/test-get_events.R

diff --git a/tests/testthat/test-get_events.R b/tests/testthat/test-get_events.R
new file mode 100644
index 0000000..b66d8ee
--- /dev/null
+++ b/tests/testthat/test-get_events.R
@@ -0,0 +1,43 @@
+test_that("get_events works as expected", {
+  skip("get_events requires API call")
+
+  res <- get_events(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id,
+    method = "export",
+    batch_size = 50000,
+    wait = 2,
+    file_type = "json"
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(2L, 34L))
+  expect_true(
+    all(c(
+      "id", "dateOfReporting", "isDateOfReportingApproximate", "createdAt",
+      "createdBy", "updatedAt", "updatedBy", "deleted", "deletedAt",
+      "createdOn", "type", "numberOfExposures", "numberOfContacts", "name",
+      "date", "description", "responsibleUserId", "eventCategory", "endDate",
+      "address.typeId", "address.locationId", "address.Identifiers",
+      "address.Location geographical level", "address.Parent location",
+      "address.geoLocationAccurate", "address.date", "address.country",
+      "address.city", "address.addressLine1", "address.postalCode",
+      "address.phoneNumber", "address.emailAddress", "address.geoLocation.lat",
+      "address.geoLocation.lng"
+    ) %in% colnames(res))
+  )
+
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "character", "logical", "character", "character",
+      "character", "character", "logical", "logical", "character", "character",
+      "integer", "integer", "character", "character", "logical", "logical",
+      "logical", "character", "character", "character", "list", "list",
+      "list", "logical", "character", "logical", "logical", "logical",
+      "logical", "logical", "logical", "numeric", "numeric"))
+
+})

From 810789b1584b5879734720094aa457f97d306adb Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:05:19 +0000
Subject: [PATCH 120/203] linted get_teams

---
 R/get_teams.R    | 31 ++++++++++++++++++++-----------
 man/get_teams.Rd |  3 ++-
 2 files changed, 22 insertions(+), 12 deletions(-)

diff --git a/R/get_teams.R b/R/get_teams.R
index d6b799e..dbb5279 100644
--- a/R/get_teams.R
+++ b/R/get_teams.R
@@ -6,7 +6,8 @@
 #' endpoint). This function relies on the
 #' `\teams` API endpoint.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
 #'
@@ -30,17 +31,25 @@
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
 #' @export
+get_teams <- function(url = url,
+                      username = username,
+                      password = password) {
 
-
-get_teams <- function(url=url,
-                      username=username,
-                      password=password) {
-
-  teams <- GET(paste0(url,"api/teams",
-                      "?access_token=",get_access_token(url=url, username=username, password=password))) %>%
-    content(as="text") %>%
-    fromJSON(flatten=TRUE) %>%
-    filter(deleted!=TRUE)
+  teams <- GET(
+    paste0(
+      url,
+      "api/teams",
+      "?access_token=",
+      get_access_token(
+        url = url,
+        username = username,
+        password = password
+      )
+    )
+  ) %>%
+    content(as = "text") %>%
+    fromJSON(flatten = TRUE) %>%
+    filter(.data$deleted != TRUE)
 
   return(teams)
 
diff --git a/man/get_teams.Rd b/man/get_teams.Rd
index add05f6..36993cc 100644
--- a/man/get_teams.Rd
+++ b/man/get_teams.Rd
@@ -7,7 +7,8 @@
 get_teams(url = url, username = username, password = password)
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 

From 7b83f3636e08bfb6e95b5fdfc1d5e42851c2ee6a Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:06:44 +0000
Subject: [PATCH 121/203] removed recursive default arguments in get_teams

---
 R/get_teams.R    | 6 +++---
 man/get_teams.Rd | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/get_teams.R b/R/get_teams.R
index dbb5279..43aaa16 100644
--- a/R/get_teams.R
+++ b/R/get_teams.R
@@ -31,9 +31,9 @@
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
 #' @export
-get_teams <- function(url = url,
-                      username = username,
-                      password = password) {
+get_teams <- function(url,
+                      username,
+                      password) {
 
   teams <- GET(
     paste0(
diff --git a/man/get_teams.Rd b/man/get_teams.Rd
index 36993cc..f6436d5 100644
--- a/man/get_teams.Rd
+++ b/man/get_teams.Rd
@@ -4,7 +4,7 @@
 \alias{get_teams}
 \title{#' Get teams data from Go.Data}
 \usage{
-get_teams(url = url, username = username, password = password)
+get_teams(url, username, password)
 }
 \arguments{
 \item{url}{Insert the base URL for your instance of Go.Data here. Don't

From d5f51dd113ec5252757b7c5ddd88ce0562a068f6 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:09:23 +0000
Subject: [PATCH 122/203] removed pipe from get_teams

---
 R/get_teams.R | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/R/get_teams.R b/R/get_teams.R
index 43aaa16..71d3436 100644
--- a/R/get_teams.R
+++ b/R/get_teams.R
@@ -35,7 +35,7 @@ get_teams <- function(url,
                       username,
                       password) {
 
-  teams <- GET(
+  teams_request <- GET(
     paste0(
       url,
       "api/teams",
@@ -46,11 +46,10 @@ get_teams <- function(url,
         password = password
       )
     )
-  ) %>%
-    content(as = "text") %>%
-    fromJSON(flatten = TRUE) %>%
-    filter(.data$deleted != TRUE)
+  )
+  teams_content <- content(teams_request, as = "text")
+  teams <- fromJSON(teams_content, flatten = TRUE)
+  teams <- filter(teams, .data$deleted != TRUE)
 
   return(teams)
-
 }

From 4c41361f3795132cf117c86cb18cc59bd727252e Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:10:49 +0000
Subject: [PATCH 123/203] used explicit namespace instead of import in
 get_teams

---
 R/get_teams.R | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/R/get_teams.R b/R/get_teams.R
index 71d3436..0c52325 100644
--- a/R/get_teams.R
+++ b/R/get_teams.R
@@ -24,18 +24,12 @@
 #'                    username=username,
 #'                    password=password)
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
 #' @export
 get_teams <- function(url,
                       username,
                       password) {
 
-  teams_request <- GET(
+  teams_request <- httr::GET(
     paste0(
       url,
       "api/teams",
@@ -47,9 +41,9 @@ get_teams <- function(url,
       )
     )
   )
-  teams_content <- content(teams_request, as = "text")
-  teams <- fromJSON(teams_content, flatten = TRUE)
-  teams <- filter(teams, .data$deleted != TRUE)
+  teams_content <- httr::content(teams_request, as = "text")
+  teams <- jsonlite::fromJSON(teams_content, flatten = TRUE)
+  teams <- dplyr::filter(teams, .data$deleted != TRUE)
 
   return(teams)
 }

From 8addbebefa2fb5a6ca5ab457f6684fe63ad7b7c1 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:12:01 +0000
Subject: [PATCH 124/203] ensure get_teams returns a tibble

---
 R/get_teams.R    | 9 ++++++---
 man/get_teams.Rd | 8 +++++---
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/R/get_teams.R b/R/get_teams.R
index 0c52325..72ffd34 100644
--- a/R/get_teams.R
+++ b/R/get_teams.R
@@ -20,9 +20,11 @@
 #' username <- "myemail@email.com"
 #' password <- "mypassword"
 #'
-#' teams <- get_teams(url=url,
-#'                    username=username,
-#'                    password=password)
+#' teams <- get_teams(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
 #' }
 #' @export
 get_teams <- function(url,
@@ -44,6 +46,7 @@ get_teams <- function(url,
   teams_content <- httr::content(teams_request, as = "text")
   teams <- jsonlite::fromJSON(teams_content, flatten = TRUE)
   teams <- dplyr::filter(teams, .data$deleted != TRUE)
+  teams <- tibble::as_tibble(teams)
 
   return(teams)
 }
diff --git a/man/get_teams.Rd b/man/get_teams.Rd
index f6436d5..2879e2d 100644
--- a/man/get_teams.Rd
+++ b/man/get_teams.Rd
@@ -30,8 +30,10 @@ url <- "https://MyGoDataServer.com/"
 username <- "myemail@email.com"
 password <- "mypassword"
 
-teams <- get_teams(url=url,
-                   username=username,
-                   password=password)
+teams <- get_teams(
+  url = url,
+  username = username,
+  password = password
+)
 }
 }

From 1b26a090bea5a883aa3e8734c9dc0c3403b42bed Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:15:25 +0000
Subject: [PATCH 125/203] added test for get_teams

---
 tests/testthat/test-get_teams.R | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 tests/testthat/test-get_teams.R

diff --git a/tests/testthat/test-get_teams.R b/tests/testthat/test-get_teams.R
new file mode 100644
index 0000000..efc960b
--- /dev/null
+++ b/tests/testthat/test-get_teams.R
@@ -0,0 +1,22 @@
+test_that("get_teams works as expected", {
+  skip("get_teams requires API call")
+
+
+  res <- get_teams(url = url, username = username, password = password)
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(3L, 10L))
+  expect_true(
+    all(c(
+      "name", "userIds", "locationIds", "id", "createdAt", "createdBy",
+      "updatedAt", "updatedBy", "createdOn", "deleted"
+    ) %in% colnames(res))
+  )
+
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "list", "list", "character", "character", "character",
+      "character", "character", "character", "logical"))
+})

From d6167e563c4db5100bca166b37583e011ff22d87 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:15:56 +0000
Subject: [PATCH 126/203] updated NAMESPACE

---
 NAMESPACE | 1 -
 1 file changed, 1 deletion(-)

diff --git a/NAMESPACE b/NAMESPACE
index 4ce71b1..2120a66 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -37,7 +37,6 @@ import(jsonlite)
 import(lubridate)
 import(purrr)
 import(stringr)
-import(tibble)
 import(tidyr)
 import(urltools)
 importFrom(jsonlite,fromJSON)

From b6b4a79b6659bc8186e1fcd9451e93f1a477c32b Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:20:24 +0000
Subject: [PATCH 127/203] linted get_locations

---
 R/get_locations.R    | 37 +++++++++++++++++++++++++------------
 man/get_locations.Rd | 11 +++++++----
 2 files changed, 32 insertions(+), 16 deletions(-)

diff --git a/R/get_locations.R b/R/get_locations.R
index 1489ba7..c16ee7b 100644
--- a/R/get_locations.R
+++ b/R/get_locations.R
@@ -6,7 +6,8 @@
 #' endpoint). This function relies on the `\locations`
 #' API endpoint.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
 #'
@@ -19,9 +20,11 @@
 #' username <- "myemail@email.com"
 #' password <- "mypassword"
 #'
-#' locations <- get_locations(url=url,
-#'                            username=username,
-#'                            password=password)
+#' locations <- get_locations(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
 #' }
 #' @importFrom magrittr %>%
 #' @import dplyr
@@ -32,15 +35,25 @@
 #' @export
 
 
-get_locations <- function(url=url,
-                          username=username,
-                          password=password) {
+get_locations <- function(url = url,
+                          username = username,
+                          password = password) {
 
-  locations <- GET(paste0(url,"api/locations",
-                      "?access_token=",godataR::get_access_token(url=url, username=username, password=password))) %>%
-    content(as="text") %>%
-    fromJSON(flatten=TRUE) %>%
-    filter(deleted!=TRUE)
+  locations <- GET(
+    paste0(
+      url,
+      "api/locations",
+      "?access_token=",
+      godataR::get_access_token(
+        url = url,
+        username = username,
+        password = password
+      )
+    )
+  ) %>%
+    content(as = "text") %>%
+    fromJSON(flatten = TRUE) %>%
+    filter(.data$deleted != TRUE)
 
   return(locations)
 
diff --git a/man/get_locations.Rd b/man/get_locations.Rd
index 67cb4db..e035f4f 100644
--- a/man/get_locations.Rd
+++ b/man/get_locations.Rd
@@ -7,7 +7,8 @@
 get_locations(url = url, username = username, password = password)
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
@@ -29,8 +30,10 @@ url <- "https://MyGoDataServer.com/"
 username <- "myemail@email.com"
 password <- "mypassword"
 
-locations <- get_locations(url=url,
-                           username=username,
-                           password=password)
+locations <- get_locations(
+  url = url,
+  username = username,
+  password = password
+)
 }
 }

From ee83866667bda44f5cbf8fb45789a70729cd0e5e Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:21:07 +0000
Subject: [PATCH 128/203] removed recursive arugment defaults for get_locations

---
 R/get_locations.R    | 6 +++---
 man/get_locations.Rd | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/get_locations.R b/R/get_locations.R
index c16ee7b..577f90b 100644
--- a/R/get_locations.R
+++ b/R/get_locations.R
@@ -35,9 +35,9 @@
 #' @export
 
 
-get_locations <- function(url = url,
-                          username = username,
-                          password = password) {
+get_locations <- function(url,
+                          username,
+                          password) {
 
   locations <- GET(
     paste0(
diff --git a/man/get_locations.Rd b/man/get_locations.Rd
index e035f4f..77b1f98 100644
--- a/man/get_locations.Rd
+++ b/man/get_locations.Rd
@@ -4,7 +4,7 @@
 \alias{get_locations}
 \title{Get location data from Go.Data}
 \usage{
-get_locations(url = url, username = username, password = password)
+get_locations(url, username, password)
 }
 \arguments{
 \item{url}{Insert the base URL for your instance of Go.Data here. Don't

From 113a45fcbd8a0d046a88b88ce3c0c1a10fe7cc4b Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:23:02 +0000
Subject: [PATCH 129/203] removed pipe from get_locations

---
 R/get_locations.R | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/R/get_locations.R b/R/get_locations.R
index 577f90b..4db6005 100644
--- a/R/get_locations.R
+++ b/R/get_locations.R
@@ -33,13 +33,11 @@
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
 #' @export
-
-
 get_locations <- function(url,
                           username,
                           password) {
 
-  locations <- GET(
+  locations_request <- GET(
     paste0(
       url,
       "api/locations",
@@ -50,11 +48,10 @@ get_locations <- function(url,
         password = password
       )
     )
-  ) %>%
-    content(as = "text") %>%
-    fromJSON(flatten = TRUE) %>%
-    filter(.data$deleted != TRUE)
+  )
+  locations_content <- content(locations_request, as = "text")
+  locations <- fromJSON(locations_content, flatten = TRUE)
+  locations <- filter(locations, .data$deleted != TRUE)
 
   return(locations)
-
 }

From e26c7ec02cb0f84e5d1c6da040c2f743e9f180d7 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:24:06 +0000
Subject: [PATCH 130/203] used explicit namespace instead of import in
 get_locations

---
 R/get_locations.R | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/R/get_locations.R b/R/get_locations.R
index 4db6005..9aa8c52 100644
--- a/R/get_locations.R
+++ b/R/get_locations.R
@@ -26,18 +26,12 @@
 #'   password = password
 #' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
 #' @export
 get_locations <- function(url,
                           username,
                           password) {
 
-  locations_request <- GET(
+  locations_request <- httr::GET(
     paste0(
       url,
       "api/locations",
@@ -49,9 +43,9 @@ get_locations <- function(url,
       )
     )
   )
-  locations_content <- content(locations_request, as = "text")
-  locations <- fromJSON(locations_content, flatten = TRUE)
-  locations <- filter(locations, .data$deleted != TRUE)
+  locations_content <- httr::content(locations_request, as = "text")
+  locations <- jsonlite::fromJSON(locations_content, flatten = TRUE)
+  locations <- dplyr::filter(locations, .data$deleted != TRUE)
 
   return(locations)
 }

From c0a6a8cd233b9862091cb1d162755319d2bcc0ca Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:24:56 +0000
Subject: [PATCH 131/203] ensure get_locations returns a tibble

---
 R/get_locations.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/get_locations.R b/R/get_locations.R
index 9aa8c52..decf897 100644
--- a/R/get_locations.R
+++ b/R/get_locations.R
@@ -46,6 +46,7 @@ get_locations <- function(url,
   locations_content <- httr::content(locations_request, as = "text")
   locations <- jsonlite::fromJSON(locations_content, flatten = TRUE)
   locations <- dplyr::filter(locations, .data$deleted != TRUE)
+  locations <- tibble::as_tibble(locations)
 
   return(locations)
 }

From 2dd80e32f7026ced32e21c24ba62ba1df7dfe111 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:28:53 +0000
Subject: [PATCH 132/203] added test for get_locations

---
 tests/testthat/test-get_locations.R | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 tests/testthat/test-get_locations.R

diff --git a/tests/testthat/test-get_locations.R b/tests/testthat/test-get_locations.R
new file mode 100644
index 0000000..fc610d0
--- /dev/null
+++ b/tests/testthat/test-get_locations.R
@@ -0,0 +1,24 @@
+test_that("get_locations works as expected", {
+  skip("get_locations requires API call")
+
+  res <- get_locations(url = url, username = username, password = password)
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(11L, 16L))
+  expect_true(
+    all(c(
+      "name", "synonyms", "identifiers", "active", "populationDensity",
+      "parentLocationId", "geographicalLevelId", "id", "createdAt",
+      "createdBy", "updatedAt", "updatedBy", "createdOn", "deleted",
+      "geoLocation.lat", "geoLocation.lng"
+    ) %in% colnames(res))
+  )
+
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "list", "list", "logical", "integer", "character",
+      "character", "character", "character", "character", "character",
+      "character", "character", "logical", "numeric", "numeric"))
+})

From b7f722dfca344e98de281220fc7c4a5837a5ca08 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:33:17 +0000
Subject: [PATCH 133/203] linted get_reference_data

---
 R/get_reference_data.R    | 40 ++++++++++++++++++++++++---------------
 man/get_reference_data.Rd | 11 +++++++----
 2 files changed, 32 insertions(+), 19 deletions(-)

diff --git a/R/get_reference_data.R b/R/get_reference_data.R
index 5e2f0b7..b56b288 100644
--- a/R/get_reference_data.R
+++ b/R/get_reference_data.R
@@ -6,7 +6,8 @@
 #' endpoint). This function relies on the
 #' `\reference-data` API endpoint.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
 #'
@@ -19,9 +20,11 @@
 #' username <- "myemail@email.com"
 #' password <- "mypassword"
 #'
-#' reference_data <- get_reference_data(url=url,
-#'                                      username=username,
-#'                                      password=password)
+#' reference_data <- get_reference_data(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
 #' }
 #' @importFrom magrittr %>%
 #' @import dplyr
@@ -30,18 +33,25 @@
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
 #' @export
+get_reference_data <- function(url = url,
+                               username = username,
+                               password = password) {
 
-
-get_reference_data <- function(url=url,
-                               username=username,
-                               password=password) {
-
-  reference_data <- GET(paste0(url,"api/reference-data",
-                      "?access_token=",get_access_token(url=url, username=username, password=password))) %>%
-    content(as="text") %>%
-    fromJSON(flatten=TRUE) %>%
-    filter(deleted!=TRUE)
+  reference_data <- GET(
+    paste0(
+      url,
+      "api/reference-data",
+      "?access_token=",
+      get_access_token(
+        url = url,
+        username = username,
+        password = password
+      )
+    )
+  ) %>%
+    content(as = "text") %>%
+    fromJSON(flatten = TRUE) %>%
+    filter(.data$deleted != TRUE)
 
     return(reference_data)
-
 }
diff --git a/man/get_reference_data.Rd b/man/get_reference_data.Rd
index 2b42b35..b5a5832 100644
--- a/man/get_reference_data.Rd
+++ b/man/get_reference_data.Rd
@@ -7,7 +7,8 @@
 get_reference_data(url = url, username = username, password = password)
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
@@ -29,8 +30,10 @@ url <- "https://MyGoDataServer.com/"
 username <- "myemail@email.com"
 password <- "mypassword"
 
-reference_data <- get_reference_data(url=url,
-                                     username=username,
-                                     password=password)
+reference_data <- get_reference_data(
+  url = url,
+  username = username,
+  password = password
+)
 }
 }

From d203ca81f5372ea71a06dedf702ce3b46908c4e8 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:33:59 +0000
Subject: [PATCH 134/203] removed recursive default arguments in
 get_reference_data

---
 R/get_reference_data.R    | 6 +++---
 man/get_reference_data.Rd | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/get_reference_data.R b/R/get_reference_data.R
index b56b288..9b523a8 100644
--- a/R/get_reference_data.R
+++ b/R/get_reference_data.R
@@ -33,9 +33,9 @@
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
 #' @export
-get_reference_data <- function(url = url,
-                               username = username,
-                               password = password) {
+get_reference_data <- function(url,
+                               username,
+                               password) {
 
   reference_data <- GET(
     paste0(
diff --git a/man/get_reference_data.Rd b/man/get_reference_data.Rd
index b5a5832..e21b311 100644
--- a/man/get_reference_data.Rd
+++ b/man/get_reference_data.Rd
@@ -4,7 +4,7 @@
 \alias{get_reference_data}
 \title{Get reference data from Go.Data}
 \usage{
-get_reference_data(url = url, username = username, password = password)
+get_reference_data(url, username, password)
 }
 \arguments{
 \item{url}{Insert the base URL for your instance of Go.Data here. Don't

From 54f00e54f8d590161e9290c305cfffe5c5bd80dc Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:36:54 +0000
Subject: [PATCH 135/203] removed pipe from get_reference_data

---
 R/get_reference_data.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/get_reference_data.R b/R/get_reference_data.R
index 9b523a8..7714ce6 100644
--- a/R/get_reference_data.R
+++ b/R/get_reference_data.R
@@ -37,7 +37,7 @@ get_reference_data <- function(url,
                                username,
                                password) {
 
-  reference_data <- GET(
+  reference_data_request <- GET(
     paste0(
       url,
       "api/reference-data",
@@ -48,10 +48,10 @@ get_reference_data <- function(url,
         password = password
       )
     )
-  ) %>%
-    content(as = "text") %>%
-    fromJSON(flatten = TRUE) %>%
-    filter(.data$deleted != TRUE)
+  )
+  reference_data_content <- content(reference_data_request, as = "text")
+  reference_data <- fromJSON(reference_data_content, flatten = TRUE)
+  reference_data <- filter(reference_data, .data$deleted != TRUE)
 
     return(reference_data)
 }

From e4d0627c98d0950eaa77ab807fff45fdbbe25836 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:38:04 +0000
Subject: [PATCH 136/203] used explicit namespace instead of import for
 get_reference_data

---
 R/get_reference_data.R | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/R/get_reference_data.R b/R/get_reference_data.R
index 7714ce6..1ad0afe 100644
--- a/R/get_reference_data.R
+++ b/R/get_reference_data.R
@@ -26,18 +26,12 @@
 #'   password = password
 #' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
 #' @export
 get_reference_data <- function(url,
                                username,
                                password) {
 
-  reference_data_request <- GET(
+  reference_data_request <- httr::GET(
     paste0(
       url,
       "api/reference-data",
@@ -49,9 +43,9 @@ get_reference_data <- function(url,
       )
     )
   )
-  reference_data_content <- content(reference_data_request, as = "text")
-  reference_data <- fromJSON(reference_data_content, flatten = TRUE)
-  reference_data <- filter(reference_data, .data$deleted != TRUE)
+  reference_data_content <- httr::content(reference_data_request, as = "text")
+  reference_data <- jsonlite::fromJSON(reference_data_content, flatten = TRUE)
+  reference_data <- dplyr::filter(reference_data, .data$deleted != TRUE)
 
     return(reference_data)
 }

From cc3dbe671399b243cb170ad841809d37b031b418 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:39:10 +0000
Subject: [PATCH 137/203] ensure get_reference_data returns a tibble

---
 R/get_reference_data.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/get_reference_data.R b/R/get_reference_data.R
index 1ad0afe..bfaf798 100644
--- a/R/get_reference_data.R
+++ b/R/get_reference_data.R
@@ -46,6 +46,7 @@ get_reference_data <- function(url,
   reference_data_content <- httr::content(reference_data_request, as = "text")
   reference_data <- jsonlite::fromJSON(reference_data_content, flatten = TRUE)
   reference_data <- dplyr::filter(reference_data, .data$deleted != TRUE)
+  reference_data <- tibble::as_tibble(reference_data)
 
     return(reference_data)
 }

From 175c6cb880912de3992693e8c2e284a20d499852 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 11:44:04 +0000
Subject: [PATCH 138/203] added test for get_reference_data

---
 tests/testthat/test-get_reference_data.R | 25 ++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 tests/testthat/test-get_reference_data.R

diff --git a/tests/testthat/test-get_reference_data.R b/tests/testthat/test-get_reference_data.R
new file mode 100644
index 0000000..864014b
--- /dev/null
+++ b/tests/testthat/test-get_reference_data.R
@@ -0,0 +1,25 @@
+test_that("get_reference_data works as expected", {
+  skip("get_reference_data requires API call")
+
+  res <- get_reference_data(url = url, username = username, password = password)
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(391L, 19L))
+  expect_true(
+    all(c(
+      "categoryId", "value", "description", "readOnly", "active",
+      "isDefaultReferenceData", "id", "createdAt", "createdBy", "updatedAt",
+      "updatedBy", "createdOn", "deleted", "colorCode", "order",
+      "isOutbreakTemplateReferenceData", "deletedAt", "iconId", "code"
+    ) %in% colnames(res))
+  )
+
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "character", "character", "logical", "logical", "logical",
+      "character", "character", "character", "character", "character",
+      "character", "logical", "character", "integer", "logical", "logical",
+      "character", "character"))
+})

From 36cb8df8b04fa7bbcc2e5119ff43b7a9c3a8fd26 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 14:56:34 +0000
Subject: [PATCH 139/203] linting tests

---
 R/get_reference_data.R                    |  2 +-
 tests/testthat/test-batch_downloader.R    | 14 +++++++-------
 tests/testthat/test-get_access_token.R    |  1 -
 tests/testthat/test-get_all_outbreaks.R   |  2 +-
 tests/testthat/test-get_godata_version.R  |  2 +-
 tests/testthat/test-get_language_tokens.R |  2 +-
 6 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/R/get_reference_data.R b/R/get_reference_data.R
index bfaf798..4f78ee6 100644
--- a/R/get_reference_data.R
+++ b/R/get_reference_data.R
@@ -48,5 +48,5 @@ get_reference_data <- function(url,
   reference_data <- dplyr::filter(reference_data, .data$deleted != TRUE)
   reference_data <- tibble::as_tibble(reference_data)
 
-    return(reference_data)
+  return(reference_data)
 }
diff --git a/tests/testthat/test-batch_downloader.R b/tests/testthat/test-batch_downloader.R
index e7da9d4..0d5168e 100644
--- a/tests/testthat/test-batch_downloader.R
+++ b/tests/testthat/test-batch_downloader.R
@@ -30,7 +30,7 @@ test_that("batch_downloader works as expected", {
       "dateBecomeCase", "wasCase", "active", "followUpHistory",
       "isDateOfOnsetApproximate", "outcomeId", "riskReason", "pregnancyStatus",
       "dateOfOutcome", "dateOfInfection", "middleName",
-      "questionnaireAnswers.would_you_like_to_complete_who_basic_case_questionnaire",
+      "questionnaireAnswers.would_you_like_to_complete_who_basic_case_questionnaire", # nolint
       "questionnaireAnswers.Case_WhichForm",
       "questionnaireAnswers.report_test_reason",
       "questionnaireAnswers.Comcond_present",
@@ -38,7 +38,7 @@ test_that("batch_downloader works as expected", {
       "questionnaireAnswers.expo_travel",
       "questionnaireAnswers.expo_visit_healthcare",
       "questionnaireAnswers.patcourse", "questionnaireAnswers.Comcond_select",
-      "questionnaireAnswers.specify_places_and_dates_for_up_to_3_locations_below",
+      "questionnaireAnswers.specify_places_and_dates_for_up_to_3_locations_below", # nolint
       "questionnaireAnswers.expo_travel_country1",
       "questionnaireAnswers.expo_travel_city1",
       "questionnaireAnswers.expo_travel_date1",
@@ -107,14 +107,14 @@ test_that("batch_downloader works as expected", {
       "questionnaireAnswers.FA1_preexistingconditions_diabetes",
       "questionnaireAnswers.FA1_preexistingconditions_HIVotherimmunedeficiency",
       "questionnaireAnswers.FA1_preexistingconditions_heartdisease",
-      "questionnaireAnswers.FA1_preexistingconditions_asthmarequiringmedication",
-      "questionnaireAnswers.FA1_preexistingconditions_chroniclungdiseasenonasthma",
+      "questionnaireAnswers.FA1_preexistingconditions_asthmarequiringmedication", # nolint
+      "questionnaireAnswers.FA1_preexistingconditions_chroniclungdiseasenonasthma", # nolint
       "questionnaireAnswers.FA1_preexistingconditions_chronicliverdisease",
-      "questionnaireAnswers.FA1_preexistingconditions_chronichaematologicaldisorder",
+      "questionnaireAnswers.FA1_preexistingconditions_chronichaematologicaldisorder", # nolint
       "questionnaireAnswers.FA1_preexistingconditions_chronickidneydisease",
       "questionnaireAnswers.FA1_preexistingconditions_chronicneurological",
-      "questionnaireAnswers.FA1_preexistingconditions_organorbonemarrowrecipient",
-      "questionnaireAnswers.FA1_preexistingconditions_otherpreexistingcondition",
+      "questionnaireAnswers.FA1_preexistingconditions_organorbonemarrowrecipient", # nolint
+      "questionnaireAnswers.FA1_preexistingconditions_otherpreexistingcondition", # nolint
       "questionnaireAnswers.FA1_healthcareinteractions_contactemergencynumber",
       "questionnaireAnswers.FA1_priorXdayexposure_travelleddomestically",
       "questionnaireAnswers.FA1_priorXdayexposure_travelledinternationally",
diff --git a/tests/testthat/test-get_access_token.R b/tests/testthat/test-get_access_token.R
index d342755..a3c8943 100644
--- a/tests/testthat/test-get_access_token.R
+++ b/tests/testthat/test-get_access_token.R
@@ -15,4 +15,3 @@ test_that("get_access_token works as expected", {
   # character string cannot contain spaces
   expect_false(grepl(pattern = "\\s", x = res))
 })
-
diff --git a/tests/testthat/test-get_all_outbreaks.R b/tests/testthat/test-get_all_outbreaks.R
index af05858..06f40f9 100644
--- a/tests/testthat/test-get_all_outbreaks.R
+++ b/tests/testthat/test-get_all_outbreaks.R
@@ -12,7 +12,7 @@ test_that("get_all_outbreaks works as expected", {
   expect_identical(dim(res), c(10L, 5L))
   expect_identical(
     colnames(res),
-    c("id", "name", "description", "createdBy", "createdAt" )
+    c("id", "name", "description", "createdBy", "createdAt")
   )
   expect_identical(
     unname(sapply(res[1, ], class)),
diff --git a/tests/testthat/test-get_godata_version.R b/tests/testthat/test-get_godata_version.R
index 6a8e862..cc90c58 100644
--- a/tests/testthat/test-get_godata_version.R
+++ b/tests/testthat/test-get_godata_version.R
@@ -5,7 +5,7 @@ test_that("get_godata_versions works as expected", {
 
   expect_type(res, "character")
   # character string can contain digits
-  expect_true(grepl(pattern = "\\d",x = res))
+  expect_true(grepl(pattern = "\\d", x = res))
   # character string can contain full stops
   expect_true(grepl(pattern = ".", x = res))
   # character string cannot contain alphabetic characters
diff --git a/tests/testthat/test-get_language_tokens.R b/tests/testthat/test-get_language_tokens.R
index 23e975d..4985c6e 100644
--- a/tests/testthat/test-get_language_tokens.R
+++ b/tests/testthat/test-get_language_tokens.R
@@ -19,6 +19,6 @@ test_that("get_language_tokens works as expected", {
     unname(sapply(res[1, ], class)),
     c("character", "character", "data.frame")
   )
-  expect_identical(colnames(res$tokens),c("token", "translation"))
+  expect_identical(colnames(res$tokens), c("token", "translation"))
   expect_identical(dim(res$tokens), c(13641L, 2L))
 })

From 20141048e47919a55ffb3b68cf01c3412448379d Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 15:03:18 +0000
Subject: [PATCH 140/203] linted get_users

---
 R/get_users.R    | 45 ++++++++++++++++++++++++++++-----------------
 man/get_users.Rd | 15 ++++++++++-----
 2 files changed, 38 insertions(+), 22 deletions(-)

diff --git a/R/get_users.R b/R/get_users.R
index b318be1..5490a01 100644
--- a/R/get_users.R
+++ b/R/get_users.R
@@ -6,12 +6,15 @@
 #' endpoint). This function relies on the
 #' `\users` API endpoint.
 #'
-#' @param url Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!
+#' @param url Insert the base URL for your instance of Go.Data here. Don't
+#' forget the forward slash "/" at end!
 #' @param username The email address for your Go.Data login.
 #' @param password The password for your Go.Data login
 #'
 #' @return
-#' Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+#' Returns a data frame. Some fields, such as addresses, hospitalization
+#' history, and questionnaire fields may require further unnesting. See
+#' \code{\link[tidyr]{nest}} for assitance with unnesting.
 #' @export
 #' @examples
 #' \dontrun{
@@ -19,9 +22,11 @@
 #' username <- "myemail@email.com"
 #' password <- "mypassword"
 #'
-#' users <- get_users(url=url,
-#'                    username=username,
-#'                    password=password)
+#' users <- get_users(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
 #' }
 #' @importFrom magrittr %>%
 #' @import dplyr
@@ -30,19 +35,25 @@
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
 #' @export
+get_users <- function(url = url,
+                      username = username,
+                      password = password) {
 
+  users <- GET(
+    paste0(
+      url,
+      "api/users",
+      "?access_token=",
+      godataR::get_access_token(
+        url = url,
+        username = username,
+        password = password
+      )
+    )
+  ) %>%
+    content(as = "text") %>%
+    fromJSON(flatten = TRUE) %>%
+    filter(.data$deleted != TRUE)
 
-
-get_users <- function(url=url,
-                      username=username,
-                      password=password) {
-
-  users <- GET(paste0(url,"api/users",
-                          "?access_token=",godataR::get_access_token(url=url, username=username, password=password))) %>%
-    content(as="text") %>%
-    fromJSON(flatten=TRUE) %>%
-    filter(deleted!=TRUE) %>%
-    #select(id, firstName, lastName, email, roleIds, lastLoginDate, institutionName, disregardGeographicRestrictions, activeOutbreakId, createdBy, createdAt)
   return(users)
-
 }
diff --git a/man/get_users.Rd b/man/get_users.Rd
index 0710668..bb42eef 100644
--- a/man/get_users.Rd
+++ b/man/get_users.Rd
@@ -7,14 +7,17 @@
 get_users(url = url, username = username, password = password)
 }
 \arguments{
-\item{url}{Insert the base URL for your instance of Go.Data here. Don't forget the forward slash "/" at end!}
+\item{url}{Insert the base URL for your instance of Go.Data here. Don't
+forget the forward slash "/" at end!}
 
 \item{username}{The email address for your Go.Data login.}
 
 \item{password}{The password for your Go.Data login}
 }
 \value{
-Returns a data frame. Some fields, such as addresses, hospitalization history, and questionnaire fields may require further unnesting. See \code{\link[tidyr]{nest}} for assitance with unnesting.
+Returns a data frame. Some fields, such as addresses, hospitalization
+history, and questionnaire fields may require further unnesting. See
+\code{\link[tidyr]{nest}} for assitance with unnesting.
 }
 \description{
 A function to retrieve a list of all user
@@ -29,8 +32,10 @@ url <- "https://MyGoDataServer.com/"
 username <- "myemail@email.com"
 password <- "mypassword"
 
-users <- get_users(url=url,
-                   username=username,
-                   password=password)
+users <- get_users(
+  url = url,
+  username = username,
+  password = password
+)
 }
 }

From 4d0a0d027264eb843702afbd1b95c72dcda1aaec Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 15:04:07 +0000
Subject: [PATCH 141/203] removed recursive argument defaults in get_users

---
 R/get_users.R    | 6 +++---
 man/get_users.Rd | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/get_users.R b/R/get_users.R
index 5490a01..2fc7e77 100644
--- a/R/get_users.R
+++ b/R/get_users.R
@@ -35,9 +35,9 @@
 #' @importFrom jsonlite fromJSON
 #' @importFrom purrr pluck
 #' @export
-get_users <- function(url = url,
-                      username = username,
-                      password = password) {
+get_users <- function(url,
+                      username,
+                      password) {
 
   users <- GET(
     paste0(
diff --git a/man/get_users.Rd b/man/get_users.Rd
index bb42eef..69f4cb8 100644
--- a/man/get_users.Rd
+++ b/man/get_users.Rd
@@ -4,7 +4,7 @@
 \alias{get_users}
 \title{Get user data from Go.Data}
 \usage{
-get_users(url = url, username = username, password = password)
+get_users(url, username, password)
 }
 \arguments{
 \item{url}{Insert the base URL for your instance of Go.Data here. Don't

From 2569d5b7b539ff4de3fd1e16581a030608377986 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 15:05:58 +0000
Subject: [PATCH 142/203] removed pipe from get_users

---
 R/get_users.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/get_users.R b/R/get_users.R
index 2fc7e77..f5696a7 100644
--- a/R/get_users.R
+++ b/R/get_users.R
@@ -39,7 +39,7 @@ get_users <- function(url,
                       username,
                       password) {
 
-  users <- GET(
+  users_request <- GET(
     paste0(
       url,
       "api/users",
@@ -50,10 +50,10 @@ get_users <- function(url,
         password = password
       )
     )
-  ) %>%
-    content(as = "text") %>%
-    fromJSON(flatten = TRUE) %>%
-    filter(.data$deleted != TRUE)
+  )
+  users_content <- content(users_request, as = "text")
+  users <- fromJSON(users_content, flatten = TRUE)
+  users <- filter(users, .data$deleted != TRUE)
 
   return(users)
 }

From 3d042349306101ec19e8ed1db80ccaa17a666a0b Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 15:06:58 +0000
Subject: [PATCH 143/203] used explicit namespace instead of import for
 get_users

---
 R/get_users.R | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/R/get_users.R b/R/get_users.R
index f5696a7..9fc311b 100644
--- a/R/get_users.R
+++ b/R/get_users.R
@@ -28,18 +28,12 @@
 #'   password = password
 #' )
 #' }
-#' @importFrom magrittr %>%
-#' @import dplyr
-#' @import tidyr
-#' @import httr
-#' @importFrom jsonlite fromJSON
-#' @importFrom purrr pluck
 #' @export
 get_users <- function(url,
                       username,
                       password) {
 
-  users_request <- GET(
+  users_request <- httr::GET(
     paste0(
       url,
       "api/users",
@@ -51,9 +45,9 @@ get_users <- function(url,
       )
     )
   )
-  users_content <- content(users_request, as = "text")
-  users <- fromJSON(users_content, flatten = TRUE)
-  users <- filter(users, .data$deleted != TRUE)
+  users_content <- httr::content(users_request, as = "text")
+  users <- jsonlite::fromJSON(users_content, flatten = TRUE)
+  users <- dplyr::filter(users, .data$deleted != TRUE)
 
   return(users)
 }

From 39ab66d5dc88f3aabd0ae785f3682bfa74cec18d Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 15:07:46 +0000
Subject: [PATCH 144/203] ensure get_users returns a tibble

---
 R/get_users.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/get_users.R b/R/get_users.R
index 9fc311b..8f1765b 100644
--- a/R/get_users.R
+++ b/R/get_users.R
@@ -48,6 +48,7 @@ get_users <- function(url,
   users_content <- httr::content(users_request, as = "text")
   users <- jsonlite::fromJSON(users_content, flatten = TRUE)
   users <- dplyr::filter(users, .data$deleted != TRUE)
+  users <- tibble::as_tibble(users)
 
   return(users)
 }

From f6ecc5e684d12ded45a933f316cd67540eba5f96 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 15:15:41 +0000
Subject: [PATCH 145/203] added test for get_users

---
 tests/testthat/test-get_users.R | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 tests/testthat/test-get_users.R

diff --git a/tests/testthat/test-get_users.R b/tests/testthat/test-get_users.R
new file mode 100644
index 0000000..d3d69ac
--- /dev/null
+++ b/tests/testthat/test-get_users.R
@@ -0,0 +1,30 @@
+test_that("get_users works as expected", {
+  skip("get_users requires API call")
+
+  res <- get_users(url = url, username = username, password = password)
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(20L, 67L))
+  expect_true(
+    all(c(
+      "id", "firstName", "lastName", "roleIds", "activeOutbreakId",
+      "languageId", "passwordChange", "loginRetriesCount", "lastLoginDate",
+      "disregardGeographicRestrictions", "dontCacheFilters", "email",
+      "createdAt", "createdBy", "updatedAt", "updatedBy", "deleted",
+      "createdOn", "securityQuestions", "outbreakIds", "institutionName"
+    ) %in% colnames(res))
+  )
+
+  expect_true(
+    all(grepl(pattern = "^settings", x = colnames(res)[22:66]))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "character", "character", "list", "character", "character",
+      "logical", "integer", "character", "logical", "logical", "character",
+      "character", "character", "character", "character", "logical",
+      "character", "list", "list", "character", rep("list", 12), "logical",
+      rep("list", 29), "logical", "list", "list", "character"))
+})

From 6c0cd734422681dcffe901c4ba3087b5c6f3a828 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 15:56:35 +0000
Subject: [PATCH 146/203] linted mongify_date

---
 R/mongify_date.R    | 25 +++++++++++++------------
 man/mongify_date.Rd |  3 ++-
 2 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/R/mongify_date.R b/R/mongify_date.R
index 7006a9d..b4d6cda 100644
--- a/R/mongify_date.R
+++ b/R/mongify_date.R
@@ -33,7 +33,8 @@
 #' must be in the same format).
 #'
 #' Dates with and without a time-stamp are both accepted. Dates which do include
-#' a time stamp must include hours, minutes and seconds in the format **HH:mm:ss**
+#' a time stamp must include hours, minutes and seconds in the format
+#' **HH:mm:ss**
 #'
 #' @md
 #'
@@ -57,32 +58,32 @@
 #'
 #' @export
 mongify_date <- function(dates,
-                        dateformat = "undefined"){
+                         dateformat = "undefined") {
 
   # Define format of input dates:
-  if(dateformat == "undefined"){
-    format2search = c("ymd_HMS", "dmy_HMS", "mdy_HMS")}
-  if(dateformat == "ymd"){format2search = "ymd_HMS"}
-  if(dateformat == "dmy"){format2search = "dmy_HMS"}
-  if(dateformat == "mdy"){format2search = "mdy_HMS"}
+  if (dateformat == "undefined") {
+    format2search <- c("ymd_HMS", "dmy_HMS", "mdy_HMS")
+  }
+  if (dateformat == "ymd") format2search <- "ymd_HMS"
+  if (dateformat == "dmy") format2search <- "dmy_HMS"
+  if (dateformat == "mdy") format2search <- "mdy_HMS"
 
   # Make sure dates are strings:
-  dates = as.character(dates)
+  dates <- as.character(dates)
 
   # Check if dates already have a time-stamp, if not add time:
-  dflong = ifelse(nchar(dates) %in% c(8, 10),
+  dflong <- ifelse(nchar(dates) %in% c(8, 10),
                   paste0(dates, " 00:00:00"),
                   dates)
 
   # Convert date-times to posixct format:
-  dfpct = lubridate::parse_date_time(x = dflong,
+  dfpct <- lubridate::parse_date_time(x = dflong,
                                      orders = format2search,
                                      tz = "UTC")
 
   # Add the Godata / Mongodb specific format ending for date-time:
-  dfmongo = format(x = dfpct, format = "%Y-%m-%dT%H:%M:%S.000Z")
+  dfmongo <- format(x = dfpct, format = "%Y-%m-%dT%H:%M:%S.000Z")
 
   # Return the formatted dates:
   return(dfmongo)
-
 }
diff --git a/man/mongify_date.Rd b/man/mongify_date.Rd
index 59bde2d..26f79bf 100644
--- a/man/mongify_date.Rd
+++ b/man/mongify_date.Rd
@@ -49,7 +49,8 @@ element order can be selected (i.e. all dates in the column to be converted
 must be in the same format).
 
 Dates with and without a time-stamp are both accepted. Dates which do include
-a time stamp must include hours, minutes and seconds in the format \strong{HH:mm:ss}
+a time stamp must include hours, minutes and seconds in the format
+\strong{HH:mm:ss}
 }
 \examples{
 # Create dummy dataframe with dates to convert:

From 483a81c5092aaff68ffb234a9b49c6e23ec4bce4 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 16:21:42 +0000
Subject: [PATCH 147/203] added tests for mongify_date and linted mongify_date

---
 R/mongify_date.R                   | 16 +++++---
 tests/testthat/test-mongify_date.R | 66 ++++++++++++++++++++++++++++++
 2 files changed, 76 insertions(+), 6 deletions(-)
 create mode 100644 tests/testthat/test-mongify_date.R

diff --git a/R/mongify_date.R b/R/mongify_date.R
index b4d6cda..90e07cf 100644
--- a/R/mongify_date.R
+++ b/R/mongify_date.R
@@ -72,14 +72,18 @@ mongify_date <- function(dates,
   dates <- as.character(dates)
 
   # Check if dates already have a time-stamp, if not add time:
-  dflong <- ifelse(nchar(dates) %in% c(8, 10),
-                  paste0(dates, " 00:00:00"),
-                  dates)
+  dflong <- ifelse(
+    nchar(dates) %in% c(8, 10),
+    paste0(dates, " 00:00:00"),
+    dates
+  )
 
   # Convert date-times to posixct format:
-  dfpct <- lubridate::parse_date_time(x = dflong,
-                                     orders = format2search,
-                                     tz = "UTC")
+  dfpct <- lubridate::parse_date_time(
+    x = dflong,
+    orders = format2search,
+    tz = "UTC"
+  )
 
   # Add the Godata / Mongodb specific format ending for date-time:
   dfmongo <- format(x = dfpct, format = "%Y-%m-%dT%H:%M:%S.000Z")
diff --git a/tests/testthat/test-mongify_date.R b/tests/testthat/test-mongify_date.R
new file mode 100644
index 0000000..35b7ca4
--- /dev/null
+++ b/tests/testthat/test-mongify_date.R
@@ -0,0 +1,66 @@
+test_that("mongify_date works as expected", {
+
+  dates <- c("08/01/2022", "08/31/2022")
+  converted_dates <- mongify_date(dates = dates, dateformat = "mdy")
+
+  expect_type(converted_dates, "character")
+  expect_length(converted_dates, length(dates))
+  expect_true(
+    all(grepl(
+      pattern = "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}.\\d{3}Z",
+      x = converted_dates
+    ))
+  )
+})
+
+test_that("mongify_date works as expected with undefined format", {
+
+  dates <- c("08/01/2022", "08/31/2022")
+  converted_dates <- mongify_date(dates = dates, dateformat = "undefined")
+
+  expect_type(converted_dates, "character")
+  expect_length(converted_dates, length(dates))
+  expect_true(
+    all(grepl(
+      pattern = "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}.\\d{3}Z",
+      x = converted_dates
+    ))
+  )
+})
+
+test_that("mongify_date works as expected with ymd format", {
+
+  dates <- c("2022/08/01", "2022/08/31")
+  converted_dates <- mongify_date(dates = dates, dateformat = "ymd")
+
+  expect_type(converted_dates, "character")
+  expect_length(converted_dates, length(dates))
+  expect_true(
+    all(grepl(
+      pattern = "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}.\\d{3}Z",
+      x = converted_dates
+    ))
+  )
+})
+
+test_that("mongify_date throws warning with incorrect format", {
+
+  # second date cannot be dmy format
+  dates <- c("08/01/2022", "08/31/2022")
+  expect_warning(
+    converted_dates <- mongify_date(dates = dates, dateformat = "dmy"),
+    regexp = "1 failed to parse."
+  )
+
+  expect_type(converted_dates, "character")
+  expect_true(anyNA(converted_dates))
+  expect_length(converted_dates, length(dates))
+  # conforms to expected format or is NA
+  expect_true(
+    all(grepl(
+      pattern = "^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}.\\d{3}Z",
+      x = converted_dates
+    ) | is.na(converted_dates)
+    )
+  )
+})

From 2fabad6b6b956c82be216a1c12adb94c3a774539 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 16:28:07 +0000
Subject: [PATCH 148/203] linted get_date_range

---
 R/get_date_range.R | 71 +++++++++++++++++++++++-----------------------
 1 file changed, 35 insertions(+), 36 deletions(-)

diff --git a/R/get_date_range.R b/R/get_date_range.R
index de11e1b..3597c38 100644
--- a/R/get_date_range.R
+++ b/R/get_date_range.R
@@ -1,59 +1,58 @@
-#' Get minimum and maximum date for a vector of dates 
-#' 
+#' Get minimum and maximum date for a vector of dates
+#'
 #' @author Amy Mikhail, \email{amy.mikhail@@gmail.com}
-#' 
-#' @description 
-#' This function will attempt to auto-detect the date format using lubridate, 
-#' then determine the minimum and maximum for the submitted vector of dates.  
+#'
+#' @description
+#' This function will attempt to auto-detect the date format using lubridate,
+#' then determine the minimum and maximum for the submitted vector of dates.
 #' It is intended as a helper function for selecting date ranges and adding
 #' them to queries.
-#' 
+#'
 #' @md
-#'  
+#'
 #' @param dates character vector of dates to extract the date range from
-#' 
-#' @return 
-#' Returns a list object with two values (minimum and maximum date)  
-#' 
+#'
+#' @return
+#' Returns a list object with two values (minimum and maximum date)
+#'
 #' @import lubridate
-#' 
-#' @examples 
+#'
+#' @examples
 #' # Create a character vector of dates:
 #' x <- c("2022-07-15", "2021-08-09", NA, "2022-08-03")
-#' 
+#'
 #' # Get date range:
 #' daterange <- get_date_range(dates = x)
-#' 
+#'
 #' # View the result:
 #' daterange
 #' @export
-get_date_range <- function(dates){
-  
+get_date_range <- function(dates) {
+
   # Check if the input variable is already in date format:
-  if(any(class(dates) %in% c("Date", "POSIXt"))){
-    
+  if (any(class(dates) %in% c("Date", "POSIXt"))) {
+
     # If yes, no need to format:
-    dates2range = dates
-    
+    dates2range <- dates
+
   } else {
-    
+
     # If no, convert to date format with lubridate:
-    dates2range = lubridate::parse_date_time(x = dates, 
-                                             orders = c("ymd", 
-                                                        "dmy", 
-                                                        "mdy"))
+    dates2range <- lubridate::parse_date_time(
+      x = dates,
+      orders = c("ymd", "dmy", "mdy")
+    )
   }
-  
+
   # Get the minimum date:
-  mindate = min(dates2range, na.rm = TRUE)
-  
+  mindate <- min(dates2range, na.rm = TRUE)
+
   # Get the maximum date:
-  maxdate = max(dates2range, na.rm = TRUE)
-  
+  maxdate <- max(dates2range, na.rm = TRUE)
+
   # Compile results:
-  daterange = list(mindate = mindate, maxdate = maxdate)
-  
+  daterange <- list(mindate = mindate, maxdate = maxdate)
+
   # Return the results:
   return(daterange)
-  
-}
\ No newline at end of file
+}

From f07b89e6a22fe685bba8da79ad6702c985519ac9 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Feb 2023 16:58:38 +0000
Subject: [PATCH 149/203] added tests for get_date_range

---
 tests/testthat/test-get_date_range.R | 77 ++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)
 create mode 100644 tests/testthat/test-get_date_range.R

diff --git a/tests/testthat/test-get_date_range.R b/tests/testthat/test-get_date_range.R
new file mode 100644
index 0000000..41593d9
--- /dev/null
+++ b/tests/testthat/test-get_date_range.R
@@ -0,0 +1,77 @@
+test_that("get_date_range works as expected", {
+  x <- c("2020-07-15", "2021-08-09", "2022-08-03")
+  date_range <- get_date_range(dates = x)
+
+  expect_type(date_range, "list")
+  expect_named(date_range, c("mindate", "maxdate"))
+  expect_identical(
+    date_range,
+    list(
+      mindate = as.POSIXct("2020-07-15", tz = "UTC"),
+      maxdate = as.POSIXct("2022-08-03", tz = "UTC")
+    )
+  )
+})
+
+test_that("get_date_range works as expected with missing values", {
+  x <- c("2020-07-15", NA, "2021-08-09", "2022-08-03", NA)
+  date_range <- get_date_range(dates = x)
+
+  expect_type(date_range, "list")
+  expect_named(date_range, c("mindate", "maxdate"))
+  expect_identical(
+    date_range,
+    list(
+      mindate = as.POSIXct("2020-07-15", tz = "UTC"),
+      maxdate = as.POSIXct("2022-08-03", tz = "UTC")
+    )
+  )
+})
+
+test_that("get_date_range works as expected with different formats", {
+  # first 3 are ymd, last is dmy
+  x <- c("2020-07-15", "2021-08-09", "2022-08-03", "13-04-2023")
+  date_range <- get_date_range(dates = x)
+
+  expect_type(date_range, "list")
+  expect_named(date_range, c("mindate", "maxdate"))
+  expect_identical(
+    date_range,
+    list(
+      mindate = as.POSIXct("2020-07-15", tz = "UTC"),
+      maxdate = as.POSIXct("2023-04-13", tz = "UTC")
+    )
+  )
+})
+
+test_that("get_date_range cannot handle ambiguous mixed formats", {
+  # last two are dmy and mdy, so max date should be the last one
+  x <- c("2020-07-15", "2021-08-09", "2022-08-03", "01-04-2023", "05-01-2023")
+  date_range <- get_date_range(dates = x)
+
+  expect_type(date_range, "list")
+  expect_named(date_range, c("mindate", "maxdate"))
+  expect_identical(
+    date_range,
+    list(
+      mindate = as.POSIXct("2020-07-15", tz = "UTC"),
+      maxdate = as.POSIXct("2023-04-01", tz = "UTC")
+    )
+  )
+})
+
+test_that("get_date_range throws warning with incorrect dates", {
+  x <- c("2020-07-15", "2021-08-09", "2022-08-03", "2023-13-01")
+  expect_warning(date_range <- get_date_range(dates = x))
+
+  expect_type(date_range, "list")
+  expect_named(date_range, c("mindate", "maxdate"))
+  expect_identical(
+    date_range,
+    list(
+      mindate = as.POSIXct("2020-07-15", tz = "UTC"),
+      maxdate = as.POSIXct("2022-08-03", tz = "UTC")
+    )
+  )
+})
+

From 3b9277e0ad1d9678594d0f4e0a51e613a699ebde Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 16 Feb 2023 11:45:43 +0000
Subject: [PATCH 150/203] added clean_locations function, documentation and a
 test

---
 R/clean_locations.R                   | 125 ++++++++++++++++++++++++++
 man/clean_locations.Rd                |  34 +++++++
 tests/testthat/test-clean_locations.R |  35 ++++++++
 3 files changed, 194 insertions(+)
 create mode 100644 R/clean_locations.R
 create mode 100644 man/clean_locations.Rd
 create mode 100644 tests/testthat/test-clean_locations.R

diff --git a/R/clean_locations.R b/R/clean_locations.R
new file mode 100644
index 0000000..b008684
--- /dev/null
+++ b/R/clean_locations.R
@@ -0,0 +1,125 @@
+#' Cleans location data
+#'
+#' @description Rearrange via joins to get into more usable hierarchy format,
+#' these can then be joined to cases, contacts, etc for further analysis
+#'
+#' @param locations A [`tibble`] containing locations data. This is the data
+#' returned from [`get_locations()`]
+#'
+#' @return A `tibble` containing the cleaned and rearranged location data.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#'
+#' locations <- get_locations(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
+#'
+#' clean_locations(locations = locations)
+#' }
+clean_locations <- function(locations) {
+
+  # filter out delete and inactive (or NA) values
+  clean_locations <- dplyr::filter(
+    locations,
+    .data$deleted == FALSE | is.na(.data$deleted)
+  )
+  clean_locations <- dplyr::filter(
+    clean_locations,
+    .data$active == TRUE | is.na(.data$active)
+  )
+
+  # add admin-level column
+  clean_locations <- dplyr::mutate(
+    .data = clean_locations,
+    admin_level = sub(".*LEVEL_", "", .data$geographicalLevelId)
+  )
+
+  # select columns
+  clean_locations <- dplyr::select(
+    .data = clean_locations,
+    location_id = "id",
+    "admin_level",
+    "name",
+    parent_location_id = "parentLocationId",
+    lat = "geoLocation.lat",
+    long = "geoLocation.lng"
+  )
+
+  clean_locations <- dplyr::filter(
+    .data = clean_locations,
+    !is.na(.data$admin_level)
+  )
+
+  # split locations data frames into separate data frames by admin level
+  locations_split <- dplyr::group_by(
+    .data = clean_locations,
+    .data$admin_level
+  )
+  locations_split <- dplyr::group_split(locations_split)
+
+  # rename columns by appending admin level
+  locations_split <- purrr::imap(.x = locations_split, .f = function(x, idx) {
+    colnames(x) <- paste("admin", idx - 1, colnames(x), sep = "_")
+    x
+  })
+
+  # add location_id and parent_location_id columns
+  locations_split <- purrr::imap(.x = locations_split, .f = function(x, idx) {
+    x$location_id <- dplyr::pull(
+      x, paste("admin", idx - 1, "location_id", sep = "_")
+    )
+    x
+  })
+  locations_split <- purrr::imap(.x = locations_split, .f = function(x, idx) {
+    if (idx - 1 != 0) {
+      x$parent_location_id <- dplyr::pull(
+        x, paste("admin", idx - 1, "parent_location_id", sep = "_")
+      )
+    }
+    x
+  })
+
+  # loop over list of admin specific data frames and join them
+  for (i in seq(from = length(locations_split), to = 2L)) {
+
+    for (x in 1:(i - 1)) {
+
+      join_index <- i - x
+
+      locations_split[[i]] <- dplyr::left_join(
+        x = locations_split[[i]],
+        y = locations_split[[join_index]],
+        by = c("parent_location_id" = "location_id")
+      )
+
+      # first table (admin level 0) does not contain parent_location_id so skip
+      if (join_index != 1) {
+        # use parent_location_id from right table
+        locations_split[[i]]$parent_location_id <-
+          locations_split[[i]]$parent_location_id.y
+        # remove extra parent_location_id column
+        locations_split[[i]]$parent_location_id.y <- NULL
+      }
+    }
+    locations_split[[i]]$parent_location_id <- NULL
+  }
+
+  # bind the admin level tables by row
+  full <- do.call(dplyr::bind_rows, locations_split)
+
+  # join cleaned location with new table
+  clean_locations <- left_join(
+    x = clean_locations,
+    y = full,
+    by = "location_id"
+  )
+
+  return(locations_clean)
+}
diff --git a/man/clean_locations.Rd b/man/clean_locations.Rd
new file mode 100644
index 0000000..0e2578b
--- /dev/null
+++ b/man/clean_locations.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_locations.R
+\name{clean_locations}
+\alias{clean_locations}
+\title{Cleans location data}
+\usage{
+clean_locations(locations)
+}
+\arguments{
+\item{locations}{A \code{\link{tibble}} containing locations data. This is the data
+returned from \code{\link[=get_locations]{get_locations()}}}
+}
+\value{
+A \code{tibble} containing the cleaned and rearranged location data.
+}
+\description{
+Rearrange via joins to get into more usable hierarchy format,
+these can then be joined to cases, contacts, etc for further analysis
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+
+locations <- get_locations(
+  url = url,
+  username = username,
+  password = password
+)
+
+clean_locations(locations = locations)
+}
+}
diff --git a/tests/testthat/test-clean_locations.R b/tests/testthat/test-clean_locations.R
new file mode 100644
index 0000000..9e6648c
--- /dev/null
+++ b/tests/testthat/test-clean_locations.R
@@ -0,0 +1,35 @@
+test_that("clean_locations works as expected", {
+  skip("get_locations requires API call")
+
+  res <- get_locations(
+    url = url,
+    username = username,
+    password = password
+  )
+  res <- clean_locations(locations = res)
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(11L, 24L))
+  expect_true(
+    all(c(
+      "location_id", "admin_level", "name", "parent_location_id", "lat",
+      "long", "admin_0_location_id", "admin_0_admin_level", "admin_0_name",
+      "admin_0_parent_location_id", "admin_0_lat", "admin_0_long",
+      "admin_1_location_id", "admin_1_admin_level", "admin_1_name",
+      "admin_1_parent_location_id", "admin_1_lat", "admin_1_long",
+      "admin_2_location_id", "admin_2_admin_level", "admin_2_name",
+      "admin_2_parent_location_id", "admin_2_lat", "admin_2_long"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c(
+      "character", "character", "character", "character", "numeric", "numeric",
+      "character", "character", "character", "character", "numeric", "numeric",
+      "character", "character", "character", "character", "numeric", "numeric",
+      "character", "character", "character", "character", "numeric", "numeric"
+    )
+  )
+})

From 05501773f15ca5c18d8792bc990f0850b5164196 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 16 Feb 2023 12:08:34 +0000
Subject: [PATCH 151/203] added clean_case_address_history function,
 documentation and test

---
 R/clean_case_address_history.R                | 98 +++++++++++++++++++
 man/clean_case_address_history.Rd             | 37 +++++++
 .../test-clean_case_address_history.R         | 31 ++++++
 3 files changed, 166 insertions(+)
 create mode 100644 R/clean_case_address_history.R
 create mode 100644 man/clean_case_address_history.Rd
 create mode 100644 tests/testthat/test-clean_case_address_history.R

diff --git a/R/clean_case_address_history.R b/R/clean_case_address_history.R
new file mode 100644
index 0000000..815d3fd
--- /dev/null
+++ b/R/clean_case_address_history.R
@@ -0,0 +1,98 @@
+#' Extract address information from case data
+#'
+#' @description This function un-nests and cleans the address data and stores
+#' it in a standalone table with all addresses, even if there is more than 1
+#' per person.
+#'
+#' @param cases A tibble with case data. Case data is returned by
+#' [`get_cases()`].
+#'
+#' @return A tibble with address information from cases data.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' cases <- get_cases(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' case_address_history <- clean_case_address_history(cases = cases)
+#' }
+clean_case_address_history <- function(cases) {
+
+  cases_address_history_clean <- dplyr::filter(
+    .data = cases,
+    .data$deleted == FALSE | is.na(.data$deleted)
+  )
+
+  cases_address_history_clean <- dplyr::select(
+    .data = cases_address_history_clean,
+    "id", "visualId", "addresses"
+  )
+
+  cases_address_history_clean <- tidyr::unnest(
+    data = cases_address_history_clean,
+    cols = "addresses",
+    names_sep = "_")
+
+  cases_address_history_clean <- dplyr::select_all(
+    .tbl = cases_address_history_clean,
+    .funs = ~gsub("\\.", "_", tolower(.))
+  )
+
+  cases_address_history_clean <- dplyr::select_if(
+    .tbl = cases_address_history_clean,
+    purrr::negate(is.list)
+  )
+
+  cases_address_history_clean <- dplyr::mutate(
+    .data = cases_address_history_clean,
+    addresses_typeid = sub(".*TYPE_", "", .data$addresses_typeid)
+  )
+
+  cases_address_history_clean <- dplyr::left_join(
+    cases_address_history_clean,
+    locations_clean,
+    by = c("addresses_locationid" = "location_id")
+  )
+
+  # bring in GPS from locations in case blank from case record, otherwise use
+  # case
+  cases_address_history_clean <- dplyr::mutate(
+    .data = cases_address_history_clean,
+    lat = dplyr::case_when(
+      is.na(addresses_geolocation_lat) ~ lat,
+      TRUE ~ addresses_geolocation_lat
+    ),
+    long = dplyr::case_when(
+      is.na(addresses_geolocation_lng) ~ lat,
+      TRUE ~ addresses_geolocation_lng
+    )
+  )
+
+  cases_address_history_clean <- dplyr::select(
+    .data = cases_address_history_clean,
+    "id",
+    "visualid",
+    "addresses_locationid",
+    "addresses_typeid",
+    "lat",
+    "long",
+    address = "addresses_addressline1",
+    postal_code = "addresses_postalcode",
+    city = "addresses_city",
+    telephone = "addresses_phonenumber",
+    email = "addresses_emailaddress",
+    dplyr::matches("^admin_.*name$")
+  )
+
+  return(cases_address_history_clean)
+}
diff --git a/man/clean_case_address_history.Rd b/man/clean_case_address_history.Rd
new file mode 100644
index 0000000..cd9369f
--- /dev/null
+++ b/man/clean_case_address_history.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_case_address_history.R
+\name{clean_case_address_history}
+\alias{clean_case_address_history}
+\title{Extract address information from case data}
+\usage{
+clean_case_address_history(cases)
+}
+\arguments{
+\item{cases}{A tibble with case data. Case data is returned by
+\code{\link[=get_cases]{get_cases()}}.}
+}
+\value{
+A tibble with address information from cases data.
+}
+\description{
+This function un-nests and cleans the address data and stores
+it in a standalone table with all addresses, even if there is more than 1
+per person.
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+cases <- get_cases(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+case_address_history <- clean_case_address_history(cases = cases)
+}
+}
diff --git a/tests/testthat/test-clean_case_address_history.R b/tests/testthat/test-clean_case_address_history.R
new file mode 100644
index 0000000..a0c5467
--- /dev/null
+++ b/tests/testthat/test-clean_case_address_history.R
@@ -0,0 +1,31 @@
+test_that("clean_case_address_history works as expected", {
+  skip("get_cases requires API call")
+
+  res <- get_cases(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+  res <- clean_case_address_history(cases = res)
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(15L, 14L))
+  expect_true(
+    all(c(
+      "id", "visualid", "addresses_locationid", "addresses_typeid", "lat",
+      "long", "address", "postal_code", "city", "telephone", "email",
+      "admin_0_name", "admin_1_name", "admin_2_name"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c(
+      "character", "character", "character", "character", "numeric", "numeric",
+      "character", "character", "character", "character", "character",
+      "character", "character", "character"
+    )
+  )
+})

From 7e375e68a415021900cf1b660906367f664c29e7 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 16 Feb 2023 13:50:04 +0000
Subject: [PATCH 152/203] added clean_case_med_history function, documentation
 and test

---
 R/clean_case_med_history.R                   | 79 ++++++++++++++++++++
 man/clean_case_med_history.Rd                | 36 +++++++++
 tests/testthat/test-clean_case_med_history.R | 30 ++++++++
 3 files changed, 145 insertions(+)
 create mode 100644 R/clean_case_med_history.R
 create mode 100644 man/clean_case_med_history.Rd
 create mode 100644 tests/testthat/test-clean_case_med_history.R

diff --git a/R/clean_case_med_history.R b/R/clean_case_med_history.R
new file mode 100644
index 0000000..82c335e
--- /dev/null
+++ b/R/clean_case_med_history.R
@@ -0,0 +1,79 @@
+#' Extracts and cleans medical history from case data
+#'
+#' @description This function un-nests and cleans date ranges of isolation and
+#' hospitalization history and stores it in a standalone table.
+#'
+#' @param cases A tibble with case data. Case data is returned by
+#' [`get_cases()`].
+#'
+#' @return A tibble with information on isolation and hospitalization history.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' cases <- get_cases(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' cases_med_history <- clean_case_med_history(cases = cases)
+#' }
+clean_case_med_history <- function(cases) {
+
+  cases_dateranges_history_clean <- dplyr::filter(
+    .data = cases,
+    .data$deleted == FALSE | is.na(.data$deleted)
+  )
+
+  # cannot unnest on mix of data frames and lists so change empty lists to empty
+  # data frames
+  cases_dateranges_history_clean$dateRanges <- purrr::map(
+    cases_dateranges_history_clean$dateRanges,
+    .f = function(x) {
+      if (length(x) == 0) x <- data.frame()
+      x
+    }
+  )
+
+  cases_dateranges_history_clean <- tidyr::unnest(
+    data = cases_dateranges_history_clean,
+    cols = dateRanges,
+    names_sep = "_"
+  )
+
+  cases_dateranges_history_clean <- dplyr::select_at(
+    .tbl = cases_dateranges_history_clean,
+    dplyr::vars(id, visualId, starts_with("dateRanges")),
+    tolower
+  )
+
+  cases_dateranges_history_clean <- dplyr::mutate(
+    .data = cases_dateranges_history_clean,
+    dateranges_typeid = sub(".*TYPE_", "", dateranges_typeid)
+  )
+
+  cases_dateranges_history_clean <- dplyr::mutate(
+    .data = cases_dateranges_history_clean,
+    dateranges_centername = sub(".*NAME_", "", dateranges_centername)
+  )
+
+  cases_dateranges_history_clean <- dplyr::mutate_at(
+    .tbl = cases_dateranges_history_clean,
+    dplyr::vars(dateranges_startdate, dateranges_enddate),
+    as.Date
+  )
+
+  cases_dateranges_history_clean <- dplyr::select_if(
+    .tbl = cases_dateranges_history_clean,
+    purrr::negate(is.list)
+  )
+
+  return(cases_dateranges_history_clean)
+}
diff --git a/man/clean_case_med_history.Rd b/man/clean_case_med_history.Rd
new file mode 100644
index 0000000..bf1fa66
--- /dev/null
+++ b/man/clean_case_med_history.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_case_med_history.R
+\name{clean_case_med_history}
+\alias{clean_case_med_history}
+\title{Extracts and cleans medical history from case data}
+\usage{
+clean_case_med_history(cases)
+}
+\arguments{
+\item{cases}{A tibble with case data. Case data is returned by
+\code{\link[=get_cases]{get_cases()}}.}
+}
+\value{
+A tibble with information on isolation and hospitalization history.
+}
+\description{
+This function un-nests and cleans date ranges of isolation and
+hospitalization history and stores it in a standalone table.
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+cases <- get_cases(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+cases_med_history <- clean_case_med_history(cases = cases)
+}
+}
diff --git a/tests/testthat/test-clean_case_med_history.R b/tests/testthat/test-clean_case_med_history.R
new file mode 100644
index 0000000..895dcd0
--- /dev/null
+++ b/tests/testthat/test-clean_case_med_history.R
@@ -0,0 +1,30 @@
+test_that("clean_case_med_history works as expected", {
+  skip("get_cases requires API call")
+
+  res <- get_cases(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+  res <- clean_case_med_history(cases = res)
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(7L, 9L))
+  expect_true(
+    all(c(
+      "id", "visualid", "dateranges_typeid", "dateranges_centername",
+      "dateranges_locationid", "dateranges_startdate", "dateranges_enddate",
+      "dateranges_comments", "dateranges_id"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c(
+      "character", "character", "character", "character", "character", "Date",
+      "Date", "logical", "logical"
+    )
+  )
+})

From ef57c7e5db11bf5ba2d0a3af947822257665aa56 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 16 Feb 2023 17:19:25 +0000
Subject: [PATCH 153/203] added clean_case_vax_history function, documentation
 and test

---
 R/clean_case_vax_history.R                   | 78 ++++++++++++++++++++
 man/clean_case_vax_history.Rd                | 35 +++++++++
 tests/testthat/test-clean_case_vax_history.R | 26 +++++++
 3 files changed, 139 insertions(+)
 create mode 100644 R/clean_case_vax_history.R
 create mode 100644 man/clean_case_vax_history.Rd
 create mode 100644 tests/testthat/test-clean_case_vax_history.R

diff --git a/R/clean_case_vax_history.R b/R/clean_case_vax_history.R
new file mode 100644
index 0000000..d70f9c8
--- /dev/null
+++ b/R/clean_case_vax_history.R
@@ -0,0 +1,78 @@
+#' Cleans vaccination data from case data
+#'
+#' @description Cleans and un-nests vaccination history, where vaccination is
+#' complete, from case data. Case data is returned from [`get_cases()`].
+#'
+#' @param cases A tibble with address information from cases data.
+#'
+#' @return A tibble with cleaned and un-nested vaccination history data.
+#' @export
+#'
+#' @examples
+#' #' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' cases <- get_cases(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' vax_history <- clean_case_vax_history(cases = cases)
+#' }
+clean_case_vax_history <- function(cases) {
+
+  cases_vacc_history_clean <- dplyr::filter(
+    .data = cases,
+    .data$deleted == FALSE | is.na(.data$deleted)
+  )
+
+  # cannot unnest on mix of data frames and lists so change empty lists to empty
+  # data frames
+  cases_vacc_history_clean$vaccinesReceived <- purrr::map(
+    cases_vacc_history_clean$vaccinesReceived,
+    .f = function(x) {
+      if (length(x) == 0) x <- data.frame()
+      x
+    }
+  )
+
+  cases_vacc_history_clean <- tidyr::unnest(
+    data = cases_vacc_history_clean,
+    "vaccinesReceived",
+    names_sep = "_"
+  )
+
+  cases_vacc_history_clean <- dplyr::select(
+    .data = cases_vacc_history_clean,
+    "id",
+    "visualId",
+    dplyr::starts_with("vaccinesReceived")
+  )
+
+  cases_vacc_history_clean <- dplyr::rename_with(
+    .data = cases_vacc_history_clean,
+    .fn = tolower
+  )
+
+  cases_vacc_history_clean <- dplyr::mutate(
+    .data = cases_vacc_history_clean,
+    vaccinesreceived_vaccine = sub(".*VACCINE_", "", vaccinesreceived_vaccine)
+  )
+
+  cases_vacc_history_clean <- dplyr::mutate(
+    .data = cases_vacc_history_clean,
+    vaccinesreceived_status = sub(".*STATUS_", "", vaccinesreceived_status)
+  )
+
+  cases_vacc_history_clean <- dplyr::mutate(
+    .data = cases_vacc_history_clean,
+    dplyr::across("vaccinesreceived_date", as.Date)
+  )
+
+  return(cases_vacc_history_clean)
+}
diff --git a/man/clean_case_vax_history.Rd b/man/clean_case_vax_history.Rd
new file mode 100644
index 0000000..c72e851
--- /dev/null
+++ b/man/clean_case_vax_history.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_case_vax_history.R
+\name{clean_case_vax_history}
+\alias{clean_case_vax_history}
+\title{Cleans vaccinations data from case data}
+\usage{
+clean_case_vax_history(cases)
+}
+\arguments{
+\item{cases}{A tibble with address information from cases data.}
+}
+\value{
+A tibble with cleaned and un-nested vaccination history data.
+}
+\description{
+Cleans and un-nests vaccination history, where vaccination is
+complete, from case data. Case data is returned from \code{\link[=get_cases]{get_cases()}}.
+}
+\examples{
+#' \dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+cases <- get_cases(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+vax_history <- clean_case_vax_history(cases = cases)
+}
+}
diff --git a/tests/testthat/test-clean_case_vax_history.R b/tests/testthat/test-clean_case_vax_history.R
new file mode 100644
index 0000000..c2b9fc2
--- /dev/null
+++ b/tests/testthat/test-clean_case_vax_history.R
@@ -0,0 +1,26 @@
+test_that("clean_case_vax_history works as expected", {
+  skip("get_cases requires API call")
+
+  res <- get_cases(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+  res <- clean_case_vax_history(cases = res)
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(1L, 5L))
+  expect_true(
+    all(c(
+      "id", "visualid", "vaccinesreceived_vaccine", "vaccinesreceived_status",
+      "vaccinesreceived_date"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "character", "character", "character", "Date")
+  )
+})

From 8589d3a5cc5cc278d7c39ee9acf61a4ca7679f91 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Mar 2023 15:42:52 +0000
Subject: [PATCH 154/203] added clean_cases function, documentation and test

---
 R/clean_cases.R                   | 245 ++++++++++++++++++++++++++++++
 man/clean_cases.Rd                |  50 ++++++
 tests/testthat/test-clean_cases.R |  51 +++++++
 3 files changed, 346 insertions(+)
 create mode 100644 R/clean_cases.R
 create mode 100644 man/clean_cases.Rd
 create mode 100644 tests/testthat/test-clean_cases.R

diff --git a/R/clean_cases.R b/R/clean_cases.R
new file mode 100644
index 0000000..e99748c
--- /dev/null
+++ b/R/clean_cases.R
@@ -0,0 +1,245 @@
+#' Cleans case data
+#'
+#' @description Cleans and un-nests case data. Case data is returned by
+#' [`get_cases()`].
+#'
+#' @param cases A `tibble` containing the case data.
+#'
+#' @return A `tibble` containing the cleaned case data.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' cases <- get_cases(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' # other cleaned data required for `clean_cases()`
+#' cases_vacc_history_clean <- clean_case_vax_history(cases = cases)
+#' cases_address_history_clean <- clean_case_address_history(cases = cases)
+#' cases_dateranges_history_clean <- clean_case_med_history(cases = cases)
+#'
+#' cases_clean <- clean_cases(
+#'   cases = cases,
+#'   cases_address_history_clean = cases_address_history_clean,
+#'   cases_vacc_history_clean = cases_vacc_history_clean,
+#'   cases_dateranges_history_clean = cases_dateranges_history_clean
+#' )
+#' }
+clean_cases <- function(cases,
+                        cases_address_history_clean,
+                        cases_vacc_history_clean,
+                        cases_dateranges_history_clean) {
+
+  # Remove all deleted records
+  cases_clean <- dplyr::filter(
+    .data = cases,
+    .data$deleted == FALSE | is.na(.data$deleted)
+  )
+
+  # Remove all nested fields, otherwise problems with exporting to excel
+  cases_clean <- dplyr::select_if(
+    .tbl = cases_clean,
+    purrr::negate(is.list)
+  )
+
+  # take out all that are not core variables, otherwise diff versions and
+  # problems exporting to excel
+  cases_clean <- dplyr::select(
+    .data = cases_clean,
+    -dplyr::contains("questionnaireAnswers")
+  )
+
+  # standardize column name syntax
+  cases_clean <- janitor::clean_names(cases_clean)
+
+  # label timestamps as datetime
+  cases_clean <- dplyr::rename(
+    .data = cases_clean,
+    date_of_birth = "dob",
+    datetime_updated_at = "updated_at",
+    datetime_created_at = "created_at"
+  )
+
+  # take out other unnecessary vars that are unnecessary and may confuse
+  # (i.e. was_case for cases)
+  cases_clean <- dplyr::select(
+    .data = cases_clean,
+    -c("is_date_of_onset_approximate",
+       "is_date_of_reporting_approximate",
+       "was_case",
+       "deleted",
+       "created_on")
+  )
+
+  #clean up all blank fields
+  cases_clean <- dplyr::mutate(
+    .data = cases_clean,
+    dplyr::across(dplyr::where(is.character), dplyr::na_if, "")
+  )
+
+  # clean date formats (TODO: edit this so that we can see time stamps)
+  cases_clean <- dplyr::mutate_at(
+    .tbl = cases_clean,
+    dplyr::vars(dplyr::starts_with("date_")), list(~ as.Date(substr(., 1, 10)))
+  )
+  cases_clean <- dplyr::mutate(
+    .data = cases_clean,
+    datetime_updated_at = as.POSIXct(datetime_updated_at, format = "%Y-%m-%dT%H:%M")
+  )
+  cases_clean <- dplyr::mutate(
+    .data = cases_clean,
+    datetime_created_at = as.POSIXct(datetime_created_at,format="%Y-%m-%dT%H:%M")
+  )
+
+  #  truncate responses of categorical vars so easier to read
+  cases_clean <- dplyr::mutate(
+    .data = cases_clean,
+    classification = sub(".*CLASSIFICATION_", "", classification),
+    gender = sub(".*GENDER_", "", gender),
+    occupation = sub(".*OCCUPATION_", "", occupation),
+    outcome = sub(".*OUTCOME_", "", outcome_id),
+    pregnancy_status = sub(".*STATUS_", "", pregnancy_status),
+    risk_level = sub(".*LEVEL_", "", risk_level)
+  )
+
+  cases_clean <- dplyr::mutate(
+    .data = cases_clean,
+    isolated = case_when(id %in% cases_dateranges_history_clean$id[cases_dateranges_history_clean$dateranges_typeid == "ISOLATION"] ~ TRUE, TRUE ~ FALSE)
+  )
+
+  cases_clean <- dplyr::mutate(
+    .data = cases_clean,
+    hospitalized = case_when(id %in% cases_dateranges_history_clean$id[cases_dateranges_history_clean$dateranges_typeid == "HOSPITALIZATION"] ~ TRUE, TRUE ~ FALSE)
+  )
+
+  cases_clean <- dplyr::mutate(
+    .data = cases_clean,
+    icu = case_when(id %in% cases_dateranges_history_clean$id[cases_dateranges_history_clean$dateranges_typeid == "ICU_ADMISSION"] ~ TRUE, TRUE ~ FALSE)
+  )
+
+  cases_address_history_clean <- dplyr::filter(
+    .data = cases_address_history_clean,
+    addresses_typeid == "USUAL_PLACE_OF_RESIDENCE"
+  )
+
+  # join in current address from address history, only current place of residence
+  cases_clean <- dplyr::left_join(x = cases_clean, y = cases_address_history_clean, by = "id")
+
+  # join in info from vacc block
+  cases_clean <- dplyr::mutate(
+    .data = cases_clean,
+    vaccinated = dplyr::case_when(id %in% cases_vacc_history_clean$id[cases_vacc_history_clean$vaccinesreceived_status == "VACCINATED"] ~ TRUE, TRUE ~ FALSE)
+  )
+
+  # force NA ages to appear as NA, not as 0 like sometimes occurs
+  cases_clean <- dplyr::mutate(
+    .data = cases_clean,
+    age_years = as.numeric(age_years)
+  )
+  cases_clean <- dplyr::mutate(
+    .data = cases_clean,
+    age_years = dplyr::na_if(age_years, 0)
+  )
+  cases_clean <- dplyr::mutate(
+    .data = cases_clean,
+    age_months = as.numeric(age_months)
+  )
+  cases_clean <- dplyr::mutate(
+    .data = cases_clean,
+    age_months = dplyr::na_if(age_months, 0)
+  )
+
+  # standardize age vars into just one var, round by 1 decimal
+  cases_clean <- dplyr::mutate(
+    .data = cases_clean,
+    age = dplyr::case_when(!is.na(age_months) ~ round(age_months / 12, digits = 1), TRUE ~ age_years)
+  )
+
+  # WHO age categories updated Sept 2020:
+  # 0-4, 5-9, 10-14, 15-19, 20-29, 30-39, 40-49, 50-59, 60-64, 65-69, 70-74,
+  # 75-79, 80+
+  # these categories below match that of detailed WHO surveillance dash:
+  # <5, 5-14, 15-24, 25-64, 65+
+  cases_clean <- dplyr::mutate(
+    .data = cases_clean,
+    age_class = factor(
+      case_when(
+        age <= 4 ~ "<5",
+        age <= 14 ~ "5-14",
+        age <= 24 ~ "15-24",
+        age <= 64 ~ "25-64",
+        is.finite(age) ~ "65+",
+        TRUE ~ "unknown"
+      ),
+      levels = c(
+        "<5",
+        "5-14",
+        "15-24",
+        "25-64",
+        "65+",
+        "unknown"
+      )
+    ),
+    age_class = factor(
+      age_class,
+      levels = rev(levels(age_class))
+    )
+  )
+
+  # organize order of vars, only bring in what we need, take away confusing vars
+  cases_clean <- dplyr::select(
+    .data = cases_clean,
+    id, # identifier
+    visual_id, # identifier
+    classification, # identifier
+    first_name, # demographics
+    middle_name, # demographics
+    last_name, # demographics
+    gender, # demographics
+    age, # demographics
+    age_class, # demographics
+    occupation, # demographics
+    pregnancy_status, # demographics
+    date_of_reporting, # dates
+    date_of_onset, # dates
+    date_of_infection, # dates
+    date_become_case, # dates
+    date_of_burial, # dates
+    was_contact, # epi
+    risk_level, # epi
+    risk_reason, # epi
+    safe_burial, # epi
+    transfer_refused, # epi
+    responsible_user_id, # assigned contact tracer
+    matches("^admin_.*name$"), # address
+    lat, # address
+    long, # address
+    address, # address
+    postal_code, # address
+    city, # address
+    telephone, # address
+    email, # address
+    vaccinated, # vaccination & dateRanges block
+    isolated, # vaccination & dateRanges block
+    hospitalized, # vaccination & dateRanges block
+    icu, # vaccination & dateRanges block
+    outcome, # outcome
+    date_of_outcome, # outcome
+    location_id = addresses_locationid, # uuid in case need later for joining of whatever sort
+    created_by, # record modification
+    datetime_created_at, # record modification
+    updated_by, # record modification
+    datetime_updated_at # record modification
+  )
+
+  return(cases_clean)
+}
diff --git a/man/clean_cases.Rd b/man/clean_cases.Rd
new file mode 100644
index 0000000..96b9a54
--- /dev/null
+++ b/man/clean_cases.Rd
@@ -0,0 +1,50 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_cases.R
+\name{clean_cases}
+\alias{clean_cases}
+\title{Cleans case data}
+\usage{
+clean_cases(
+  cases,
+  cases_address_history_clean,
+  cases_vacc_history_clean,
+  cases_dateranges_history_clean
+)
+}
+\arguments{
+\item{cases}{A \code{tibble} containing the case data.}
+}
+\value{
+A \code{tibble} containing the cleaned case data.
+}
+\description{
+Cleans and un-nests case data. Case data is returned by
+\code{\link[=get_cases]{get_cases()}}.
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+cases <- get_cases(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+# other cleaned data required for `clean_cases()`
+cases_vacc_history_clean <- clean_case_vax_history(cases = cases)
+cases_address_history_clean <- clean_case_address_history(cases = cases)
+cases_dateranges_history_clean <- clean_case_med_history(cases = cases)
+
+cases_clean <- clean_cases(
+  cases = cases,
+  cases_address_history_clean = cases_address_history_clean,
+  cases_vacc_history_clean = cases_vacc_history_clean,
+  cases_dateranges_history_clean = cases_dateranges_history_clean
+)
+}
+}
diff --git a/tests/testthat/test-clean_cases.R b/tests/testthat/test-clean_cases.R
new file mode 100644
index 0000000..a29ce82
--- /dev/null
+++ b/tests/testthat/test-clean_cases.R
@@ -0,0 +1,51 @@
+test_that("clean_cases works as expected", {
+  skip("get_cases requires API call")
+
+  cases <- get_cases(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+
+  cases_vacc_history_clean <- clean_case_vax_history(cases = cases)
+  cases_address_history_clean <- clean_case_address_history(cases = cases)
+  cases_dateranges_history_clean <- clean_case_med_history(cases = cases)
+
+  res <- clean_cases(
+    cases = cases,
+    cases_address_history_clean = cases_address_history_clean,
+    cases_vacc_history_clean = cases_vacc_history_clean,
+    cases_dateranges_history_clean = cases_dateranges_history_clean
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(14L, 43L))
+  expect_true(
+    all(c(
+      "id", "visual_id", "classification", "first_name", "middle_name",
+      "last_name", "gender", "age", "age_class", "occupation",
+      "pregnancy_status", "date_of_reporting", "date_of_onset",
+      "date_of_infection", "date_become_case", "date_of_burial", "was_contact",
+      "risk_level", "risk_reason", "safe_burial", "transfer_refused",
+      "responsible_user_id", "admin_0_name", "admin_1_name", "admin_2_name",
+      "lat", "long", "address", "postal_code", "city", "telephone", "email",
+      "vaccinated", "isolated", "hospitalized", "icu", "outcome",
+      "date_of_outcome", "location_id", "created_by", "datetime_created_at",
+      "updated_by", "datetime_updated_at"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], function(x) class(x)[1])),
+    c(
+      rep("character", 7), "numeric", "factor", "character", "character",
+      rep("Date", 5), "logical", "character", "character", "logical", "logical",
+      "character", "character", "character", "character", "numeric", "numeric",
+      "character", "character", "character", "character", "character",
+      "logical", "logical", "logical", "logical", "character", "Date",
+      "character", "character", "POSIXct", "character", "POSIXct"
+    )
+  )
+})

From 5bcb9dbba8aac9899f2787d3c9a7b68c75f8be72 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Mar 2023 16:24:27 +0000
Subject: [PATCH 155/203] added cases_from_contacts function, documentation and
 test

---
 R/cases_from_contacts.R                   | 106 ++++++++++++++++++++++
 man/cases_from_contacts.Rd                |  47 ++++++++++
 tests/testthat/test-cases_from_contacts.R |  53 +++++++++++
 3 files changed, 206 insertions(+)
 create mode 100644 R/cases_from_contacts.R
 create mode 100644 man/cases_from_contacts.Rd
 create mode 100644 tests/testthat/test-cases_from_contacts.R

diff --git a/R/cases_from_contacts.R b/R/cases_from_contacts.R
new file mode 100644
index 0000000..7cd9fdb
--- /dev/null
+++ b/R/cases_from_contacts.R
@@ -0,0 +1,106 @@
+#' Pull out all cases that used to be contacts
+#'
+#' @param cases_clean The cleaned case data. Case data is returned by
+#' [`get_cases()`] and cleaned by [`clean_cases()`].
+#'
+#' @return A tibble containing the cases that used to be contacts.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' cases <- get_cases(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' # other cleaned data required for `clean_cases()`
+#' cases_vacc_history_clean <- clean_case_vax_history(cases = cases)
+#' cases_address_history_clean <- clean_case_address_history(cases = cases)
+#' cases_dateranges_history_clean <- clean_case_med_history(cases = cases)
+#'
+#' cases_clean <- clean_cases(
+#'   cases = cases,
+#'   cases_address_history_clean = cases_address_history_clean,
+#'   cases_vacc_history_clean = cases_vacc_history_clean,
+#'   cases_dateranges_history_clean = cases_dateranges_history_clean
+#' )
+#'
+#' cases_from_contacts <- cases_from_contacts(cases_clean = cases_clean)
+#' }
+cases_from_contacts <- function(cases_clean) {
+
+  contacts_becoming_cases <- dplyr::filter(
+    .data = cases_clean,
+    .data$was_contact == TRUE
+  )
+
+  # set this status to became case and no longer active
+  contacts_becoming_cases <- dplyr::mutate(
+    .data = contacts_becoming_cases,
+    follow_up_status = "BECAME_CASE",
+    was_case = NA,
+    date_of_last_contact = NA,
+    follow_up_team_id = NA,
+    relationship_exposure_type = NA,
+    relationship_context_of_transmission = NA,
+    relationship_exposure_duration = NA,
+    relationship_exposure_frequency = NA,
+    relationship_certainty_level = NA,
+    relationship_cluster_id = NA,
+  )
+
+  # organize order of vars, only bring in what we need, take away confusing vars
+  contacts_becoming_cases <- dplyr::select(
+    .data = contacts_becoming_cases,
+    "id", # identifier
+    "visual_id", # identifier
+    "classification", # identifier
+    "follow_up_status", # identifier
+    "first_name", # demographics
+    "middle_name", # demographics
+    "last_name", # demographics
+    "gender", # demographics
+    "age", # demographics
+    "age_class", # demographics
+    "occupation", # demographics
+    "pregnancy_status", # demographics
+    "date_of_reporting", # dates
+    "date_of_last_contact", # dates
+    "date_of_burial", # dates
+    "risk_level", # epi
+    "risk_reason", # epi
+    "responsible_user_id", # assigned contact tracer
+    "follow_up_team_id", # assigned contact tracer
+    dplyr::matches("^admin_.*name$"), # address
+    "lat", # address
+    "long", # address
+    "address", # address
+    "postal_code", # address
+    "city", # address
+    "telephone", # address
+    "email", # address
+    "vaccinated",
+    "outcome", # outcome
+    "date_of_outcome", # outcome
+    "relationship_exposure_type",
+    "relationship_context_of_transmission",
+    "relationship_exposure_duration",
+    "relationship_exposure_frequency",
+    "relationship_certainty_level",
+    "relationship_cluster_id",
+    "location_id", # uuid in case need later for joining of whatever sort
+    "created_by", # record modification
+    "datetime_created_at", # record modification
+    "updated_by", # record modification
+    "datetime_updated_at" # record modification
+  )
+
+  return(contacts_becoming_cases)
+}
diff --git a/man/cases_from_contacts.Rd b/man/cases_from_contacts.Rd
new file mode 100644
index 0000000..e9a91d6
--- /dev/null
+++ b/man/cases_from_contacts.Rd
@@ -0,0 +1,47 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/cases_from_contacts.R
+\name{cases_from_contacts}
+\alias{cases_from_contacts}
+\title{Pull out all cases that used to be contacts}
+\usage{
+cases_from_contacts(cases_clean)
+}
+\arguments{
+\item{cases_clean}{The cleaned case data. Case data is returned by
+\code{\link[=get_cases]{get_cases()}} and cleaned by \code{\link[=clean_cases]{clean_cases()}}.}
+}
+\value{
+A tibble containing the cases that used to be contacts.
+}
+\description{
+Pull out all cases that used to be contacts
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+cases <- get_cases(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+# other cleaned data required for `clean_cases()`
+cases_vacc_history_clean <- clean_case_vax_history(cases = cases)
+cases_address_history_clean <- clean_case_address_history(cases = cases)
+cases_dateranges_history_clean <- clean_case_med_history(cases = cases)
+
+cases_clean <- clean_cases(
+  cases = cases,
+  cases_address_history_clean = cases_address_history_clean,
+  cases_vacc_history_clean = cases_vacc_history_clean,
+  cases_dateranges_history_clean = cases_dateranges_history_clean
+)
+
+cases_from_contacts <- cases_from_contacts(cases_clean = cases_clean)
+}
+}
diff --git a/tests/testthat/test-cases_from_contacts.R b/tests/testthat/test-cases_from_contacts.R
new file mode 100644
index 0000000..f5c3570
--- /dev/null
+++ b/tests/testthat/test-cases_from_contacts.R
@@ -0,0 +1,53 @@
+test_that("cases_from_contacts works as expected", {
+  skip("get_cases requires API call")
+
+  cases <- get_cases(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+
+  cases_vacc_history_clean <- clean_case_vax_history(cases = cases)
+  cases_address_history_clean <- clean_case_address_history(cases = cases)
+  cases_dateranges_history_clean <- clean_case_med_history(cases = cases)
+
+  cases_clean <- clean_cases(
+    cases = cases,
+    cases_address_history_clean = cases_address_history_clean,
+    cases_vacc_history_clean = cases_vacc_history_clean,
+    cases_dateranges_history_clean = cases_dateranges_history_clean
+  )
+
+  res <- cases_from_contacts(cases_clean = cases_clean)
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(3L, 43L))
+  expect_true(
+    all(c(
+      "id", "visual_id", "classification", "follow_up_status", "first_name",
+      "middle_name", "last_name", "gender", "age", "age_class", "occupation",
+      "pregnancy_status", "date_of_reporting", "date_of_last_contact",
+      "date_of_burial", "risk_level", "risk_reason", "responsible_user_id",
+      "follow_up_team_id", "admin_0_name", "admin_1_name", "admin_2_name",
+      "lat", "long", "address", "postal_code", "city", "telephone", "email",
+      "vaccinated", "outcome", "date_of_outcome", "relationship_exposure_type",
+      "relationship_context_of_transmission", "relationship_exposure_duration",
+      "relationship_exposure_frequency", "relationship_certainty_level",
+      "relationship_cluster_id", "location_id", "created_by",
+      "datetime_created_at", "updated_by", "datetime_updated_at"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], function(x) class(x)[1])),
+    c(
+      rep("character", 8), "numeric", "factor", "character", "character",
+      "Date", "logical", "Date", "character", "character", "character",
+      "logical", "character", "character", "character", "numeric", "numeric",
+      rep("character", 5), "logical", "character", "Date", rep("logical", 6),
+      "character", "character", "POSIXct", "character", "POSIXct"
+    )
+  )
+})

From d1974e3aed0974d1e17b5b298b5d7afbf69ce28b Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Mar 2023 17:19:13 +0000
Subject: [PATCH 156/203] added clean_contact_address_history function,
 documentation and test

---
 R/clean_contact_address_history.R             | 107 ++++++++++++++++++
 man/clean_contact_address_history.Rd          |  50 ++++++++
 .../test-clean_contact_address_history.R      |  42 +++++++
 3 files changed, 199 insertions(+)
 create mode 100644 R/clean_contact_address_history.R
 create mode 100644 man/clean_contact_address_history.Rd
 create mode 100644 tests/testthat/test-clean_contact_address_history.R

diff --git a/R/clean_contact_address_history.R b/R/clean_contact_address_history.R
new file mode 100644
index 0000000..15222b2
--- /dev/null
+++ b/R/clean_contact_address_history.R
@@ -0,0 +1,107 @@
+#' Extracts address information from contact data
+#'
+#' @description This function un-nests and cleans the address data and stores
+#' it in a standalone table with all addresses, even if there is more than 1
+#' per person.
+#'
+#' @param contacts A tibble with contacts data. Contacts data is returned by
+#' [`get_contacts()`].
+#' @param locations_clean A tibble with cleaned locations data. Locations data
+#' is returned by [`get_locations()`] and cleaned by [`clean_locations()`].
+#'
+#' @return A tibble with address information from contacts data.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' contacts <- get_contacts(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' locations <- get_locations(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
+#' locations_clean <- clean_locations(locations = locations)
+#'
+#' contact_address_history <- clean_contact_address_history(
+#'   contacts = contacts,
+#'   locations_clean = locations_clean
+#' )
+#' }
+clean_contact_address_history <- function(contacts,
+                                          locations_clean) {
+
+  contacts_address_history_clean <- dplyr::filter(
+    .data = contacts,
+    .data$deleted == FALSE | is.na(.data$deleted)
+  )
+
+  contacts_address_history_clean <- dplyr::select(
+    .data = contacts_address_history_clean,
+    "id", "visualId", "addresses"
+  )
+
+  contacts_address_history_clean <- tidyr::unnest(
+    data = contacts_address_history_clean,
+    cols = "addresses",
+    names_sep = "_"
+  )
+
+  contacts_address_history_clean <- dplyr::select_all(
+    .tbl = contacts_address_history_clean,
+    .funs = ~gsub("\\.", "_", tolower(.))
+  )
+
+  contacts_address_history_clean <- dplyr::select_if(
+    .tbl = contacts_address_history_clean,
+    purrr::negate(is.list)
+  )
+
+  contacts_address_history_clean <- dplyr::mutate(
+    .data = contacts_address_history_clean,
+    addresses_typeid = sub(".*TYPE_", "", addresses_typeid)
+  )
+
+  contacts_address_history_clean <- dplyr::left_join(
+    x = contacts_address_history_clean,
+    y = locations_clean,
+    by = c("addresses_locationid" = "location_id")
+  )
+
+  # bring in GPS from locations if blank in contact record, otherwise use
+  # contact address block
+  contacts_address_history_clean <- dplyr::mutate(
+    .data = contacts_address_history_clean,
+    lat = dplyr::case_when(
+      is.na(addresses_geolocation_lat) ~ lat, TRUE ~ addresses_geolocation_lat),
+    long = dplyr::case_when(
+      is.na(addresses_geolocation_lng) ~ lat, TRUE ~ addresses_geolocation_lng)
+    )
+
+  contacts_address_history_clean <- dplyr::select(
+    .data = contacts_address_history_clean,
+    "id",
+    "addresses_locationid",
+    "addresses_typeid",
+    "lat",
+    "long",
+    "address" = addresses_addressline1,
+    "postal_code" = addresses_postalcode,
+    "city" = addresses_city,
+    "telephone" = addresses_phonenumber,
+    "email" = addresses_emailaddress,
+    dplyr::matches("^admin_.*name$")
+  )
+
+  return(contacts_address_history_clean)
+}
diff --git a/man/clean_contact_address_history.Rd b/man/clean_contact_address_history.Rd
new file mode 100644
index 0000000..1209f5a
--- /dev/null
+++ b/man/clean_contact_address_history.Rd
@@ -0,0 +1,50 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_contact_address_history.R
+\name{clean_contact_address_history}
+\alias{clean_contact_address_history}
+\title{Extracts address information from contact data}
+\usage{
+clean_contact_address_history(contacts, locations_clean)
+}
+\arguments{
+\item{contacts}{A tibble with contacts data. Contacts data is returned by
+\code{\link[=get_contacts]{get_contacts()}}.}
+
+\item{locations_clean}{A tibble with cleaned locations data. Locations data
+is returned by \code{\link[=get_locations]{get_locations()}} and cleaned by \code{\link[=clean_locations]{clean_locations()}}.}
+}
+\value{
+A tibble with address information from contacts data.
+}
+\description{
+This function un-nests and cleans the address data and stores
+it in a standalone table with all addresses, even if there is more than 1
+per person.
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+contacts <- get_contacts(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+locations <- get_locations(
+  url = url,
+  username = username,
+  password = password
+)
+locations_clean <- clean_locations(locations = locations)
+
+contact_address_history <- clean_contact_address_history(
+  contacts = contacts,
+  locations_clean = locations_clean
+)
+}
+}
diff --git a/tests/testthat/test-clean_contact_address_history.R b/tests/testthat/test-clean_contact_address_history.R
new file mode 100644
index 0000000..50930ab
--- /dev/null
+++ b/tests/testthat/test-clean_contact_address_history.R
@@ -0,0 +1,42 @@
+test_that("clean_contact_address_history works as expected", {
+  skip("get_contacts requires API call")
+
+  contacts <- get_contacts(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+
+  locations <- get_locations(
+    url = url,
+    username = username,
+    password = password
+  )
+  locations_clean <- clean_locations(locations = locations)
+
+  res <- clean_contact_address_history(
+    contacts = contacts,
+    locations_clean = locations_clean
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(15L, 13L))
+  expect_true(
+    all(c(
+      "id", "addresses_locationid", "addresses_typeid", "lat", "long",
+      "address", "postal_code", "city", "telephone", "email", "admin_0_name",
+      "admin_1_name", "admin_2_name"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c(
+      "character", "character", "character", "numeric", "numeric",
+      "character", "logical", "character", "character", "character",
+      "character", "character", "character"
+    )
+  )
+})

From 19ddad5d7b473a4b37512075809dbae9f302cef0 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Tue, 14 Mar 2023 18:01:09 +0000
Subject: [PATCH 157/203] added clean_contact_vax_history function,
 documentation and test

---
 R/clean_contact_vax_history.R                 | 77 +++++++++++++++++++
 man/clean_contact_vax_history.Rd              | 36 +++++++++
 .../testthat/test-clean_contact_vax_history.R | 27 +++++++
 3 files changed, 140 insertions(+)
 create mode 100644 R/clean_contact_vax_history.R
 create mode 100644 man/clean_contact_vax_history.Rd
 create mode 100644 tests/testthat/test-clean_contact_vax_history.R

diff --git a/R/clean_contact_vax_history.R b/R/clean_contact_vax_history.R
new file mode 100644
index 0000000..32ea9da
--- /dev/null
+++ b/R/clean_contact_vax_history.R
@@ -0,0 +1,77 @@
+#' Cleans vaccination data from contact data
+#'
+#' @description Cleans and un-nests vaccination history, where vaccination is
+#' complete, from contact data. Contact data is returned from
+#' [`get_contacts()`].
+#'
+#' @param contacts A tibble with address information from contact data.
+#'
+#' @return A tibble with cleaned and un-nested vaccination history data.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' contacts <- get_contacts(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' vax_history <- clean_contact_vax_history(contacts = contacts)
+#' }
+clean_contact_vax_history <- function(contacts) {
+
+  contacts_vax_history_clean <- dplyr::filter(
+    .data = contacts,
+    .data$deleted == FALSE | is.na(.data$deleted)
+  )
+
+  # cannot unnest on mix of data frames and lists so change empty lists to empty
+  # data frames
+  contacts_vax_history_clean$vaccinesReceived <- purrr::map(
+    contacts_vax_history_clean$vaccinesReceived,
+    .f = function(x) {
+      if (length(x) == 0) x <- data.frame()
+      x
+    }
+  )
+
+  contacts_vax_history_clean <- tidyr::unnest(
+    data = contacts_vax_history_clean,
+    cols = "vaccinesReceived",
+    names_sep = "_"
+  )
+
+  contacts_vax_history_clean <- dplyr::select_at(
+    .tbl = contacts_vax_history_clean,
+    dplyr::vars(
+      "id",
+      "visualId",
+      dplyr::starts_with("vaccinesReceived")
+    ),
+    .funs = tolower
+  )
+
+  contacts_vax_history_clean <- dplyr::mutate(
+    .data = contacts_vax_history_clean,
+    vaccinesreceived_vaccine = sub(".*VACCINE_", "", vaccinesreceived_vaccine)
+  )
+
+  contacts_vax_history_clean <- dplyr::mutate(
+    .data = contacts_vax_history_clean,
+    vaccinesreceived_status = sub(".*STATUS_", "", vaccinesreceived_status)
+  )
+
+  contacts_vax_history_clean <- dplyr::mutate_at(
+    .tbl = contacts_vax_history_clean,
+    dplyr::vars(vaccinesreceived_date), as.Date
+  )
+
+  return(contacts_vax_history_clean)
+}
diff --git a/man/clean_contact_vax_history.Rd b/man/clean_contact_vax_history.Rd
new file mode 100644
index 0000000..a24cd21
--- /dev/null
+++ b/man/clean_contact_vax_history.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_contact_vax_history.R
+\name{clean_contact_vax_history}
+\alias{clean_contact_vax_history}
+\title{Cleans vaccination data from contact data}
+\usage{
+clean_contact_vax_history(contacts)
+}
+\arguments{
+\item{contacts}{A tibble with address information from contact data.}
+}
+\value{
+A tibble with cleaned and un-nested vaccination history data.
+}
+\description{
+Cleans and un-nests vaccination history, where vaccination is
+complete, from contact data. Contact data is returned from
+\code{\link[=get_contacts]{get_contacts()}}.
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+contacts <- get_contacts(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+vax_history <- clean_contact_vax_history(contacts = contacts)
+}
+}
diff --git a/tests/testthat/test-clean_contact_vax_history.R b/tests/testthat/test-clean_contact_vax_history.R
new file mode 100644
index 0000000..3b53f8e
--- /dev/null
+++ b/tests/testthat/test-clean_contact_vax_history.R
@@ -0,0 +1,27 @@
+test_that("clean_contact_vax_history works as expected", {
+  skip("get_contacts requires API call")
+
+  contacts <- get_contacts(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+
+  res <- clean_contact_vax_history(contacts = contacts)
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(1L, 5L))
+  expect_true(
+    all(c(
+      "id", "visualid", "vaccinesreceived_vaccine", "vaccinesreceived_date",
+      "vaccinesreceived_status"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "character", "character", "Date", "character")
+  )
+})

From aff39432d13f014100e3ac58aac7eb8bcd070a2a Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 15 Mar 2023 14:32:36 +0000
Subject: [PATCH 158/203] added clean_contacts_of_contacts_address_history
 function, documentation and test

---
 ...ean_contacts_of_contacts_address_history.R | 107 ++++++++++++++++++
 ...an_contacts_of_contacts_address_history.Rd |  53 +++++++++
 ...ean_contacts_of_contacts_address_history.R |  41 +++++++
 3 files changed, 201 insertions(+)
 create mode 100644 R/clean_contacts_of_contacts_address_history.R
 create mode 100644 man/clean_contacts_of_contacts_address_history.Rd
 create mode 100644 tests/testthat/test-clean_contacts_of_contacts_address_history.R

diff --git a/R/clean_contacts_of_contacts_address_history.R b/R/clean_contacts_of_contacts_address_history.R
new file mode 100644
index 0000000..b749a71
--- /dev/null
+++ b/R/clean_contacts_of_contacts_address_history.R
@@ -0,0 +1,107 @@
+#' Extracts address information from contacts of contacts data
+#'
+#' @description This function un-nests and cleans the address data and stores
+#' it in a standalone table with all addresses, even if there is more than 1
+#' per person.
+#'
+#' @param contacts_of_contacts A`tibble` with contacts of contacts data.
+#' Contacts of contacts data is returned by [`get_contacts_of_contacts()`].
+#' @param locations_clean A `tibble` with cleaned location data. Location data
+#' is returned by [`get_locations()`] and cleaned by [`clean_locations()`].
+#'
+#' @return A `tibble` with address information from contacts of contacts data.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' contacts_of_contacts <- get_contacts_of_contacts(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' locations <- get_locations(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
+#' locations_clean <- clean_locations(locations = locations)
+#'
+#' contact_of_contacts_add_hist <- clean_contacts_of_contacts_address_history(
+#'   contacts_of_contacts = contacts_of_contacts,
+#'   locations_clean = locations_clean
+#' )
+#' }
+clean_contacts_of_contacts_address_history <- function(contacts_of_contacts,
+                                                       locations_clean) {
+
+  coc_add_hist <- dplyr::filter(
+    .data = contacts_of_contacts,
+    .data$deleted == FALSE | is.na(.data$deleted)
+  )
+
+  coc_add_hist <- dplyr::select(
+    .data = coc_add_hist,
+    "id", "visualId", "addresses"
+  )
+
+  coc_add_hist <- tidyr::unnest(
+    data = coc_add_hist,
+    "addresses",
+    names_sep = "_"
+  )
+
+  coc_add_hist <- dplyr::select_all(
+    .tbl = coc_add_hist,
+    .funs = ~gsub("\\.", "_", tolower(.))
+  )
+
+  coc_add_hist <- dplyr::select_if(
+    .tbl = coc_add_hist,
+    .predicate = purrr::negate(is.list)
+  )
+
+  coc_add_hist <- dplyr::mutate(
+    .data = coc_add_hist,
+    addresses_typeid = sub(".*TYPE_", "", addresses_typeid)
+  )
+
+  coc_add_hist <- dplyr::left_join(
+    x = coc_add_hist,
+    y = locations_clean,
+    by = c("addresses_locationid" = "location_id")
+  )
+
+  # bring in GPS from locations if blank in contact record, otherwise use
+  # contact address block
+  coc_add_hist <- dplyr::mutate(
+    .data = coc_add_hist,
+    lat = case_when(
+      is.na(addresses_geolocation_lat) ~ lat, TRUE ~ addresses_geolocation_lat),
+    long = case_when(
+      is.na(addresses_geolocation_lng) ~ lat, TRUE ~ addresses_geolocation_lng)
+  )
+
+  coc_add_hist <- dplyr::select(
+    .data = coc_add_hist,
+    "id",
+    "addresses_locationid",
+    "addresses_typeid",
+    "lat",
+    "long",
+    address = "addresses_addressline1",
+    postal_code = "addresses_postalcode",
+    city = "addresses_city",
+    telephone = "addresses_phonenumber",
+    email = "addresses_emailaddress",
+    dplyr::matches("^admin_.*name$")
+  )
+
+  return(coc_add_hist)
+}
diff --git a/man/clean_contacts_of_contacts_address_history.Rd b/man/clean_contacts_of_contacts_address_history.Rd
new file mode 100644
index 0000000..a4923b4
--- /dev/null
+++ b/man/clean_contacts_of_contacts_address_history.Rd
@@ -0,0 +1,53 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_contacts_of_contacts_address_history.R
+\name{clean_contacts_of_contacts_address_history}
+\alias{clean_contacts_of_contacts_address_history}
+\title{Extracts address information from contacts of contacts data}
+\usage{
+clean_contacts_of_contacts_address_history(
+  contacts_of_contacts,
+  locations_clean
+)
+}
+\arguments{
+\item{contacts_of_contacts}{A\code{tibble} with contacts of contacts data.
+Contacts of contacts data is returned by \code{\link[=get_contacts_of_contacts]{get_contacts_of_contacts()}}.}
+
+\item{locations_clean}{A \code{tibble} with cleaned location data. Location data
+is returned by \code{\link[=get_locations]{get_locations()}} and cleaned by \code{\link[=clean_locations]{clean_locations()}}.}
+}
+\value{
+A \code{tibble} with address information from contacts of contacts data.
+}
+\description{
+This function un-nests and cleans the address data and stores
+it in a standalone table with all addresses, even if there is more than 1
+per person.
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+contacts_of_contacts <- get_contacts_of_contacts(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+locations <- get_locations(
+  url = url,
+  username = username,
+  password = password
+)
+locations_clean <- clean_locations(locations = locations)
+
+contact_of_contacts_address_history <- clean_contacts_of_contacts_address_history(
+  contacts_of_contacts = contacts_of_contacts,
+  locations_clean = locations_clean
+)
+}
+}
diff --git a/tests/testthat/test-clean_contacts_of_contacts_address_history.R b/tests/testthat/test-clean_contacts_of_contacts_address_history.R
new file mode 100644
index 0000000..c8a0589
--- /dev/null
+++ b/tests/testthat/test-clean_contacts_of_contacts_address_history.R
@@ -0,0 +1,41 @@
+test_that("clean_contacts_of_contacts_address_history works as expected", {
+  skip("get_contacts_of_contacts requires API call")
+
+  contacts_of_contacts <- get_contacts_of_contacts(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+
+  locations <- get_locations(
+    url = url,
+    username = username,
+    password = password
+  )
+  locations_clean <- clean_locations(locations = locations)
+
+  res <- clean_contacts_of_contacts_address_history(
+    contacts_of_contacts = contacts_of_contacts,
+    locations_clean = locations_clean
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(1L, 13L))
+  expect_true(
+    all(c(
+      "id", "addresses_locationid", "addresses_typeid", "lat", "long",
+      "address", "postal_code", "city", "telephone", "email", "admin_0_name",
+      "admin_1_name", "admin_2_name"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c(
+      "character", "character", "character", "numeric", "numeric",
+      rep("logical", 5), "character", "character", "character"
+    )
+  )
+})

From 6f70b4deab73ea92d4e61e7860b24779cb3811d5 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 15 Mar 2023 14:51:24 +0000
Subject: [PATCH 159/203] added clean_contacts_of_contacts_vax_history
 function, documentation and test

---
 R/clean_contacts_of_contacts_vax_history.R    | 67 +++++++++++++++++++
 man/clean_contacts_of_contacts_vax_history.Rd | 39 +++++++++++
 ...t-clean_contacts_of_contacts_vax_history.R | 29 ++++++++
 3 files changed, 135 insertions(+)
 create mode 100644 R/clean_contacts_of_contacts_vax_history.R
 create mode 100644 man/clean_contacts_of_contacts_vax_history.Rd
 create mode 100644 tests/testthat/test-clean_contacts_of_contacts_vax_history.R

diff --git a/R/clean_contacts_of_contacts_vax_history.R b/R/clean_contacts_of_contacts_vax_history.R
new file mode 100644
index 0000000..44e75c7
--- /dev/null
+++ b/R/clean_contacts_of_contacts_vax_history.R
@@ -0,0 +1,67 @@
+#' Cleans vaccination data from contacts of contacts data
+#'
+#' @description Cleans and un-nests vaccination history, where vaccination is
+#' complete, from contacts of contacts data. Contacts of contacts data is
+#' returned from [`get_contacts_of_contacts()`].
+#'
+#' @param contacts_of_contacts A `tibble` with address information from contacts
+#' of contacts data.
+#'
+#' @return A `tibble` with cleaned and un-nested vaccination history data.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' contacts_of_contacts <- get_contacts_of_contacts(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' vax_history <- clean_contacts_of_contacts_vax_history(
+#'   contacts_of_contacts = contacts_of_contacts
+#' )
+#' }
+clean_contacts_of_contacts_vax_history <- function(contacts_of_contacts) {
+
+  coc_vacc_hist <- dplyr::filter(
+    .data = contacts_of_contacts,
+    .data$deleted == FALSE | is.na(.data$deleted)
+  )
+
+  coc_vacc_hist <- tidyr::unnest(
+    data = coc_vacc_hist,
+    cols = "vaccinesReceived",
+    names_sep = "_"
+  )
+
+  coc_vacc_hist <- dplyr::select_at(
+    .tbl = coc_vacc_hist,
+    .vars = dplyr::vars(id, visualId, dplyr::starts_with("vaccinesReceived")),
+    tolower
+  )
+
+  coc_vacc_hist <- dplyr::mutate(
+    .data = coc_vacc_hist,
+    vaccinesreceived_vaccine = sub(".*VACCINE_", "", vaccinesreceived_vaccine)
+  )
+
+  coc_vacc_hist <- dplyr::mutate(
+    .data = coc_vacc_hist,
+    vaccinesreceived_status = sub(".*STATUS_", "", vaccinesreceived_status)
+  )
+
+  coc_vacc_hist <- dplyr::mutate_at(
+    .tbl = coc_vacc_hist,
+    dplyr::vars(vaccinesreceived_date),
+    as.Date
+  )
+
+  return(coc_vacc_hist)
+}
diff --git a/man/clean_contacts_of_contacts_vax_history.Rd b/man/clean_contacts_of_contacts_vax_history.Rd
new file mode 100644
index 0000000..43cb262
--- /dev/null
+++ b/man/clean_contacts_of_contacts_vax_history.Rd
@@ -0,0 +1,39 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_contacts_of_contacts_vax_history.R
+\name{clean_contacts_of_contacts_vax_history}
+\alias{clean_contacts_of_contacts_vax_history}
+\title{Cleans vaccination data from contacts of contacts data}
+\usage{
+clean_contacts_of_contacts_vax_history(contacts_of_contacts)
+}
+\arguments{
+\item{contacts_of_contacts}{A \code{tibble} with address information from contacts
+of contacts data.}
+}
+\value{
+A \code{tibble} with cleaned and un-nested vaccination history data.
+}
+\description{
+Cleans and un-nests vaccination history, where vaccination is
+complete, from contacts of contacts data. Contacts of contacts data is
+returned from \code{\link[=get_contacts_of_contacts]{get_contacts_of_contacts()}}.
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+contacts_of_contacts <- get_contacts_of_contacts(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+vax_history <- clean_contacts_of_contacts_vax_history(
+  contacts_of_contacts = contacts_of_contacts
+)
+}
+}
diff --git a/tests/testthat/test-clean_contacts_of_contacts_vax_history.R b/tests/testthat/test-clean_contacts_of_contacts_vax_history.R
new file mode 100644
index 0000000..e537ec7
--- /dev/null
+++ b/tests/testthat/test-clean_contacts_of_contacts_vax_history.R
@@ -0,0 +1,29 @@
+test_that("clean_contacts_of_contacts_vax_history works as expected", {
+  skip("get_contacts_of_contacts requires API call")
+
+  contacts_of_contacts <- get_contacts_of_contacts(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+
+  res <- clean_contacts_of_contacts_vax_history(
+    contacts_of_contacts = contacts_of_contacts
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(1L, 5L))
+  expect_true(
+    all(c(
+      "id", "visualid", "vaccinesreceived_vaccine", "vaccinesreceived_date",
+      "vaccinesreceived_status"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "character", "character", "Date", "character")
+  )
+})

From 78d1f539fda7d4fa69c5a3398340832108403bf1 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 15 Mar 2023 16:04:03 +0000
Subject: [PATCH 160/203] added clean_contacts_of_contacts function,
 documentation and test (WIP as function currently errors)

---
 R/clean_contacts_of_contacts.R                | 229 ++++++++++++++++++
 man/clean_contacts_of_contacts.Rd             |  69 ++++++
 .../test-clean_contacts_of_contacts.R         |  62 +++++
 3 files changed, 360 insertions(+)
 create mode 100644 R/clean_contacts_of_contacts.R
 create mode 100644 man/clean_contacts_of_contacts.Rd
 create mode 100644 tests/testthat/test-clean_contacts_of_contacts.R

diff --git a/R/clean_contacts_of_contacts.R b/R/clean_contacts_of_contacts.R
new file mode 100644
index 0000000..c9c6444
--- /dev/null
+++ b/R/clean_contacts_of_contacts.R
@@ -0,0 +1,229 @@
+#' Clean contacts of contacts data
+#'
+#' @description Cleans and un-nests contacts of contacts data. Contacts of
+#' contacts data is returned by [`get_contacts_of_contacts()`].
+#'
+#' @param contacts_of_contacts A `tibble` containing the contacts of contacts
+#' data.
+#' @param contacts_of_contacts_address_history_clean A `tibble` containing the
+#' cleaned address history data from contacts of contacts (data is cleaned by
+#' [`clean_contacts_of_contacts_address_history()`]).
+#' @param contacts_of_contacts_vacc_history_clean A `tibble` containing the
+#' cleaned vaccination history from contacts of contacts (data is cleaned by
+#' [`clean_contacts_of_contacts_vax_history()`]).
+#'
+#' @return A `tibble` containing the cleaned contacts of contacts data.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#'   url <- "https://MyGoDataServer.com/"
+#'   username <- "myemail@email.com"
+#'   password <- "mypassword"
+#'   outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' contacts_of_contacts <- get_contacts_of_contacts(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' locations <- get_locations(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
+#'
+#' locations_clean <- clean_locations(locations = locations)
+#'
+#' contacts_of_contacts_address_history_clean <- clean_contacts_of_contacts_address_history(
+#'   contacts_of_contacts = contacts_of_contacts,
+#'   locations_clean = locations_clean
+#' )
+#'
+#' contacts_of_contacts_vacc_history_clean <- clean_contacts_of_contacts_vax_history(
+#'   contacts_of_contacts = contacts_of_contacts
+#' )
+#'
+#' contacts_of_contacts_clean <- clean_contacts_of_contacts(
+#'   contacts_of_contacts = contacts_of_contacts,
+#'   contacts_of_contacts_address_history_clean = contacts_of_contacts_address_history_clean,
+#'   contacts_of_contacts_vacc_history_clean = contacts_of_contacts_vacc_history_clean
+#' )
+#' }
+clean_contacts_of_contacts <- function(contacts_of_contacts,
+                                       contacts_of_contacts_address_history_clean,
+                                       contacts_of_contacts_vacc_history_clean) {
+
+  # Remove all deleted records
+  coc_clean <- dplyr::filter(
+    .data = contacts_of_contacts,
+    .data$deleted == FALSE | is.na(.data$deleted)
+  )
+
+  # Remove all nested fields, otherwise problems with exporting to excel
+  coc_clean <- dplyr::select_if(
+    .tbl = coc_clean,
+    .predicate = purrr::negate(is.list)
+  )
+
+  # standardize column name syntax
+  coc_clean <- janitor::clean_names(dat = coc_clean)
+
+  # label timestamps as datetime
+  coc_clean <- dplyr::rename(
+    .data = coc_clean,
+    date_of_birth = "dob",
+    datetime_updated_at = "updated_at",
+    datetime_created_at = "created_at"
+  )
+
+  # clean up all character fields
+  coc_clean <- dplyr::mutate(
+    .data = coc_clean,
+    dplyr::across(dplyr::where(is.character), na_if, "")
+  )
+
+  # clean date formats (TODO: edit this so that we can see time stamps)
+  coc_clean <- dplyr::mutate_at(
+    .tbl = coc_clean,
+    .vars = dplyr::vars(dplyr::starts_with("date_")),
+    list(~ as.Date(substr(., 1, 10)))
+  )
+
+  coc_clean <- dplyr::mutate(
+    .data = coc_clean,
+    datetime_updated_at = as.POSIXct(datetime_updated_at,format="%Y-%m-%dT%H:%M")
+  )
+
+  coc_clean <- dplyr::mutate(
+    .data = coc_clean,
+    datetime_created_at = as.POSIXct(datetime_created_at,format="%Y-%m-%dT%H:%M")
+  )
+
+  #  truncate responses of categorical vars so easier to read
+  coc_clean <- dplyr::mutate(
+    .data = coc_clean,
+    classification = sub(".*CLASSIFICATION_", "", classification),
+    gender = sub(".*GENDER_", "", gender),
+    occupation = sub(".*OCCUPATION_", "", occupation),
+    outcome = sub(".*OUTCOME_", "", outcome_id),
+    pregnancy_status = sub(".*STATUS_", "", pregnancy_status),
+    risk_level = sub(".*LEVEL_", "", risk_level),
+    relationship_certainty_level = sub(".*LEVEL_", "", relationship_certainty_level_id),
+    relationship_exposure_type = sub(".*TYPE_", "", relationship_exposure_type_id),
+    relationship_context_of_transmission = sub(".*TRANSMISSION_", "", relationship_social_relationship_type_id),
+    relationship_exposure_frequency = sub(".*FREQUENCY_", "", relationship_exposure_frequency_id),
+    relationship_exposure_duration = sub(".*DURATION_", "", relationship_exposure_duration_id)
+  )
+
+  contacts_of_contacts_address_history_clean <- dplyr::filter(
+    .data = contacts_of_contacts_address_history_clean,
+    addresses_typeid == "USUAL_PLACE_OF_RESIDENCE"
+  )
+
+  # join in current address from address history, only current place of
+  # residence
+  coc_clean <- left_join(
+    x = coc_clean,
+    y = contacts_of_contacts_address_history_clean,
+    by="id"
+  )
+
+  # join in info from vacc block
+  coc_clean <- dplyr::mutate(
+    .data = coc_clean,
+    vaccinated = case_when(id %in% contacts_of_contacts_vacc_history_clean$id[contacts_of_contacts_vacc_history_clean$vaccinesreceived_status == "VACCINATED"] ~ TRUE, TRUE ~ FALSE)
+  )
+
+  # force NA ages to appear as NA, not as 0 like sometimes occurs
+  coc_clean <- dplyr::mutate(.data = coc_clean, age_years = as.numeric(age_years))
+  coc_clean <- dplyr::mutate(.data = coc_clean, age_years = na_if(age_years,0))
+  coc_clean <- dplyr::mutate(.data = coc_clean, age_months = as.numeric(age_months))
+  coc_clean <- dplyr::mutate(.data = coc_clean, age_months = na_if(age_months,0))
+
+  # standardize age vars into just one var, round by 1 decimal
+  coc_clean <- dplyr::mutate(
+    .data = coc_clean,
+    age = case_when(!is.na(age_months) ~  round(age_months / 12, digits = 1),
+                    TRUE ~ age_years)
+  )
+
+  # WHO age categories updated Sept 2020:
+  # 0-4, 5-9, 10-14, 15-19, 20-29, 30-39, 40-49, 50-59, 60-64, 65-69, 70-74,
+  # 75-79, 80+
+  # these categories below match that of detailed WHO surveillance dash:
+  # <5, 5-14, 15-24, 25-64, 65+
+  coc_clean <- dplyr::mutate(
+    .data = coc_clean,
+    age_class = factor(
+      case_when(
+        age <= 4 ~ "<5",
+        age <= 14 ~ "5-14",
+        age <= 24 ~ "15-24",
+        age <= 64 ~ "25-64",
+        is.finite(age) ~ "65+",
+        TRUE ~ "unknown"
+      ), levels = c(
+        "<5",
+        "5-14",
+        "15-24",
+        "25-64",
+        "65+",
+        "unknown"
+      )),
+    age_class = factor(
+      age_class,
+      levels = rev(levels(age_class)))
+  )
+
+  # organize order of vars, only bring in what we need, take away confusing vars
+  coc_clean <- dplyr::select(
+    .data = coc_clean,
+    "id", # identifier
+    "visual_id", # identifier
+    "classification", # identifier
+    "first_name", # demographics
+    "middle_name", # demographics
+    "last_name", # demographics
+    "gender", # demographics
+    "age", # demographics
+    "age_class", # demographics
+    "occupation", # demographics
+    "pregnancy_status", # demographics
+    "date_of_reporting", # dates
+    "date_of_last_contact", # dates
+    "date_of_burial", # dates
+    "was_case", # epi
+    "risk_level", # epi
+    "risk_reason", # epi
+    "safe_burial", # epi
+    "transfer_refused", # epi
+    "responsible_user_id", # assigned contact tracer
+    dplyr::matches("^admin_.*name$"), # address
+    "lat",# address
+    "long", # address
+    "address", # address
+    "postal_code", # address
+    "city", # address
+    "telephone", # address
+    "email", # address
+    "vaccinated", # vaccination
+    "outcome", # outcome
+    "date_of_outcome",  # outcome
+    "relationship_exposure_type",
+    "relationship_context_of_transmission",
+    "relationship_exposure_duration",
+    "relationship_exposure_frequency",
+    "relationship_certainty_level",
+    "relationship_cluster_id",
+    location_id = "addresses_locationid",  # uuid in case need later for joining of whatever sort.
+    "created_by",
+    "datetime_created_at",
+    "updated_by",
+    "datetime_updated_at"
+  )
+
+  return(coc_clean)
+}
diff --git a/man/clean_contacts_of_contacts.Rd b/man/clean_contacts_of_contacts.Rd
new file mode 100644
index 0000000..2cada00
--- /dev/null
+++ b/man/clean_contacts_of_contacts.Rd
@@ -0,0 +1,69 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_contacts_of_contacts.R
+\name{clean_contacts_of_contacts}
+\alias{clean_contacts_of_contacts}
+\title{Clean contacts of contacts data}
+\usage{
+clean_contacts_of_contacts(
+  contacts_of_contacts,
+  contacts_of_contacts_address_history_clean,
+  contacts_of_contacts_vacc_history_clean
+)
+}
+\arguments{
+\item{contacts_of_contacts}{A \code{tibble} containing the contacts of contacts
+data.}
+
+\item{contacts_of_contacts_address_history_clean}{A \code{tibble} containing the
+cleaned address history data from contacts of contacts (data is cleaned by
+\code{\link[=clean_contacts_of_contacts_address_history]{clean_contacts_of_contacts_address_history()}}).}
+
+\item{contacts_of_contacts_vacc_history_clean}{A \code{tibble} containing the
+cleaned vaccination history from contacts of contacts (data is cleaned by
+\code{\link[=clean_contacts_of_contacts_vax_history]{clean_contacts_of_contacts_vax_history()}}).}
+}
+\value{
+A \code{tibble} containing the cleaned contacts of contacts data.
+}
+\description{
+Cleans and un-nests contacts of contacts data. Contacts of
+contacts data is returned by \code{\link[=get_contacts_of_contacts]{get_contacts_of_contacts()}}.
+}
+\examples{
+\dontrun{
+  url <- "https://MyGoDataServer.com/"
+  username <- "myemail@email.com"
+  password <- "mypassword"
+  outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+contacts_of_contacts <- get_contacts_of_contacts(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+locations <- get_locations(
+  url = url,
+  username = username,
+  password = password
+)
+
+locations_clean <- clean_locations(locations = locations)
+
+contacts_of_contacts_address_history_clean <- clean_contacts_of_contacts_address_history(
+  contacts_of_contacts = contacts_of_contacts,
+  locations_clean = locations_clean
+)
+
+contacts_of_contacts_vacc_history_clean <- clean_contacts_of_contacts_vax_history(
+  contacts_of_contacts = contacts_of_contacts
+)
+
+contacts_of_contacts_clean <- clean_contacts_of_contacts(
+  contacts_of_contacts = contacts_of_contacts,
+  contacts_of_contacts_address_history_clean = contacts_of_contacts_address_history_clean,
+  contacts_of_contacts_vacc_history_clean = contacts_of_contacts_vacc_history_clean
+)
+}
+}
diff --git a/tests/testthat/test-clean_contacts_of_contacts.R b/tests/testthat/test-clean_contacts_of_contacts.R
new file mode 100644
index 0000000..740bfc9
--- /dev/null
+++ b/tests/testthat/test-clean_contacts_of_contacts.R
@@ -0,0 +1,62 @@
+test_that("clean_contacts_of_contacts works as expected", {
+  skip("get_contacts_of_contacts requires API call")
+
+  contacts_of_contacts <- get_contacts_of_contacts(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+
+  locations <- get_locations(
+    url = url,
+    username = username,
+    password = password
+  )
+  locations_clean <- clean_locations(locations = locations)
+
+  contacts_of_contacts_address_history_clean <- clean_contacts_of_contacts_address_history(
+    contacts_of_contacts = contacts_of_contacts,
+    locations_clean = locations_clean
+  )
+
+  contacts_of_contacts_vacc_history_clean <- clean_contacts_of_contacts_vax_history(
+    contacts_of_contacts = contacts_of_contacts
+  )
+
+  res <- clean_contacts_of_contacts(
+    contacts_of_contacts = contacts_of_contacts,
+    contacts_of_contacts_address_history_clean = contacts_of_contacts_address_history_clean,
+    contacts_of_contacts_vacc_history_clean = contacts_of_contacts_vacc_history_clean
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(14L, 43L))
+  expect_true(
+    all(c(
+      "id", "visual_id", "classification", "first_name", "middle_name",
+      "last_name", "gender", "age", "age_class", "occupation",
+      "pregnancy_status", "date_of_reporting", "date_of_onset",
+      "date_of_infection", "date_become_case", "date_of_burial", "was_contact",
+      "risk_level", "risk_reason", "safe_burial", "transfer_refused",
+      "responsible_user_id", "admin_0_name", "admin_1_name", "admin_2_name",
+      "lat", "long", "address", "postal_code", "city", "telephone", "email",
+      "vaccinated", "isolated", "hospitalized", "icu", "outcome",
+      "date_of_outcome", "location_id", "created_by", "datetime_created_at",
+      "updated_by", "datetime_updated_at"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], function(x) class(x)[1])),
+    c(
+      rep("character", 7), "numeric", "factor", "character", "character",
+      rep("Date", 5), "logical", "character", "character", "logical", "logical",
+      "character", "character", "character", "character", "numeric", "numeric",
+      "character", "character", "character", "character", "character",
+      "logical", "logical", "logical", "logical", "character", "Date",
+      "character", "character", "POSIXct", "character", "POSIXct"
+    )
+  )
+})

From 442c3a4c81cf4fd43d8e0773b0db28a7aa15d761 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 15 Mar 2023 16:53:20 +0000
Subject: [PATCH 161/203] added clean_followups function, documentation and
 test

---
 R/clean_followups.R                   | 153 ++++++++++++++++++++++++++
 man/clean_followups.Rd                |  63 +++++++++++
 tests/testthat/test-clean_followups.R |  59 ++++++++++
 3 files changed, 275 insertions(+)
 create mode 100644 R/clean_followups.R
 create mode 100644 man/clean_followups.Rd
 create mode 100644 tests/testthat/test-clean_followups.R

diff --git a/R/clean_followups.R b/R/clean_followups.R
new file mode 100644
index 0000000..056d604
--- /dev/null
+++ b/R/clean_followups.R
@@ -0,0 +1,153 @@
+#' Clean followup data
+#'
+#' @description Cleans and un-nests followup data which is returned from
+#' [`get_followups()`]
+#'
+#' @param followups A `tibble` with events data. Followup data is returned by
+#' [`get_followups()`].
+#' @param contacts_address_history_clean A `tibble` with cleaned address
+#' history data from contacts. Contacts data is returned by [`get_contacts()`]
+#' and cleaned by [`clean_contact_address_history()`].
+#'
+#' @return A `tibble` with cleaned followup data.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' followups <- get_followups(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' contacts <- get_contacts(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' locations <- get_locations(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
+#'
+#' locations_clean <- clean_locations(locations = locations)
+#'
+#' contacts_address_history_clean <- clean_contact_address_history(
+#'   contacts = contacts,
+#'   locations_clean = locations_clean
+#' )
+#'
+#' followups_clean <- clean_followups(
+#'   followups = followups,
+#'   contacts_address_history_clean = contacts_address_history_clean
+#' )
+#' }
+clean_followups <- function(followups,
+                            contacts_address_history_clean) {
+
+  # Remove all deleted records
+  followups_clean <- dplyr::filter(
+    .data = followups,
+    .data$deleted == FALSE | is.na(.data$deleted)
+  )
+
+  # Remove all nested fields, otherwise problems with exporting to excel
+  followups_clean <- dplyr::select_if(
+    .tbl = followups_clean,
+    .predicate = purrr::negate(is.list)
+  )
+
+  # take out all that are not core variables, otherwise diff versions and
+  # problems exporting to excel
+  followups_clean <- dplyr::select(
+    .data = followups_clean,
+    -dplyr::contains("questionnaireAnswers")
+  )
+
+  # standardize column name syntax
+  followups_clean <- janitor::clean_names(dat = followups_clean)
+
+  # label timestamps as datetime
+  followups_clean <- dplyr::rename(
+    .data = followups_clean,
+    datetime_updated_at = "updated_at",
+    datetime_created_at = "created_at"
+  )
+
+  # clean up all character fields
+  followups_clean <- dplyr::mutate(
+    .data = followups_clean,
+    dplyr::across(dplyr::where(is.character), dplyr::na_if, "")
+  )
+
+  # clean date formats (TODO: edit this so that we can see time stamps)
+  followups_clean <- dplyr::mutate_at(
+    .tbl = followups_clean,
+    dplyr::vars(date), list(~ as.Date(substr(., 1, 10)))
+  )
+
+  followups_clean <- dplyr::mutate(
+    .data = followups_clean,
+    datetime_updated_at = as.POSIXct(datetime_updated_at, format = "%Y-%m-%dT%H:%M")
+  )
+
+  followups_clean <- dplyr::mutate(
+    .data = followups_clean,
+    datetime_created_at = as.POSIXct(datetime_created_at, format = "%Y-%m-%dT%H:%M")
+  )
+
+  #  truncate responses of categorical vars so easier to read
+  followups_clean <- dplyr::mutate(
+    .data = followups_clean,
+    followup_status = sub(".*TYPE_", "", status_id)
+  )
+
+  contacts_address_history_clean <- dplyr::filter(
+    .data = contacts_address_history_clean,
+    addresses_typeid == "USUAL_PLACE_OF_RESIDENCE"
+  )
+
+  followups_clean <- dplyr::left_join(
+    x = followups_clean,
+    y = contacts_address_history_clean,
+    by = "id"
+  )
+
+  # organize order of vars, only bring in what we need, take away confusing vars
+  followups_clean <- dplyr::select(
+    .data = followups_clean,
+    "id", # identifier
+    "contact_id", # identifier
+    "contact_visual_id", # identifier
+    "date", # dates
+    followup_number = "index", # FU status
+    "followup_status", # FU status
+    "targeted", # FU status
+    "responsible_user_id", # assigned contact tracer
+    "team_id", # assigned contact tracer
+    dplyr::matches("^admin_.*name$"), # address
+    "lat", # address
+    "long", # address
+    "address", # address
+    "postal_code", # address
+    "city", # address
+    "telephone", # address
+    "email", # address
+    location_id = "addresses_locationid",  # uuid in case need later for joining of whatever sort.
+    "created_by",  # record modification
+    "datetime_created_at",   # record modification
+    "updated_by",   # record modification
+    "datetime_updated_at"  # record modification
+  )
+
+  return(followups_clean)
+}
diff --git a/man/clean_followups.Rd b/man/clean_followups.Rd
new file mode 100644
index 0000000..074c21d
--- /dev/null
+++ b/man/clean_followups.Rd
@@ -0,0 +1,63 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_followups.R
+\name{clean_followups}
+\alias{clean_followups}
+\title{Clean followup data}
+\usage{
+clean_followups(followups, contacts_address_history_clean)
+}
+\arguments{
+\item{followups}{A \code{tibble} with events data. Followup data is returned by
+\code{\link[=get_followups]{get_followups()}}.}
+
+\item{contacts_address_history_clean}{A \code{tibble} with cleaned address
+history data from contacts. Contacts data is returned by \code{\link[=get_contacts]{get_contacts()}}
+and cleaned by \code{\link[=clean_contact_address_history]{clean_contact_address_history()}}.}
+}
+\value{
+A \code{tibble} with cleaned followup data.
+}
+\description{
+Cleans and un-nests followup data which is returned from
+\code{\link[=get_followups]{get_followups()}}
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+followups <- get_followups(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+contacts <- get_contacts(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+locations <- get_locations(
+  url = url,
+  username = username,
+  password = password
+)
+
+locations_clean <- clean_locations(locations = locations)
+
+contacts_address_history_clean <- clean_contact_address_history(
+  contacts = contacts,
+  locations_clean = locations_clean
+)
+
+followups_clean <- clean_followups(
+  followups = followups,
+  contacts_address_history_clean = contacts_address_history_clean
+)
+}
+}
diff --git a/tests/testthat/test-clean_followups.R b/tests/testthat/test-clean_followups.R
new file mode 100644
index 0000000..630f7d4
--- /dev/null
+++ b/tests/testthat/test-clean_followups.R
@@ -0,0 +1,59 @@
+test_that("clean_followups works as expected", {
+  skip("get_followups requires API call")
+
+  followups <- get_followups(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+
+  contacts <- get_contacts(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+
+  locations <- get_locations(
+    url = url,
+    username = username,
+    password = password
+  )
+
+  locations_clean <- clean_locations(locations = locations)
+
+  contacts_address_history_clean <- clean_contact_address_history(
+    contacts = contacts,
+    locations_clean = locations_clean
+  )
+
+  res <- clean_followups(
+    followups = followups,
+    contacts_address_history_clean = contacts_address_history_clean
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(49L, 24L))
+  expect_true(
+    all(c(
+      "id", "contact_id", "contact_visual_id", "date", "followup_number",
+      "followup_status", "targeted", "responsible_user_id", "team_id",
+      "admin_0_name", "admin_1_name", "admin_2_name", "lat", "long", "address",
+      "postal_code", "city", "telephone", "email", "location_id", "created_by",
+      "datetime_created_at", "updated_by", "datetime_updated_at"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], function(x) class(x)[1])),
+    c(
+      "character", "character", "character", "Date", "integer", "character",
+      "logical", "character", "character", "character", "character",
+      "character", "numeric", "numeric", "character", "logical", "character",
+      "character", "character", "character", "character", "POSIXct",
+      "character", "POSIXct"
+    )
+  )
+})

From 688d28cfef38048563dce19a3066fa2fc4700795 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Wed, 15 Mar 2023 17:32:51 +0000
Subject: [PATCH 162/203] added clean_events function, documentation and test
 (WIP function currently errors)

---
 R/clean_events.R                   | 116 +++++++++++++++++++++++++++++
 man/clean_events.Rd                |  50 +++++++++++++
 tests/testthat/test-clean_events.R |  28 +++++++
 3 files changed, 194 insertions(+)
 create mode 100644 R/clean_events.R
 create mode 100644 man/clean_events.Rd
 create mode 100644 tests/testthat/test-clean_events.R

diff --git a/R/clean_events.R b/R/clean_events.R
new file mode 100644
index 0000000..7bd02fa
--- /dev/null
+++ b/R/clean_events.R
@@ -0,0 +1,116 @@
+#' Clean events data
+#'
+#' @description Cleans and un-nests events data which is returned from
+#' [`get_events()`].
+#'
+#' @param events A `tibble` with events data. Events data is returned by
+#' [`get_events()`].
+#' @param locations_clean A `tibble` with cleaned location data. Location data
+#' is returned by [`get_locations()`] and cleaned by [`clean_locations()`].
+#' Make sure the locations data is cleaned prior to supplying it to
+#' `clean_events()`.
+#'
+#' @return A `tibble` with cleaned events data.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' events <- get_events(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' locations <- get_locations(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
+#' locations_clean <- clean_locations(locations = locations)
+#'
+#' clean_events <- clean_events(
+#'   events = events,
+#'   locations_clean = locations_clean)
+#' }
+clean_events <- function(events,
+                         locations_clean) {
+
+  # Remove all deleted records
+  clean_events <- dplyr::filter(
+    .data = events,
+    .data$deleted == FALSE | is.na(.data$deleted)
+  )
+
+  # Remove all nested fields, otherwise problems with exporting to excel
+  clean_events <- dplyr::select_if(.tbl = clean_events, purrr::negate(is.list))
+
+  # standardize column name syntax
+  clean_events <- janitor::clean_names(clean_events)
+
+  # label timestamps as datetime
+  clean_events <- dplyr::rename(
+    .data = clean_events,
+    datetime_updated_at = "updated_at",
+    datetime_created_at = "created_at"
+  )
+
+  # clean up all character fields
+  clean_events <- dplyr::mutate(
+    .data = clean_events,
+    dplyr::across(dplyr::where(is.character), na_if, "")
+  )
+
+  # clean date formats (TODO: edit this so that we can see time stamps)
+  clean_events <- mutate_at(
+    clean_events,
+    dplyr::vars(dplyr::starts_with("date_")),
+    list(~ as.Date(substr(., 1, 10)))
+  )
+  clean_events <- mutate(
+    clean_events,
+    datetime_updated_at = as.POSIXct(datetime_updated_at, format="%Y-%m-%dT%H:%M"))
+  clean_events <- mutate(
+    clean_events,
+    datetime_created_at = as.POSIXct(datetime_created_at,format="%Y-%m-%dT%H:%M"))
+
+  clean_events <- dplyr::left_join(
+    x = clean_events,
+    y = select(locations_clean,
+               location_id,
+               matches("^admin_.*name$")),
+    by = c("address_location_id" = "location_id")
+  )
+
+  # organize order of vars, only bring in what we need, take away
+  # confusing vars
+  clean_events <- dplyr::select(
+    .data = clean_events,
+    "id", # identifier
+    "name", # identifier
+    "date", # dates
+    "date_of_reporting", # dates
+    "description",
+    "responsible_user_id", # assigned contact tracer
+    matches("^admin_.*name$"),
+    lat = "address_geo_location_lat", # address
+    long = "address_geo_location_lng", # address
+    address = "address_address_line1", # address
+    postal_code = "address_postal_code", # address
+    city = "address_city", # address
+    telephone = "address_phone_number", # address
+    email = "address_email_address", # address
+    location_id = "address_location_id",  # uuid in case need later for joining of whatever sort.
+    "created_by",
+    "datetime_created_at",
+    "updated_by",
+    "datetime_updated_at"
+  )  # record modification
+
+  return(clean_events)
+}
diff --git a/man/clean_events.Rd b/man/clean_events.Rd
new file mode 100644
index 0000000..2e444d3
--- /dev/null
+++ b/man/clean_events.Rd
@@ -0,0 +1,50 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_events.R
+\name{clean_events}
+\alias{clean_events}
+\title{Clean events data}
+\usage{
+clean_events(events, locations_clean)
+}
+\arguments{
+\item{events}{A \code{tibble} with events data. Events data is returned by
+\code{\link[=get_events]{get_events()}}.}
+
+\item{locations_clean}{A \code{tibble} with cleaned location data. Location data
+is returned by \code{\link[=get_locations]{get_locations()}} and cleaned by \code{\link[=clean_locations]{clean_locations()}}.
+Make sure the locations data is cleaned prior to supplying it to
+\code{clean_events()}.}
+}
+\value{
+A \code{tibble} with cleaned events data.
+}
+\description{
+Cleans and un-nests events data which is returned from
+\code{\link[=get_events]{get_events()}}.
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+events <- get_events(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+locations <- get_locations(
+  url = url,
+  username = username,
+  password = password
+)
+locations_clean <- clean_locations(locations = locations)
+
+clean_events <- clean_events(
+  events = events,
+  locations_clean = locations_clean)
+}
+}
diff --git a/tests/testthat/test-clean_events.R b/tests/testthat/test-clean_events.R
new file mode 100644
index 0000000..90cd59c
--- /dev/null
+++ b/tests/testthat/test-clean_events.R
@@ -0,0 +1,28 @@
+test_that("clean_events works as expected", {
+  skip("get_events requires API call")
+
+  res <- get_events(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+  res <- clean_events(events = res)
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(3L, 15L))
+  expect_true(
+    all(c(
+      "id", "name", "user_ids_1", "user_ids_2", "user_ids_3", "user_ids_4",
+      "user_ids_5", "location_ids_1", "location_ids_2", "location_ids_3",
+      "location_ids_4", "created_by", "datetime_created_at", "updated_by",
+      "datetime_updated_at"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    rep("character", 15)
+  )
+})

From 05380ac88b54ceaeb3b91c4705e4cf74ba0c777c Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 16 Mar 2023 14:09:29 +0000
Subject: [PATCH 163/203] added clean_users function, documentation and test

---
 R/clean_users.R                   | 69 +++++++++++++++++++++++++++++++
 man/clean_users.Rd                | 34 +++++++++++++++
 tests/testthat/test-clean_users.R | 23 +++++++++++
 3 files changed, 126 insertions(+)
 create mode 100644 R/clean_users.R
 create mode 100644 man/clean_users.Rd
 create mode 100644 tests/testthat/test-clean_users.R

diff --git a/R/clean_users.R b/R/clean_users.R
new file mode 100644
index 0000000..3653110
--- /dev/null
+++ b/R/clean_users.R
@@ -0,0 +1,69 @@
+#' Cleans users data
+#'
+#' @description Cleans and un-nests users data. Users data is returned by
+#' [`get_users()`].
+#'
+#' @param users A `tibble` containing users data. Users data is returned by
+#' [`get_users()`].
+#'
+#' @return A `tibble` with cleaned users data.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#'
+#' users <- get_users(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
+#'
+#' clean_users <- clean_users(users)
+#' }
+clean_users <- function(users) {
+
+  # standardize column name syntax
+  clean_users <- janitor::clean_names(clean_users)
+
+  # label timestamps as datetime
+  clean_users <- dplyr::rename(
+    clean_users,
+    datetime_last_login = "last_login_date",
+    datetime_created_at = "created_at"
+  )
+
+  # clean up all character fields
+  clean_users <- dplyr::mutate(
+    .data = clean_users,
+    dplyr::across(dplyr::where(is.character), dplyr::na_if, "")
+  )
+
+  clean_users <- tidyr::unnest_wider(clean_users, "role_ids", names_sep = "_")
+
+  #  truncate responses of categorical vars so easier to read
+  clean_users <- dplyr::mutate(
+    clean_users,
+    institution_name = sub(".*NAME_", "", .data$institution_name)
+  )
+
+  # organize order of vars, only bring in what we need, take away confusing vars
+  clean_users <- dplyr::select(
+    .data = clean_users,
+    "id",
+    "first_name",
+    "last_name",
+    "email",
+    "institution_name",
+    "disregard_geographic_restrictions",
+    dplyr::starts_with("role_ids"),
+    "active_outbreak_id",
+    "created_by",
+    "datetime_created_at",
+    "datetime_last_login"
+  )
+
+  return(clean_users)
+}
diff --git a/man/clean_users.Rd b/man/clean_users.Rd
new file mode 100644
index 0000000..d06731b
--- /dev/null
+++ b/man/clean_users.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_users.R
+\name{clean_users}
+\alias{clean_users}
+\title{Cleans users data}
+\usage{
+clean_users(users)
+}
+\arguments{
+\item{users}{A \code{tibble} containing users data. Users data is returned by
+\code{\link[=get_users]{get_users()}}.}
+}
+\value{
+A \code{tibble} with cleaned users data.
+}
+\description{
+Cleans and un-nests users data. Users data is returned by
+\code{\link[=get_users]{get_users()}}.
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+
+users <- get_users(
+  url = url,
+  username = username,
+  password = password
+)
+
+clean_users <- clean_users(users)
+}
+}
diff --git a/tests/testthat/test-clean_users.R b/tests/testthat/test-clean_users.R
new file mode 100644
index 0000000..876963a
--- /dev/null
+++ b/tests/testthat/test-clean_users.R
@@ -0,0 +1,23 @@
+test_that("clean_users works as expected", {
+  skip("get_users requires API call")
+
+  users <- get_users(url = url, username = username, password = password)
+  res <- clean_users(users = users)
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(20L, 24L))
+  expect_true(
+    all(c(
+      "id", "first_name", "last_name", "email", "institution_name",
+      "disregard_geographic_restrictions", paste0("role_ids_", 1:14),
+      "active_outbreak_id", "created_by", "datetime_created_at",
+      "datetime_last_login"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c(rep("character", 5), "logical", rep("character", 18))
+  )
+})

From 0de513ac86856479848fac16dba3b110fe9f7ad5 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 16 Mar 2023 14:11:03 +0000
Subject: [PATCH 164/203] fixed bug in clean_users

---
 R/clean_users.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/clean_users.R b/R/clean_users.R
index 3653110..cca13d3 100644
--- a/R/clean_users.R
+++ b/R/clean_users.R
@@ -26,7 +26,7 @@
 clean_users <- function(users) {
 
   # standardize column name syntax
-  clean_users <- janitor::clean_names(clean_users)
+  clean_users <- janitor::clean_names(users)
 
   # label timestamps as datetime
   clean_users <- dplyr::rename(

From fc1180d8f84982579a1265ddedb897c3fe771d5e Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 16 Mar 2023 14:16:18 +0000
Subject: [PATCH 165/203] added clean_teams function, documentation and test

---
 R/clean_teams.R                   | 75 +++++++++++++++++++++++++++++++
 man/clean_teams.Rd                | 34 ++++++++++++++
 tests/testthat/test-clean_teams.R | 23 ++++++++++
 3 files changed, 132 insertions(+)
 create mode 100644 R/clean_teams.R
 create mode 100644 man/clean_teams.Rd
 create mode 100644 tests/testthat/test-clean_teams.R

diff --git a/R/clean_teams.R b/R/clean_teams.R
new file mode 100644
index 0000000..6c670d0
--- /dev/null
+++ b/R/clean_teams.R
@@ -0,0 +1,75 @@
+#' Clean teams data
+#'
+#' @description Cleans and un-nests teams data. Teams data is returned by
+#' [`get_teams()`].
+#'
+#' @param teams A `tibble` containing teams data. Teams data is returned by
+#' [`get_teams()`].
+#'
+#' @return A `tibble` of cleaned teams data
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#'
+#' teams <- get_teams(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
+#'
+#' clean_teams <- clean_teams(teams)
+#' }
+clean_teams <- function(teams) {
+
+  # Remove all deleted records
+  clean_teams <- dplyr::filter(
+    .data = teams,
+    .data$deleted == FALSE | is.na(.data$deleted)
+  )
+
+  # standardize column name syntax
+  clean_teams <- janitor::clean_names(clean_teams)
+
+  # label timestamps as datetime
+  clean_teams <- dplyr::rename(
+    .data = clean_teams,
+    datetime_updated_at = "updated_at",
+    datetime_created_at = "created_at"
+  )
+
+  #clean up all character fields
+  clean_teams <- dplyr::mutate(
+    .data = clean_teams,
+    dplyr::across(dplyr::where(is.character), na_if, "")
+  )
+
+  clean_teams <- tidyr::unnest_wider(
+    data = clean_teams,
+    col = "user_ids",
+    names_sep = "_"
+  )
+  clean_teams <- tidyr::unnest_wider(
+    data = clean_teams,
+    col = "location_ids",
+    names_sep = "_"
+  )
+
+  # organize order of vars, only bring in what we need, take away confusing vars
+  clean_teams <- dplyr::select(
+    .data = clean_teams,
+    "id",
+    "name",
+    dplyr::starts_with("user_ids"),
+    dplyr::starts_with("location_ids"),
+    "created_by", # record modification
+    "datetime_created_at", # record modification
+    "updated_by", # record modification
+    "datetime_updated_at" # record modification
+  )
+
+  return(clean_teams)
+}
diff --git a/man/clean_teams.Rd b/man/clean_teams.Rd
new file mode 100644
index 0000000..27dfa2e
--- /dev/null
+++ b/man/clean_teams.Rd
@@ -0,0 +1,34 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_teams.R
+\name{clean_teams}
+\alias{clean_teams}
+\title{Clean teams data}
+\usage{
+clean_teams(teams)
+}
+\arguments{
+\item{teams}{A \code{tibble} containing teams data. Teams data is returned by
+\code{\link[=get_teams]{get_teams()}}.}
+}
+\value{
+A \code{tibble} of cleaned teams data
+}
+\description{
+Cleans and un-nests teams data. Teams data is returned by
+\code{\link[=get_teams]{get_teams()}}.
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+
+teams <- get_teams(
+  url = url,
+  username = username,
+  password = password
+)
+
+clean_teams <- clean_teams(teams)
+}
+}
diff --git a/tests/testthat/test-clean_teams.R b/tests/testthat/test-clean_teams.R
new file mode 100644
index 0000000..ff8a10f
--- /dev/null
+++ b/tests/testthat/test-clean_teams.R
@@ -0,0 +1,23 @@
+test_that("clean_teams works as expected", {
+  skip("get_teams requires API call")
+
+  teams <- get_teams(url = url, username = username, password = password)
+  res <- clean_teams(teams = teams)
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(4L, 15L))
+  expect_true(
+    all(c(
+      "id", "name", "user_ids_1", "user_ids_2", "user_ids_3", "user_ids_4",
+      "user_ids_5", "location_ids_1", "location_ids_2", "location_ids_3",
+      "location_ids_4", "created_by", "datetime_created_at", "updated_by",
+      "datetime_updated_at"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    rep("character", 15)
+  )
+})

From 035e7109d4100279668c798067ee5c7287265cd0 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 16 Mar 2023 14:32:47 +0000
Subject: [PATCH 166/203] added clean_relationships function, documentation and
 test

---
 R/clean_relationships.R                   | 104 ++++++++++++++++++++++
 man/clean_relationships.Rd                |  36 ++++++++
 tests/testthat/test-clean_relationships.R |  30 +++++++
 3 files changed, 170 insertions(+)
 create mode 100644 R/clean_relationships.R
 create mode 100644 man/clean_relationships.Rd
 create mode 100644 tests/testthat/test-clean_relationships.R

diff --git a/R/clean_relationships.R b/R/clean_relationships.R
new file mode 100644
index 0000000..c0cc883
--- /dev/null
+++ b/R/clean_relationships.R
@@ -0,0 +1,104 @@
+#' Cleans relationship data
+#'
+#' @description Cleans and un-nests relationship data. Relationship data is
+#' returned by [`get_relationships()`].
+#'
+#' @param relationships A `tibble` of relationship data. Relationship data is
+#' returned by [`get_relationships()`].
+#'
+#' @return A `tibble` with clean relationship data.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' relationships <- get_relationships(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' clean_relationships <- clean_relationships(relationships)
+#' }
+clean_relationships <- function(relationships) {
+
+  # Remove all deleted records
+  clean_relationships <- dplyr::filter(
+    .data = relationships,
+    .data$deleted == FALSE | is.na(.data$deleted)
+  )
+
+  # Remove all nested fields, otherwise problems with exporting to excel
+  clean_relationships <- dplyr::select_if(
+    .tbl = clean_relationships,
+    purrr::negate(is.list)
+  )
+
+  # standardize column name syntax
+  clean_relationships <- janitor::clean_names(clean_relationships)
+
+  # label timestamps as datetime
+  clean_relationships <- dplyr::rename(
+    .data = clean_relationships,
+    datetime_updated_at = "updated_at",
+    datetime_created_at = "created_at"
+  )
+
+  #clean up all character fields
+  clean_relationships <- dplyr::mutate(
+    .data = clean_relationships,
+    dplyr::across(dplyr::where(is.character), na_if, "")
+  )
+
+  # clean date formats (TODO: edit this so that we can see time stamps)
+  clean_relationships <- dplyr::mutate(
+    .data = clean_relationships,
+    dplyr::across(
+      dplyr::starts_with("date_"), list(~ as.Date(substr(., 1, 10)))
+    )
+  )
+  clean_relationships <- dplyr::mutate(
+    .data = clean_relationships,
+    datetime_updated_at = as.POSIXct(
+      datetime_updated_at,
+      format = "%Y-%m-%dT%H:%M"
+    )
+  )
+  clean_relationships <- dplyr::mutate(
+    .data = clean_relationships,
+    datetime_created_at = as.POSIXct(
+      datetime_created_at,
+      format = "%Y-%m-%dT%H:%M"
+    )
+  )
+
+  #  truncate responses of categorical vars so easier to read
+  clean_relationships <- dplyr::mutate(
+    .data = clean_relationships,
+    source_person_type = sub(".*TYPE_", "", source_person_type),
+    target_person_type = sub(".*TYPE_", "", target_person_type)
+  )
+
+  # organize order of vars, only bring in what we need, take away confusing vars
+  clean_relationships <- dplyr::select(
+    .data = clean_relationships,
+    "id", #id
+    "source_person_id", #id
+    "source_person_visual_id", #id
+    "target_person_id", #id
+    "target_person_visual_id", #id
+    "source_person_type", #id
+    "target_person_type", #id
+    "created_by", # record modification
+    "datetime_created_at", # record modification
+    "updated_by", # record modification
+    "datetime_updated_at" # record modification
+  )
+
+  return(clean_relationships)
+}
diff --git a/man/clean_relationships.Rd b/man/clean_relationships.Rd
new file mode 100644
index 0000000..e834893
--- /dev/null
+++ b/man/clean_relationships.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_relationships.R
+\name{clean_relationships}
+\alias{clean_relationships}
+\title{Cleans relationship data}
+\usage{
+clean_relationships(relationships)
+}
+\arguments{
+\item{relationships}{A \code{tibble} of relationship data. Relationship data is
+returned by \code{\link[=get_relationships]{get_relationships()}}.}
+}
+\value{
+A \code{tibble} with clean relationship data.
+}
+\description{
+Cleans and un-nests relationship data. Relationship data is
+returned by \code{\link[=get_relationships]{get_relationships()}}.
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+relationships <- get_relationships(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+clean_relationships <- clean_relationships(relationships)
+}
+}
diff --git a/tests/testthat/test-clean_relationships.R b/tests/testthat/test-clean_relationships.R
new file mode 100644
index 0000000..6fff74c
--- /dev/null
+++ b/tests/testthat/test-clean_relationships.R
@@ -0,0 +1,30 @@
+test_that("clean_relationships works as expected", {
+  skip("get_relationships requires API call")
+
+  relationships <- get_relationships(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+  res <- clean_relationships(relationships = relationships)
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(28L, 11L))
+  expect_true(
+    all(c(
+      "id", "source_person_id", "source_person_visual_id", "target_person_id",
+      "target_person_visual_id", "source_person_type", "target_person_type",
+      "created_by", "datetime_created_at", "updated_by", "datetime_updated_at"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], function(x) class(x)[1])),
+    c(
+      "character", "character", "character", "character", "character",
+      "character", "character", "character", "POSIXct", "character", "POSIXct"
+    )
+  )
+})

From 54ec892dc831f7ea416c3d91d5171495f10bfab1 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 16 Mar 2023 14:46:34 +0000
Subject: [PATCH 167/203] added contacts_per_case function, documentation and
 test

---
 R/contacts_per_case.R                   | 49 +++++++++++++++++++++++++
 man/contacts_per_case.Rd                | 41 +++++++++++++++++++++
 tests/testthat/test-contacts_per_case.R | 28 ++++++++++++++
 3 files changed, 118 insertions(+)
 create mode 100644 R/contacts_per_case.R
 create mode 100644 man/contacts_per_case.Rd
 create mode 100644 tests/testthat/test-contacts_per_case.R

diff --git a/R/contacts_per_case.R b/R/contacts_per_case.R
new file mode 100644
index 0000000..cd32caa
--- /dev/null
+++ b/R/contacts_per_case.R
@@ -0,0 +1,49 @@
+#' Counts the number of contacts per case from relationship data
+#'
+#' @description Uses cleaned relationship data to tally the number of contacts
+#' per case. Relationship data is returned by [`get_relationships()`] and
+#' cleaned by [`clean_relationships()`].
+#'
+#' @param relationships_clean A `tibble` with the cleaned relationship data.
+#' Relationship data is returned by [`get_relationships()`] and cleaned by
+#' [`clean_relationships()`].
+#'
+#' @return A `tibble` with the number of contacts associated to each source
+#' person
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' relationships <- get_relationships(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' clean_relationships <- clean_relationships(relationships)
+#'
+#' contacts_per_case <- contacts_per_case(clean_relationships)
+#' }
+contacts_per_case <- function(relationships_clean) {
+
+  contacts_per_case <- dplyr::group_by(
+    .data = relationships_clean,
+    .data$source_person_id
+  )
+
+  contacts_per_case <- dplyr::tally(x = contacts_per_case)
+
+  contacts_per_case <- dplyr::select(
+    .data = contacts_per_case,
+    "source_person_id",
+    no_contacts = n
+  )
+
+  return(contacts_per_case)
+}
diff --git a/man/contacts_per_case.Rd b/man/contacts_per_case.Rd
new file mode 100644
index 0000000..b3f7046
--- /dev/null
+++ b/man/contacts_per_case.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/contacts_per_case.R
+\name{contacts_per_case}
+\alias{contacts_per_case}
+\title{Counts the number of contacts per case from relationship data}
+\usage{
+contacts_per_case(relationships_clean)
+}
+\arguments{
+\item{relationships_clean}{A \code{tibble} with the cleaned relationship data.
+Relationship data is returned by \code{\link[=get_relationships]{get_relationships()}} and cleaned by
+\code{\link[=clean_relationships]{clean_relationships()}}.}
+}
+\value{
+A \code{tibble} with the number of contacts associated to each source
+person
+}
+\description{
+Uses cleaned relationship data to tally the number of contacts
+per case. Relationship data is returned by \code{\link[=get_relationships]{get_relationships()}} and
+cleaned by \code{\link[=clean_relationships]{clean_relationships()}}.
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+relationships <- get_relationships(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+clean_relationships <- clean_relationships(relationships)
+
+contacts_per_case <- contacts_per_case(clean_relationships)
+}
+}
diff --git a/tests/testthat/test-contacts_per_case.R b/tests/testthat/test-contacts_per_case.R
new file mode 100644
index 0000000..e6fbd0a
--- /dev/null
+++ b/tests/testthat/test-contacts_per_case.R
@@ -0,0 +1,28 @@
+test_that("contacts_per_case works as expected", {
+  skip("get_relationships requires API call")
+
+  relationships <- get_relationships(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+
+  clean_relationships <- clean_relationships(relationships)
+
+  res <- contacts_per_case(clean_relationships)
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(10L, 2L))
+  expect_true(
+    all(c(
+      "source_person_id", "no_contacts"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "integer")
+  )
+})

From e3ee64088a0763fe550670e2211903ba6925e610 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 16 Mar 2023 14:54:16 +0000
Subject: [PATCH 168/203] added exposures_per_case function, documentation and
 test

---
 R/exposures_per_case.R                   | 49 ++++++++++++++++++++++++
 man/exposures_per_case.Rd                | 41 ++++++++++++++++++++
 tests/testthat/test-exposures_per_case.R | 28 ++++++++++++++
 3 files changed, 118 insertions(+)
 create mode 100644 R/exposures_per_case.R
 create mode 100644 man/exposures_per_case.Rd
 create mode 100644 tests/testthat/test-exposures_per_case.R

diff --git a/R/exposures_per_case.R b/R/exposures_per_case.R
new file mode 100644
index 0000000..a2ef7f2
--- /dev/null
+++ b/R/exposures_per_case.R
@@ -0,0 +1,49 @@
+#' Counts the number of exposures per case from relationship data
+#'
+#' @description Uses cleaned relationship data to tally the number of contacts
+#' per case. Relationship data is returned by [`get_relationships()`] and
+#' cleaned by [`clean_relationships()`].
+#'
+#' @param relationships_clean A `tibble` with the cleaned relationship data.
+#' Relationship data is returned by [`get_relationships()`] and cleaned by
+#' [`clean_relationships()`].
+#'
+#' @return A `tibble` with the number of exposures associated to each target
+#' person
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' relationships <- get_relationships(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#'
+#' clean_relationships <- clean_relationships(relationships)
+#'
+#' exposures_per_case <- exposures_per_case(clean_relationships)
+#' }
+exposures_per_case <- function(relationships_clean) {
+
+  exposures_per_case <- dplyr::group_by(
+    .data = relationships_clean,
+    .data$target_person_id
+  )
+
+  exposures_per_case <- dplyr::tally(x = exposures_per_case)
+
+  exposures_per_case <- dplyr::select(
+    .data = exposures_per_case,
+    "target_person_id",
+    no_exposures = n
+  )
+
+  return(exposures_per_case)
+}
diff --git a/man/exposures_per_case.Rd b/man/exposures_per_case.Rd
new file mode 100644
index 0000000..51942e5
--- /dev/null
+++ b/man/exposures_per_case.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/exposures_per_case.R
+\name{exposures_per_case}
+\alias{exposures_per_case}
+\title{Counts the number of exposures per case from relationship data}
+\usage{
+exposures_per_case(relationships_clean)
+}
+\arguments{
+\item{relationships_clean}{A \code{tibble} with the cleaned relationship data.
+Relationship data is returned by \code{\link[=get_relationships]{get_relationships()}} and cleaned by
+\code{\link[=clean_relationships]{clean_relationships()}}.}
+}
+\value{
+A \code{tibble} with the number of exposures associated to each target
+person
+}
+\description{
+Uses cleaned relationship data to tally the number of contacts
+per case. Relationship data is returned by \code{\link[=get_relationships]{get_relationships()}} and
+cleaned by \code{\link[=clean_relationships]{clean_relationships()}}.
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+relationships <- get_relationships(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+clean_relationships <- clean_relationships(relationships)
+
+exposures_per_case <- exposures_per_case(clean_relationships)
+}
+}
diff --git a/tests/testthat/test-exposures_per_case.R b/tests/testthat/test-exposures_per_case.R
new file mode 100644
index 0000000..e47ab2b
--- /dev/null
+++ b/tests/testthat/test-exposures_per_case.R
@@ -0,0 +1,28 @@
+test_that("exposures_per_case works as expected", {
+  skip("get_relationships requires API call")
+
+  relationships <- get_relationships(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+
+  clean_relationships <- clean_relationships(relationships)
+
+  res <- exposures_per_case(clean_relationships)
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(23L, 2L))
+  expect_true(
+    all(c(
+      "target_person_id", "no_exposures"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], class)),
+    c("character", "integer")
+  )
+})

From bab80d634c6a5a15155719d451dfe620a3c1a6b8 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 31 Mar 2023 12:04:55 +0100
Subject: [PATCH 169/203] added clean_contacts

---
 R/clean_contacts.R    | 278 ++++++++++++++++++++++++++++++++++++++++++
 man/clean_contacts.Rd |  90 ++++++++++++++
 2 files changed, 368 insertions(+)
 create mode 100644 R/clean_contacts.R
 create mode 100644 man/clean_contacts.Rd

diff --git a/R/clean_contacts.R b/R/clean_contacts.R
new file mode 100644
index 0000000..d2907d8
--- /dev/null
+++ b/R/clean_contacts.R
@@ -0,0 +1,278 @@
+#' Clean contacts data
+#'
+#' @description Cleans and un-nests contact data. Contact data is returned by
+#' [`get_contacts()`].
+#'
+#' @param contacts A `tibble` containing the contact data.
+#' @param contacts_address_history_clean A `tibble` containing the cleaned
+#' address history data from contacts (data is cleaned by
+#' [`clean_contact_address_history()`].
+#' @param contacts_vacc_history_clean A `tibble` containing the cleaned
+#' vaccination history data from contacts (data is cleaned by
+#' [`clean_contact_vax_history()`].
+#' @param contacts_becoming_cases A `tibble` containing the cleaned data on
+#' contacts that became cases (date is produced using
+#' [`cases_from_contacts()`]).
+#'
+#' @return A `tibble` containing the cleaned case data.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#'   url <- "https://MyGoDataServer.com/"
+#'   username <- "myemail@email.com"
+#'   password <- "mypassword"
+#'   outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#'   contacts <- get_contacts(
+#'     url = url,
+#'     username = username,
+#'     password = password,
+#'     outbreak_id = outbreak_id
+#'   )
+#'
+#'   locations <- get_locations(
+#'     url = url,
+#'     username = username,
+#'     password = password
+#'   )
+#'
+#'   locations_clean <- clean_locations(locations = locations)
+#'
+#'   # other cleaned data required for `clean_contacts()`
+#'   contacts_vacc_history_clean <- clean_contact_vax_history(contacts = contacts)
+#'   contacts_address_history_clean <- clean_contact_address_history(
+#'     contacts = contacts,
+#'     locations_clean = locations_clean
+#'   )
+#'
+#'   cases <- get_cases(
+#'     url = url,
+#'     username = username,
+#'     password = password,
+#'     outbreak_id = outbreak_id
+#'   )
+#'   cases_address_history_clean <- clean_case_address_history(cases = cases)
+#'   cases_vacc_history_clean <- clean_case_vax_history(cases = cases)
+#'   cases_dateranges_history_clean <- clean_case_med_history(cases = cases)
+#'
+#'   cases_clean <- clean_cases(
+#'     cases = cases,
+#'     cases_address_history_clean = cases_address_history_clean,
+#'     cases_vacc_history_clean = cases_vacc_history_clean,
+#'     cases_dateranges_history_clean = cases_dateranges_history_clean
+#'   )
+#'   contacts_becoming_cases <- cases_from_contacts(cases_clean = cases_clean)
+#'
+#'   contacts_clean <- clean_contacts(
+#'     contacts = contacts,
+#'     contacts_address_history_clean = cases_address_history_clean,
+#'     contacts_vacc_history_clean = cases_vacc_history_clean,
+#'     contacts_becoming_cases = contacts_becoming_cases
+#'   )
+#' }
+clean_contacts <- function(contacts,
+                           contacts_address_history_clean,
+                           contacts_vacc_history_clean,
+                           contacts_becoming_cases) {
+
+  # Remove all deleted records
+  contacts_clean <- dplyr::filter(
+    .data = contacts,
+    .data$deleted == FALSE | is.na(.data$deleted)
+  )
+
+  # Remove all nested fields, otherwise problems with exporting to excel
+  contacts_clean <- dplyr::select_if(
+    .tbl = contacts_clean,
+    .predicate = purrr::negate(is.list)
+  )
+
+  # take out all that are not core variables, otherwise diff versions and
+  # problems exporting to excel
+  contacts_clean <- dplyr::select(
+    .data = contacts_clean,
+    -dplyr::contains("questionnaireAnswers")
+  )
+
+  # standardize column name syntax
+  contacts_clean <- janitor::clean_names(dat = contacts_clean)
+
+  # label timestamps as datetime
+  contacts_clean <- dplyr::rename(
+    .data = contacts_clean,
+    date_of_birth = "dob",
+    date_of_follow_up_start = "follow_up_start_date",
+    date_of_follow_up_end = "follow_up_end_date",
+    datetime_updated_at = "updated_at",
+    datetime_created_at = "created_at"
+  )
+
+  # take out other unnecessary vars that are unnecessary and may confuse
+  # (i.e. was_case for cases)
+  contacts_clean <- dplyr::select(
+    .data = contacts_clean,
+    -c(
+      "is_date_of_reporting_approximate",
+      "was_contact",
+      "follow_up_original_start_date",
+      "type",
+      "deleted",
+      "created_on"
+    )
+  )
+
+  #clean up all character fields
+  contacts_clean <- dplyr::mutate(
+    .data = contacts_clean,
+    dplyr::across(dplyr::where(is.character), na_if, "")
+  )
+
+  # clean date formats (TODO: edit this so that we can see time stamps)
+  contacts_clean <- dplyr::mutate_at(
+    .tbl = contacts_clean,
+    .vars = dplyr::vars(dplyr::starts_with("date_")),
+    list(~ as.Date(substr(., 1, 10)))
+  )
+
+  contacts_clean <- dplyr::mutate(
+    .data = contacts_clean,
+    datetime_updated_at = as.POSIXct(datetime_updated_at, format = "%Y-%m-%dT%H:%M")
+  )
+
+  contacts_clean <- dplyr::mutate(
+    .data = contacts_clean,
+    datetime_created_at = as.POSIXct(datetime_created_at, format = "%Y-%m-%dT%H:%M")
+  )
+
+  #  truncate responses of categorical vars so easier to read
+  contacts_clean <- dplyr::mutate(
+    .data = contacts_clean,
+    classification = sub(".*CLASSIFICATION_", "", classification),
+    gender = sub(".*GENDER_", "", gender),
+    occupation = sub(".*OCCUPATION_", "", occupation),
+    outcome = sub(".*OUTCOME_", "", outcome_id),
+    pregnancy_status = sub(".*STATUS_", "", pregnancy_status),
+    risk_level = sub(".*LEVEL_", "", risk_level),
+    follow_up_status = sub(".*TYPE_", "", follow_up_status),
+    relationship_certainty_level = sub(".*LEVEL_", "", relationship_certainty_level_id),
+    relationship_exposure_type = sub(".*TYPE_", "", relationship_exposure_type_id),
+    relationship_context_of_transmission = sub(".*TRANSMISSION_", "", relationship_social_relationship_type_id),
+    relationship_exposure_frequency = sub(".*FREQUENCY_", "", relationship_exposure_frequency_id),
+    relationship_exposure_duration = sub(".*DURATION_", "", relationship_exposure_duration_id)
+  )
+
+  contacts_address_history_clean <- dplyr::filter(
+    .data = contacts_address_history_clean,
+    addresses_typeid == "USUAL_PLACE_OF_RESIDENCE"
+  )
+
+  # join in current address from address history, only current place of residence
+  contacts_clean <- dplyr::left_join(
+    x = contacts_clean,
+    y = contacts_address_history_clean,
+    by = "id"
+  )
+
+  # join in info from vacc block
+  contacts_clean <- dplyr::mutate(
+    .data = contacts_clean,
+    vaccinated = case_when(id %in% contacts_vacc_history_clean$id[contacts_vacc_history_clean$vaccinesreceived_status == "VACCINATED"] ~ TRUE, TRUE ~ FALSE)
+  )
+
+  # force NA ages to appear as NA, not as 0 like sometimes occurs
+  contacts_clean <- dplyr::mutate(.data = contacts_clean, age_years = as.numeric(age_years))
+  contacts_clean <- dplyr::mutate(.data = contacts_clean, age_years = na_if(age_years,0))
+  contacts_clean <- dplyr::mutate(.data = contacts_clean, age_months = as.numeric(age_months))
+  contacts_clean <- dplyr::mutate(.data = contacts_clean, age_months = na_if(age_months,0))
+
+  # standardize age vars into just one var, round by 1 decimal
+  contacts_clean <- dplyr::mutate(
+    .data = contacts_clean,
+    age = case_when(!is.na(age_months) ~  round(age_months / 12, digits = 1),
+                    TRUE ~ age_years))
+
+  # WHO age categories updated Sept 2020:
+  # 0-4, 5-9, 10-14, 15-19, 20-29, 30-39, 40-49, 50-59, 60-64, 65-69, 70-74,
+  # 75-79, 80+
+  # these categories below match that of detailed WHO surveillance dash:
+  # <5, 5-14, 15-24, 25-64, 65+
+  contacts_clean <- dplyr::mutate(
+    .data = contacts_clean,
+    age_class = factor(
+      case_when(
+        age <= 4 ~ "<5",
+        age <= 14 ~ "5-14",
+        age <= 24 ~ "15-24",
+        age <= 64 ~ "25-64",
+        is.finite(age) ~ "65+",
+        TRUE ~ "unknown"
+      ), levels = c(
+        "<5",
+        "5-14",
+        "15-24",
+        "25-64",
+        "65+",
+        "unknown"
+      )),
+    age_class = factor(
+      age_class,
+      levels = rev(levels(age_class)))
+  )
+
+  # organize order of vars, only bring in what we need, take away confusing vars
+  contacts_clean <- dplyr::select(
+    .data = contacts_clean,
+    id, # identifier
+    visual_id, # identifier
+    classification, # identifier
+    follow_up_status, # identifier
+    first_name, # demographics
+    middle_name, # demographics
+    last_name, # demographics
+    gender, # demographics
+    age, # demographics
+    age_class, # demographics
+    occupation, # demographics
+    pregnancy_status, # demographics
+    date_of_reporting, # dates
+    date_of_last_contact, # dates
+    date_of_burial, # dates
+    date_of_follow_up_start, # dates
+    date_of_follow_up_end, # dates
+    was_case, # epi
+    risk_level, # epi
+    risk_reason, # epi
+    safe_burial, # epi
+    transfer_refused, # epi
+    responsible_user_id, # assigned contact tracer
+    follow_up_team_id, # assigned contact tracer
+    matches("^admin_.*name$"),
+    lat, # address
+    long, # address
+    address, # address
+    postal_code, # address
+    city, # address
+    telephone, # address
+    email, # address
+    vaccinated, # vaccination
+    outcome, # outcome
+    date_of_outcome,  # outcome
+    relationship_exposure_type,
+    relationship_context_of_transmission,
+    relationship_exposure_duration,
+    relationship_exposure_frequency,
+    relationship_certainty_level,
+    relationship_cluster_id,
+    location_id = addresses_locationid,  # uuid in case need later for joining of whatever sort.
+    created_by, # record modification
+    datetime_created_at, # record modification
+    updated_by, # record modification
+    datetime_updated_at # record modification
+  )
+
+  #Join in cases that used to be contacts
+  contacts_clean <- dplyr::bind_rows(contacts_clean, contacts_becoming_cases)
+
+  return(contacts_clean)
+}
diff --git a/man/clean_contacts.Rd b/man/clean_contacts.Rd
new file mode 100644
index 0000000..02de61c
--- /dev/null
+++ b/man/clean_contacts.Rd
@@ -0,0 +1,90 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clean_contacts.R
+\name{clean_contacts}
+\alias{clean_contacts}
+\title{Clean contacts data}
+\usage{
+clean_contacts(
+  contacts,
+  contacts_address_history_clean,
+  contacts_vacc_history_clean,
+  contacts_becoming_cases
+)
+}
+\arguments{
+\item{contacts}{A \code{tibble} containing the contact data.}
+
+\item{contacts_address_history_clean}{A \code{tibble} containing the cleaned
+address history data from contacts (data is cleaned by
+\code{\link[=clean_contact_address_history]{clean_contact_address_history()}}.}
+
+\item{contacts_vacc_history_clean}{A \code{tibble} containing the cleaned
+vaccination history data from contacts (data is cleaned by
+\code{\link[=clean_contact_vax_history]{clean_contact_vax_history()}}.}
+
+\item{contacts_becoming_cases}{A \code{tibble} containing the cleaned data on
+contacts that became cases (date is produced using
+\code{\link[=cases_from_contacts]{cases_from_contacts()}}).}
+}
+\value{
+A \code{tibble} containing the cleaned case data.
+}
+\description{
+Cleans and un-nests contact data. Contact data is returned by
+\code{\link[=get_contacts]{get_contacts()}}.
+}
+\examples{
+\dontrun{
+  url <- "https://MyGoDataServer.com/"
+  username <- "myemail@email.com"
+  password <- "mypassword"
+  outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+  contacts <- get_contacts(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+
+  locations <- get_locations(
+    url = url,
+    username = username,
+    password = password
+  )
+
+  locations_clean <- clean_locations(locations = locations)
+
+  # other cleaned data required for `clean_contacts()`
+  contacts_vacc_history_clean <- clean_contact_vax_history(contacts = contacts)
+  contacts_address_history_clean <- clean_contact_address_history(
+    contacts = contacts,
+    locations_clean = locations_clean
+  )
+
+  cases <- get_cases(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+  cases_address_history_clean <- clean_case_address_history(cases = cases)
+  cases_vacc_history_clean <- clean_case_vax_history(cases = cases)
+  cases_dateranges_history_clean <- clean_case_med_history(cases = cases)
+
+  cases_clean <- clean_cases(
+    cases = cases,
+    cases_address_history_clean = cases_address_history_clean,
+    cases_vacc_history_clean = cases_vacc_history_clean,
+    cases_dateranges_history_clean = cases_dateranges_history_clean
+  )
+  contacts_becoming_cases <- cases_from_contacts(cases_clean = cases_clean)
+
+  contacts_clean <- clean_contacts(
+    contacts = contacts,
+    contacts_address_history_clean = cases_address_history_clean,
+    contacts_vacc_history_clean = cases_vacc_history_clean,
+    contacts_becoming_cases = contacts_becoming_cases
+  )
+}
+}

From 6c9e113a0574986cc110b3e36c13dfb2dbcab784 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 31 Mar 2023 12:22:29 +0100
Subject: [PATCH 170/203] added dplyr namespace to case_when in clean_cases

---
 R/clean_cases.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/clean_cases.R b/R/clean_cases.R
index e99748c..1f00853 100644
--- a/R/clean_cases.R
+++ b/R/clean_cases.R
@@ -113,17 +113,17 @@ clean_cases <- function(cases,
 
   cases_clean <- dplyr::mutate(
     .data = cases_clean,
-    isolated = case_when(id %in% cases_dateranges_history_clean$id[cases_dateranges_history_clean$dateranges_typeid == "ISOLATION"] ~ TRUE, TRUE ~ FALSE)
+    isolated = dplyr::case_when(id %in% cases_dateranges_history_clean$id[cases_dateranges_history_clean$dateranges_typeid == "ISOLATION"] ~ TRUE, TRUE ~ FALSE)
   )
 
   cases_clean <- dplyr::mutate(
     .data = cases_clean,
-    hospitalized = case_when(id %in% cases_dateranges_history_clean$id[cases_dateranges_history_clean$dateranges_typeid == "HOSPITALIZATION"] ~ TRUE, TRUE ~ FALSE)
+    hospitalized = dplyr::case_when(id %in% cases_dateranges_history_clean$id[cases_dateranges_history_clean$dateranges_typeid == "HOSPITALIZATION"] ~ TRUE, TRUE ~ FALSE)
   )
 
   cases_clean <- dplyr::mutate(
     .data = cases_clean,
-    icu = case_when(id %in% cases_dateranges_history_clean$id[cases_dateranges_history_clean$dateranges_typeid == "ICU_ADMISSION"] ~ TRUE, TRUE ~ FALSE)
+    icu = dplyr::case_when(id %in% cases_dateranges_history_clean$id[cases_dateranges_history_clean$dateranges_typeid == "ICU_ADMISSION"] ~ TRUE, TRUE ~ FALSE)
   )
 
   cases_address_history_clean <- dplyr::filter(
@@ -172,7 +172,7 @@ clean_cases <- function(cases,
   cases_clean <- dplyr::mutate(
     .data = cases_clean,
     age_class = factor(
-      case_when(
+      dplyr::case_when(
         age <= 4 ~ "<5",
         age <= 14 ~ "5-14",
         age <= 24 ~ "15-24",

From 2696fd56ca0ecfead7117216b8f04f0a8fb434c6 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 31 Mar 2023 12:39:15 +0100
Subject: [PATCH 171/203] fixed clean_case_address_history by adding
 locations_clean argument to function, updated doc and test

---
 R/clean_case_address_history.R                 | 18 ++++++++++++++++--
 man/clean_case_address_history.Rd              | 18 ++++++++++++++++--
 .../testthat/test-clean_case_address_history.R | 15 +++++++++++++--
 3 files changed, 45 insertions(+), 6 deletions(-)

diff --git a/R/clean_case_address_history.R b/R/clean_case_address_history.R
index 815d3fd..fb7ac72 100644
--- a/R/clean_case_address_history.R
+++ b/R/clean_case_address_history.R
@@ -6,6 +6,8 @@
 #'
 #' @param cases A tibble with case data. Case data is returned by
 #' [`get_cases()`].
+#' @param locations_clean A tibble with cleaned locations data. Locations data
+#' is returned by [`get_locations()`] and cleaned by [`clean_locations()`].
 #'
 #' @return A tibble with address information from cases data.
 #' @export
@@ -24,9 +26,21 @@
 #'   outbreak_id = outbreak_id
 #' )
 #'
-#' case_address_history <- clean_case_address_history(cases = cases)
+#' locations <- get_locations(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
+#'
+#' locations_clean <- clean_locations(locations = locations)
+#'
+#' case_address_history <- clean_case_address_history(
+#'   cases = cases,
+#'   locations_clean = locations_clean
+#' )
 #' }
-clean_case_address_history <- function(cases) {
+clean_case_address_history <- function(cases,
+                                       locations_clean) {
 
   cases_address_history_clean <- dplyr::filter(
     .data = cases,
diff --git a/man/clean_case_address_history.Rd b/man/clean_case_address_history.Rd
index cd9369f..5c32b1b 100644
--- a/man/clean_case_address_history.Rd
+++ b/man/clean_case_address_history.Rd
@@ -4,11 +4,14 @@
 \alias{clean_case_address_history}
 \title{Extract address information from case data}
 \usage{
-clean_case_address_history(cases)
+clean_case_address_history(cases, locations_clean)
 }
 \arguments{
 \item{cases}{A tibble with case data. Case data is returned by
 \code{\link[=get_cases]{get_cases()}}.}
+
+\item{locations_clean}{A tibble with cleaned locations data. Locations data
+is returned by \code{\link[=get_locations]{get_locations()}} and cleaned by \code{\link[=clean_locations]{clean_locations()}}.}
 }
 \value{
 A tibble with address information from cases data.
@@ -32,6 +35,17 @@ cases <- get_cases(
   outbreak_id = outbreak_id
 )
 
-case_address_history <- clean_case_address_history(cases = cases)
+locations <- get_locations(
+  url = url,
+  username = username,
+  password = password
+)
+
+locations_clean <- clean_locations(locations = locations)
+
+case_address_history <- clean_case_address_history(
+  cases = cases,
+  locations_clean = locations_clean
+)
 }
 }
diff --git a/tests/testthat/test-clean_case_address_history.R b/tests/testthat/test-clean_case_address_history.R
index a0c5467..f60c2e1 100644
--- a/tests/testthat/test-clean_case_address_history.R
+++ b/tests/testthat/test-clean_case_address_history.R
@@ -7,11 +7,22 @@ test_that("clean_case_address_history works as expected", {
     password = password,
     outbreak_id = outbreak_id
   )
-  res <- clean_case_address_history(cases = res)
+
+  locations <- get_locations(
+    url = url,
+    username = username,
+    password = password
+  )
+  locations_clean <- clean_locations(locations = locations)
+
+  res <- clean_case_address_history(
+    cases = res,
+    locations_clean = locations_clean
+  )
 
   expect_s3_class(res, "tbl_df")
   expect_s3_class(res, "data.frame")
-  expect_identical(dim(res), c(15L, 14L))
+  expect_identical(dim(res), c(16L, 14L))
   expect_true(
     all(c(
       "id", "visualid", "addresses_locationid", "addresses_typeid", "lat",

From a0026634b7fa4a2454314f4248b05039d7a0bf14 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 31 Mar 2023 12:42:04 +0100
Subject: [PATCH 172/203] fixed clean_locations by fixing typo in return

---
 R/clean_locations.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/clean_locations.R b/R/clean_locations.R
index b008684..1c5afba 100644
--- a/R/clean_locations.R
+++ b/R/clean_locations.R
@@ -121,5 +121,5 @@ clean_locations <- function(locations) {
     by = "location_id"
   )
 
-  return(locations_clean)
+  return(clean_locations)
 }

From c28d3456591cf3900d554c4dc8291d707c6df47f Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 31 Mar 2023 12:48:31 +0100
Subject: [PATCH 173/203] updated check_godata_url function, doc and test to
 use success_code and avoid returning NA

---
 R/check_godata_url.R                   | 11 ++++++-----
 man/check_godata_url.Rd                |  5 ++++-
 tests/testthat/test-check_godata_url.R |  9 +++++++++
 3 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/R/check_godata_url.R b/R/check_godata_url.R
index f395640..1196961 100644
--- a/R/check_godata_url.R
+++ b/R/check_godata_url.R
@@ -6,6 +6,8 @@
 #'
 #' @param url Insert the base URL for your instance of Go.Data here. Don't
 #' forget the forward slash "/" at end!
+#' @param success_code A numeric specifying which code is returned by the API
+#' when successfully returning the status code. Default is 200.
 #'
 #' @return
 #' Boolean, where `TRUE` indicates a valid URL.
@@ -15,16 +17,15 @@
 #' check_godata_url(url = url)
 #' }
 #' @export
-check_godata_url <- function(url) {
+check_godata_url <- function(url,
+                             success_code = 200) {
 
   # Get status code for version check
   status_code <- httr::GET(paste0(url, "api/system-settings/version"))
 
   status_code <- purrr::pluck(status_code, "status_code")
 
-  # create boolean based on status code being 200 (success)
-  check <- status_code == 200
-
-  return(check)
+  # return boolean based on status code being a success
+  return(isTRUE(status_code == success_code))
 
 }
diff --git a/man/check_godata_url.Rd b/man/check_godata_url.Rd
index f64d9ce..ad76c37 100644
--- a/man/check_godata_url.Rd
+++ b/man/check_godata_url.Rd
@@ -4,11 +4,14 @@
 \alias{check_godata_url}
 \title{Check if the provided Go.Data URL is valid}
 \usage{
-check_godata_url(url)
+check_godata_url(url, success_code = 200)
 }
 \arguments{
 \item{url}{Insert the base URL for your instance of Go.Data here. Don't
 forget the forward slash "/" at end!}
+
+\item{success_code}{A numeric specifying which code is returned by the API
+when successfully returning the status code. Default is 200.}
 }
 \value{
 Boolean, where \code{TRUE} indicates a valid URL.
diff --git a/tests/testthat/test-check_godata_url.R b/tests/testthat/test-check_godata_url.R
index 80177f8..0022bf4 100644
--- a/tests/testthat/test-check_godata_url.R
+++ b/tests/testthat/test-check_godata_url.R
@@ -6,3 +6,12 @@ test_that("check_godata_url works as expected", {
   expect_type(res, "logical")
   expect_length(res, 1)
 })
+
+test_that("check_godata_url works as expected specifying success code", {
+  skip("check_godata_url requires API call")
+
+  res <- check_godata_url(url = url, success_code = 200)
+
+  expect_type(res, "logical")
+  expect_length(res, 1)
+})

From bb9c39d1e2d894249a53479d46aa43a8cba2bc3d Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 31 Mar 2023 12:59:25 +0100
Subject: [PATCH 174/203] updated check_godata_version to use strsplit, added
 version names and check

---
 R/check_godata_version.R | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/R/check_godata_version.R b/R/check_godata_version.R
index 8cdd754..d59f964 100644
--- a/R/check_godata_version.R
+++ b/R/check_godata_version.R
@@ -20,18 +20,25 @@ check_godata_version <- function(url = url) {
   gd_version <- get_godata_version(url = url)
 
   # Convert string to vector of 3 numbers
-  gd_version <- stringr::str_split(gd_version, "[.]")
+  gd_version <- strsplit(x = gd_version, split = "[.]")
 
   gd_version <- as.numeric(unlist(gd_version))
 
+  stopifnot(
+    "godata version from API does not have major, minor and patch versioning" =
+      length(gd_version) == 3
+  )
+
+  names(gd_version) <- c("major", "minor", "patch")
+
   # Check if 2.38.1 or later
   # Should be TRUE if it is version 2.38.1 or later &
   # FALSE if version 2.38.0 or earlier
-  if (gd_version[1] < 2) {
+  if (gd_version["major"] < 2) {
     return(FALSE)
-  } else if (gd_version[1] == 2 && gd_version[2] < 38) {
+  } else if (gd_version["major"] == 2 && gd_version["minor"] < 38) {
     return(FALSE)
-  } else if (gd_version[1] == 2 && gd_version[2] == 38 && gd_version[3] == 0) {
+  } else if (gd_version["major"] == 2 && gd_version["minor"] == 38 && gd_version["patch"] == 0) {
     return(FALSE)
   } else {
     return(TRUE)

From c57fbf9a8f184d93297445fdf2998bee2024e069 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 31 Mar 2023 13:06:22 +0100
Subject: [PATCH 175/203] updated batch_downloader test

---
 tests/testthat/test-batch_downloader.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-batch_downloader.R b/tests/testthat/test-batch_downloader.R
index 0d5168e..52daf07 100644
--- a/tests/testthat/test-batch_downloader.R
+++ b/tests/testthat/test-batch_downloader.R
@@ -15,7 +15,7 @@ test_that("batch_downloader works as expected", {
 
   expect_s3_class(res, "tbl_df")
   expect_s3_class(res, "data.frame")
-  expect_identical(dim(res), c(13L, 153L))
+  expect_identical(dim(res), c(14L, 153L))
   expect_identical(
     colnames(res),
     c("firstName", "gender", "wasContact", "safeBurial", "classification",

From 6c9fe8c7248a882868cb0d9cdcbaaf32bdb1e9a1 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 31 Mar 2023 14:11:59 +0100
Subject: [PATCH 176/203] fixed clean_cases test

---
 tests/testthat/test-clean_cases.R | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-clean_cases.R b/tests/testthat/test-clean_cases.R
index a29ce82..a98f56b 100644
--- a/tests/testthat/test-clean_cases.R
+++ b/tests/testthat/test-clean_cases.R
@@ -8,8 +8,19 @@ test_that("clean_cases works as expected", {
     outbreak_id = outbreak_id
   )
 
+  locations <- get_locations(
+    url = url,
+    username = username,
+    password = password
+  )
+
+  locations_clean <- clean_locations(locations = locations)
+
   cases_vacc_history_clean <- clean_case_vax_history(cases = cases)
-  cases_address_history_clean <- clean_case_address_history(cases = cases)
+  cases_address_history_clean <- clean_case_address_history(
+    cases = cases,
+    locations_clean = locations_clean
+  )
   cases_dateranges_history_clean <- clean_case_med_history(cases = cases)
 
   res <- clean_cases(

From 542109403a693c73d09b53a0a54391c406f3766e Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 31 Mar 2023 14:14:27 +0100
Subject: [PATCH 177/203] updated clean_case_address_history

---
 tests/testthat/test-clean_case_address_history.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-clean_case_address_history.R b/tests/testthat/test-clean_case_address_history.R
index f60c2e1..f1ed978 100644
--- a/tests/testthat/test-clean_case_address_history.R
+++ b/tests/testthat/test-clean_case_address_history.R
@@ -1,7 +1,7 @@
 test_that("clean_case_address_history works as expected", {
   skip("get_cases requires API call")
 
-  res <- get_cases(
+  cases <- get_cases(
     url = url,
     username = username,
     password = password,
@@ -16,7 +16,7 @@ test_that("clean_case_address_history works as expected", {
   locations_clean <- clean_locations(locations = locations)
 
   res <- clean_case_address_history(
-    cases = res,
+    cases = cases,
     locations_clean = locations_clean
   )
 

From 649f5fb6c09f9bece6e87ebe9c84eddcbb7343f3 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 31 Mar 2023 14:16:35 +0100
Subject: [PATCH 178/203] fixed cases_from_contacts test

---
 tests/testthat/test-cases_from_contacts.R | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-cases_from_contacts.R b/tests/testthat/test-cases_from_contacts.R
index f5c3570..cd09e3e 100644
--- a/tests/testthat/test-cases_from_contacts.R
+++ b/tests/testthat/test-cases_from_contacts.R
@@ -8,8 +8,19 @@ test_that("cases_from_contacts works as expected", {
     outbreak_id = outbreak_id
   )
 
+  locations <- get_locations(
+    url = url,
+    username = username,
+    password = password
+  )
+
+  locations_clean <- clean_locations(locations = locations)
+
   cases_vacc_history_clean <- clean_case_vax_history(cases = cases)
-  cases_address_history_clean <- clean_case_address_history(cases = cases)
+  cases_address_history_clean <- clean_case_address_history(
+    cases = cases,
+    locations_clean = locations_clean
+  )
   cases_dateranges_history_clean <- clean_case_med_history(cases = cases)
 
   cases_clean <- clean_cases(

From fe8b34ed6e998d4cb341772c4afcc64b5e34d3f4 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 31 Mar 2023 14:44:47 +0100
Subject: [PATCH 179/203] fixed export_downloader test

---
 tests/testthat/test-export_downloader.R | 50 ++++++++++++++-----------
 1 file changed, 28 insertions(+), 22 deletions(-)

diff --git a/tests/testthat/test-export_downloader.R b/tests/testthat/test-export_downloader.R
index 424ecbb..48ad43c 100644
--- a/tests/testthat/test-export_downloader.R
+++ b/tests/testthat/test-export_downloader.R
@@ -15,7 +15,7 @@ test_that("export_downloader works as expected", {
 
   expect_s3_class(res, "tbl_df")
   expect_s3_class(res, "data.frame")
-  expect_identical(dim(res), c(13L, 357L))
+  expect_identical(dim(res), c(14L, 363L))
   expect_true(
     all(c(
       "id", "visualId", "dateOfReporting", "isDateOfReportingApproximate",
@@ -26,16 +26,20 @@ test_that("export_downloader works as expected", {
       "outcomeId", "dateOfOutcome", "documents", "type", "dateRanges",
       "transferRefused", "addresses", "safeBurial", "dateOfBurial",
       "isDateOfOnsetApproximate", "numberOfExposures", "numberOfContacts",
-      "burialLocationId", "burialLocationId Identifiers",
+      "deathLocationId", "deathLocationId Identifiers",
+      "deathLocationId Location geographical level",
+      "deathLocationId Parent location", "burialLocationId",
+      "burialLocationId Identifiers",
       "burialLocationId Location geographical level",
       "burialLocationId Parent location", "burialPlaceName",
       "investigationStatus", "dateInvestigationCompleted", "vaccinesReceived",
-      "pregnancyStatus", "responsibleUserId", "age.years", "age.months"
+      "pregnancyStatus", "age.years", "age.months", "responsibleUser.firstName",
+      "responsibleUser.lastName", "responsibleUser.id"
     ) %in% colnames(res))
   )
 
   expect_true(
-    all(grepl(pattern = "^questionnaireAnswers", x = colnames(res)[50:357]))
+    all(grepl(pattern = "^questionnaireAnswers", x = colnames(res)[56:363]))
   )
 
   expect_identical(
@@ -47,14 +51,15 @@ test_that("export_downloader works as expected", {
       "character", "character", "character", "character", "character", "list",
       "character", "list", "logical", "list", "logical", "logical", "logical",
       "integer", "integer", "logical", "list", "list", "list", "logical",
-      "character", "logical", "list", "character", "character", "integer",
-      "integer", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "logical", "character", "logical", "list",
+      "character", "integer", "integer", "character", "character", "character",
       "list", "list", "list", "list", "list", "list", "list", "list", "list",
       "list", "list", "list", "list", "list", "list", "list", "list", "list",
       "list", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "list", "logical",
       "logical", "logical", "logical", "logical", "logical", "logical",
-      "logical", "logical", "logical", "logical", "list", "list", "list",
-      "list", "list", "list", "logical", "logical", "logical", "logical",
+      "logical", "logical", "logical", "list", "list", "list", "list", "list",
+      "list", "logical", "logical", "logical", "logical", "logical", "logical",
       "logical", "logical", "logical", "logical", "logical", "logical",
       "logical", "logical", "logical", "logical", "logical", "logical",
       "logical", "logical", "logical", "logical", "logical", "logical",
@@ -65,24 +70,23 @@ test_that("export_downloader works as expected", {
       "logical", "logical", "logical", "logical", "logical", "logical",
       "logical", "logical", "logical", "logical", "logical", "logical",
       "logical", "logical", "logical", "logical", "logical", "logical",
-      "logical", "logical", "logical", "logical", "list", "list", "list",
-      "list", "list", "list", "list", "logical", "logical", "logical",
-      "logical", "logical", "logical", "logical", "list", "list", "list",
-      "list", "list", "list", "list", "list", "list", "list", "logical",
-      "list", "list", "list", "list", "logical", "logical", "logical",
+      "logical", "logical", "list", "list", "list", "list", "list", "list",
+      "list", "logical", "logical", "logical", "logical", "logical", "logical",
+      "logical", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "logical", "list", "list", "list", "list", "logical",
       "logical", "logical", "logical", "logical", "logical", "logical",
       "logical", "logical", "logical", "logical", "logical", "logical",
       "logical", "logical", "logical", "logical", "logical", "logical",
       "logical", "logical", "logical", "logical", "logical", "logical",
-      "logical", "list", "logical", "logical", "list", "logical", "logical",
-      "logical", "list", "logical", "list", "logical", "list", "logical",
-      "list", "logical", "list", "logical", "list", "logical", "list", "list",
-      "list", "list", "list", "list", "list", "list", "list", "list", "list",
-      "list", "list", "list", "list", "logical", "list", "logical", "list",
-      "logical", "logical", "logical", "logical", "list", "logical", "logical",
-      "logical", "logical", "list", "logical", "list", "logical", "list",
+      "logical", "logical", "logical", "list", "logical", "logical", "list",
+      "logical", "logical", "logical", "list", "logical", "list", "logical",
       "list", "logical", "list", "logical", "list", "logical", "list",
-      "logical", "list", "logical", "logical", "logical", "logical", "logical",
+      "logical", "list", "list", "list", "list", "list", "list", "list", "list",
+      "list", "list", "list", "list", "list", "list", "list", "logical", "list",
+      "logical", "list", "logical", "logical", "logical", "logical", "list",
+      "logical", "logical", "logical", "logical", "list", "logical", "list",
+      "logical", "list", "list", "logical", "list", "logical", "list",
+      "logical", "list", "logical", "list", "logical", "logical", "logical",
       "logical", "logical", "logical", "logical", "logical", "logical",
       "logical", "logical", "logical", "logical", "logical", "logical",
       "logical", "logical", "logical", "logical", "logical", "logical",
@@ -93,5 +97,7 @@ test_that("export_downloader works as expected", {
       "logical", "logical", "logical", "logical", "logical", "logical",
       "logical", "logical", "logical", "logical", "logical", "logical",
       "logical", "logical", "logical", "logical", "logical", "logical",
-      "logical", "logical", "logical", "list", "list", "list"))
+      "logical", "logical", "logical", "logical", "logical", "list", "list",
+      "list")
+  )
 })

From b8344d7d944aa0b8a5fa65cc66cc520554449294 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 31 Mar 2023 14:46:32 +0100
Subject: [PATCH 180/203] fixed get_all_outbreaks test

---
 tests/testthat/test-get_all_outbreaks.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-get_all_outbreaks.R b/tests/testthat/test-get_all_outbreaks.R
index 06f40f9..4530c3f 100644
--- a/tests/testthat/test-get_all_outbreaks.R
+++ b/tests/testthat/test-get_all_outbreaks.R
@@ -9,7 +9,7 @@ test_that("get_all_outbreaks works as expected", {
 
   expect_s3_class(res, "tbl_df")
   expect_s3_class(res, "data.frame")
-  expect_identical(dim(res), c(10L, 5L))
+  expect_identical(dim(res), c(11L, 5L))
   expect_identical(
     colnames(res),
     c("id", "name", "description", "createdBy", "createdAt")

From f05251fce23ffdb42f962910d008f7668940e07d Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 31 Mar 2023 16:14:54 +0100
Subject: [PATCH 181/203] added first draft of get_cases_questionnaire

---
 R/get_cases_questionnaire.R    | 86 ++++++++++++++++++++++++++++++++++
 man/get_cases_questionnaire.Rd | 64 +++++++++++++++++++++++++
 2 files changed, 150 insertions(+)
 create mode 100644 R/get_cases_questionnaire.R
 create mode 100644 man/get_cases_questionnaire.Rd

diff --git a/R/get_cases_questionnaire.R b/R/get_cases_questionnaire.R
new file mode 100644
index 0000000..171060e
--- /dev/null
+++ b/R/get_cases_questionnaire.R
@@ -0,0 +1,86 @@
+#' Download cases from Go.Data and returns questionnaire fields
+#'
+#' A function that retrieves the questionnaire fields from case data for a
+#' specific `outbreak_id`.
+#'
+#' Unlike [`get_cases()`] this function only uses the [`export_downloader()`],
+#' and not the [`batch_downloader()`]. Therefore, this function will only work
+#' on Go.Data versions 2.38.1 or newer. This method relies on the GET
+#' outbreak/{id}/cases/export API endpoint. An export request is submitted to
+#' the server, and then when the export is ready, it will be downloaded.
+#'
+#' This function fixes the file return type to `"csv"`.
+#'
+#' @param url Insert the base URL for your instance of Go.Data here.
+#' Don't forget the forward slash "/" at end!
+#' @param username The email address for your Go.Data login.
+#' @param password The password for your Go.Data login
+#' @param outbreak_id The id number for the outbreak for which you want to
+#' download data.
+#' @param method The method to download data. `method = "export"` is the
+#' preferred and default method for Go.Data version 2.38.1 or later.
+#' See Details.
+#' @param batch_size If `method = "batches"`, then `batch_size` specifies the
+#' number of records to retrieve in each iteration.
+#' @param wait If `method = "export"`, then `wait` is the number of seconds to
+#' wait in between iterations of checking the status of the export.
+#' @param file_type If `method = "export"`, then `file_type` determines Whether
+#' the resulting data frame should contain nested fields (`file_type = "json"`,
+#' the default) or an entirely flat data structure (`file_type = "csv"`)
+#'
+#' @return Returns a `tibble`.
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#'
+#' cases <- get_cases_questionnaire(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#' }
+get_cases_questionnaire <- function(url,
+                                    username,
+                                    password,
+                                    outbreak_id,
+                                    wait = 2) {
+
+  #Check that outbreak_id is active
+  active_outbreak_id <- get_active_outbreak(
+    url = url,
+    username = username,
+    password = password
+  )
+  if (outbreak_id != active_outbreak_id) {
+    set_active_outbreak(
+      url = url,
+      username = username,
+      password = password,
+      outbreak_id = outbreak_id
+    )
+  }
+
+  #Submit an export request to the system
+  api_call_request <- paste0(
+    url, "api/outbreaks/", outbreak_id, "/cases/export"
+  )
+  df <- export_downloader(
+    url = url,
+    username = username,
+    password = password,
+    api_call_request = api_call_request,
+    file_type = "csv",
+    wait = wait
+  )
+
+  # subset columns to questionnaire
+  df_questionnaire <- df[, grep(pattern = "FA", x = colnames(df))]
+
+  return(tibble::as_tibble(df_questionnaire))
+}
diff --git a/man/get_cases_questionnaire.Rd b/man/get_cases_questionnaire.Rd
new file mode 100644
index 0000000..53c1583
--- /dev/null
+++ b/man/get_cases_questionnaire.Rd
@@ -0,0 +1,64 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get_cases_questionnaire.R
+\name{get_cases_questionnaire}
+\alias{get_cases_questionnaire}
+\title{Download cases from Go.Data and returns questionnaire fields}
+\usage{
+get_cases_questionnaire(url, username, password, outbreak_id, wait = 2)
+}
+\arguments{
+\item{url}{Insert the base URL for your instance of Go.Data here.
+Don't forget the forward slash "/" at end!}
+
+\item{username}{The email address for your Go.Data login.}
+
+\item{password}{The password for your Go.Data login}
+
+\item{outbreak_id}{The id number for the outbreak for which you want to
+download data.}
+
+\item{wait}{If \code{method = "export"}, then \code{wait} is the number of seconds to
+wait in between iterations of checking the status of the export.}
+
+\item{method}{The method to download data. \code{method = "export"} is the
+preferred and default method for Go.Data version 2.38.1 or later.
+See Details.}
+
+\item{batch_size}{If \code{method = "batches"}, then \code{batch_size} specifies the
+number of records to retrieve in each iteration.}
+
+\item{file_type}{If \code{method = "export"}, then \code{file_type} determines Whether
+the resulting data frame should contain nested fields (\code{file_type = "json"},
+the default) or an entirely flat data structure (\code{file_type = "csv"})}
+}
+\value{
+Returns a \code{tibble}.
+}
+\description{
+A function that retrieves the questionnaire fields from case data for a
+specific \code{outbreak_id}.
+}
+\details{
+Unlike \code{\link[=get_cases]{get_cases()}} this function only uses the \code{\link[=export_downloader]{export_downloader()}},
+and not the \code{\link[=batch_downloader]{batch_downloader()}}. Therefore, this function will only work
+on Go.Data versions 2.38.1 or newer. This method relies on the GET
+outbreak/{id}/cases/export API endpoint. An export request is submitted to
+the server, and then when the export is ready, it will be downloaded.
+
+This function fixes the file return type to \code{"csv"}.
+}
+\examples{
+\dontrun{
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+
+cases <- get_cases_questionnaire(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+}
+}

From fbaeeac3b07bc348cf69519478ea31c66b6d139b Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 31 Mar 2023 16:23:35 +0100
Subject: [PATCH 182/203] updated get_cases_questionnaire documentation

---
 R/get_cases_questionnaire.R    |  8 --------
 man/get_cases_questionnaire.Rd | 11 -----------
 2 files changed, 19 deletions(-)

diff --git a/R/get_cases_questionnaire.R b/R/get_cases_questionnaire.R
index 171060e..2ba125d 100644
--- a/R/get_cases_questionnaire.R
+++ b/R/get_cases_questionnaire.R
@@ -17,16 +17,8 @@
 #' @param password The password for your Go.Data login
 #' @param outbreak_id The id number for the outbreak for which you want to
 #' download data.
-#' @param method The method to download data. `method = "export"` is the
-#' preferred and default method for Go.Data version 2.38.1 or later.
-#' See Details.
-#' @param batch_size If `method = "batches"`, then `batch_size` specifies the
-#' number of records to retrieve in each iteration.
 #' @param wait If `method = "export"`, then `wait` is the number of seconds to
 #' wait in between iterations of checking the status of the export.
-#' @param file_type If `method = "export"`, then `file_type` determines Whether
-#' the resulting data frame should contain nested fields (`file_type = "json"`,
-#' the default) or an entirely flat data structure (`file_type = "csv"`)
 #'
 #' @return Returns a `tibble`.
 #' @export
diff --git a/man/get_cases_questionnaire.Rd b/man/get_cases_questionnaire.Rd
index 53c1583..658dd83 100644
--- a/man/get_cases_questionnaire.Rd
+++ b/man/get_cases_questionnaire.Rd
@@ -19,17 +19,6 @@ download data.}
 
 \item{wait}{If \code{method = "export"}, then \code{wait} is the number of seconds to
 wait in between iterations of checking the status of the export.}
-
-\item{method}{The method to download data. \code{method = "export"} is the
-preferred and default method for Go.Data version 2.38.1 or later.
-See Details.}
-
-\item{batch_size}{If \code{method = "batches"}, then \code{batch_size} specifies the
-number of records to retrieve in each iteration.}
-
-\item{file_type}{If \code{method = "export"}, then \code{file_type} determines Whether
-the resulting data frame should contain nested fields (\code{file_type = "json"},
-the default) or an entirely flat data structure (\code{file_type = "csv"})}
 }
 \value{
 Returns a \code{tibble}.

From e6be6076d08b060a99be1bf94e614ec9c55e1488 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 6 Apr 2023 15:20:16 +0100
Subject: [PATCH 183/203] updated documentation

---
 NAMESPACE                                     | 20 +++++++++++++++++++
 man/clean_case_vax_history.Rd                 |  2 +-
 ...an_contacts_of_contacts_address_history.Rd |  2 +-
 3 files changed, 22 insertions(+), 2 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 2120a66..947f78b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,12 +1,32 @@
 # Generated by roxygen2: do not edit by hand
 
+export(cases_from_contacts)
 export(check_godata_url)
+export(clean_case_address_history)
+export(clean_case_med_history)
+export(clean_case_vax_history)
+export(clean_cases)
+export(clean_contact_address_history)
+export(clean_contact_vax_history)
+export(clean_contacts)
+export(clean_contacts_of_contacts)
+export(clean_contacts_of_contacts_address_history)
+export(clean_contacts_of_contacts_vax_history)
+export(clean_events)
+export(clean_followups)
+export(clean_locations)
+export(clean_relationships)
+export(clean_teams)
+export(clean_users)
+export(contacts_per_case)
 export(expand_location_tree)
+export(exposures_per_case)
 export(get_access_token)
 export(get_active_outbreak)
 export(get_all_outbreaks)
 export(get_cases)
 export(get_cases_epiwindow)
+export(get_cases_questionnaire)
 export(get_clusters)
 export(get_contacts)
 export(get_contacts_epiwindow)
diff --git a/man/clean_case_vax_history.Rd b/man/clean_case_vax_history.Rd
index c72e851..95f6570 100644
--- a/man/clean_case_vax_history.Rd
+++ b/man/clean_case_vax_history.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/clean_case_vax_history.R
 \name{clean_case_vax_history}
 \alias{clean_case_vax_history}
-\title{Cleans vaccinations data from case data}
+\title{Cleans vaccination data from case data}
 \usage{
 clean_case_vax_history(cases)
 }
diff --git a/man/clean_contacts_of_contacts_address_history.Rd b/man/clean_contacts_of_contacts_address_history.Rd
index a4923b4..2896a5f 100644
--- a/man/clean_contacts_of_contacts_address_history.Rd
+++ b/man/clean_contacts_of_contacts_address_history.Rd
@@ -45,7 +45,7 @@ locations <- get_locations(
 )
 locations_clean <- clean_locations(locations = locations)
 
-contact_of_contacts_address_history <- clean_contacts_of_contacts_address_history(
+contact_of_contacts_add_hist <- clean_contacts_of_contacts_address_history(
   contacts_of_contacts = contacts_of_contacts,
   locations_clean = locations_clean
 )

From 7084b7167490257d27e2bf46f53c4ec1064667b4 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 6 Apr 2023 15:49:24 +0100
Subject: [PATCH 184/203] used translation function in
 clean_case_address_history

---
 R/clean_case_address_history.R                | 21 ++++++++++++++-----
 man/clean_case_address_history.Rd             | 15 +++++++++++--
 .../test-clean_case_address_history.R         | 10 ++++++++-
 3 files changed, 38 insertions(+), 8 deletions(-)

diff --git a/R/clean_case_address_history.R b/R/clean_case_address_history.R
index fb7ac72..2be9f22 100644
--- a/R/clean_case_address_history.R
+++ b/R/clean_case_address_history.R
@@ -8,6 +8,8 @@
 #' [`get_cases()`].
 #' @param locations_clean A tibble with cleaned locations data. Locations data
 #' is returned by [`get_locations()`] and cleaned by [`clean_locations()`].
+#' @param language_tokens A tibble of language tokens returned by
+#' [`get_language_tokens()`] to translate the string tokens in the data.
 #'
 #' @return A tibble with address information from cases data.
 #' @export
@@ -34,13 +36,22 @@
 #'
 #' locations_clean <- clean_locations(locations = locations)
 #'
+#' language_tokens <- get_language_tokens(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   language = "english_us"
+#' )
+#'
 #' case_address_history <- clean_case_address_history(
 #'   cases = cases,
-#'   locations_clean = locations_clean
+#'   locations_clean = locations_clean,
+#'   language_tokens = language_tokens
 #' )
 #' }
 clean_case_address_history <- function(cases,
-                                       locations_clean) {
+                                       locations_clean,
+                                       language_tokens) {
 
   cases_address_history_clean <- dplyr::filter(
     .data = cases,
@@ -67,9 +78,9 @@ clean_case_address_history <- function(cases,
     purrr::negate(is.list)
   )
 
-  cases_address_history_clean <- dplyr::mutate(
-    .data = cases_address_history_clean,
-    addresses_typeid = sub(".*TYPE_", "", .data$addresses_typeid)
+  cases_address_history_clean <- translate_categories(
+    data = cases_address_history_clean,
+    language_tokens = language_tokens
   )
 
   cases_address_history_clean <- dplyr::left_join(
diff --git a/man/clean_case_address_history.Rd b/man/clean_case_address_history.Rd
index 5c32b1b..cab3aea 100644
--- a/man/clean_case_address_history.Rd
+++ b/man/clean_case_address_history.Rd
@@ -4,7 +4,7 @@
 \alias{clean_case_address_history}
 \title{Extract address information from case data}
 \usage{
-clean_case_address_history(cases, locations_clean)
+clean_case_address_history(cases, locations_clean, language_tokens)
 }
 \arguments{
 \item{cases}{A tibble with case data. Case data is returned by
@@ -12,6 +12,9 @@ clean_case_address_history(cases, locations_clean)
 
 \item{locations_clean}{A tibble with cleaned locations data. Locations data
 is returned by \code{\link[=get_locations]{get_locations()}} and cleaned by \code{\link[=clean_locations]{clean_locations()}}.}
+
+\item{language_tokens}{A tibble of language tokens returned by
+\code{\link[=get_language_tokens]{get_language_tokens()}} to translate the string tokens in the data.}
 }
 \value{
 A tibble with address information from cases data.
@@ -43,9 +46,17 @@ locations <- get_locations(
 
 locations_clean <- clean_locations(locations = locations)
 
+language_tokens <- get_language_tokens(
+  url = url,
+  username = username,
+  password = password,
+  language = "english_us"
+)
+
 case_address_history <- clean_case_address_history(
   cases = cases,
-  locations_clean = locations_clean
+  locations_clean = locations_clean,
+  language_tokens = language_tokens
 )
 }
 }
diff --git a/tests/testthat/test-clean_case_address_history.R b/tests/testthat/test-clean_case_address_history.R
index f1ed978..97a1363 100644
--- a/tests/testthat/test-clean_case_address_history.R
+++ b/tests/testthat/test-clean_case_address_history.R
@@ -15,9 +15,17 @@ test_that("clean_case_address_history works as expected", {
   )
   locations_clean <- clean_locations(locations = locations)
 
+  language_tokens <- get_language_tokens(
+    url = url,
+    username = username,
+    password = password,
+    language = "english_us"
+  )
+
   res <- clean_case_address_history(
     cases = cases,
-    locations_clean = locations_clean
+    locations_clean = locations_clean,
+    language_tokens = language_tokens
   )
 
   expect_s3_class(res, "tbl_df")

From fe63123fb1da4cb8ebe12534235d8a6933caf078 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 6 Apr 2023 15:57:30 +0100
Subject: [PATCH 185/203] used translation function in clean_case_med_history

---
 R/clean_case_med_history.R                   | 28 +++++++++++++-------
 man/clean_case_med_history.Rd                | 17 ++++++++++--
 tests/testthat/test-clean_case_med_history.R | 15 +++++++++--
 3 files changed, 46 insertions(+), 14 deletions(-)

diff --git a/R/clean_case_med_history.R b/R/clean_case_med_history.R
index 82c335e..c9d802b 100644
--- a/R/clean_case_med_history.R
+++ b/R/clean_case_med_history.R
@@ -5,6 +5,8 @@
 #'
 #' @param cases A tibble with case data. Case data is returned by
 #' [`get_cases()`].
+#' @param language_tokens A tibble of language tokens returned by
+#' [`get_language_tokens()`] to translate the string tokens in the data.
 #'
 #' @return A tibble with information on isolation and hospitalization history.
 #' @export
@@ -23,9 +25,20 @@
 #'   outbreak_id = outbreak_id
 #' )
 #'
-#' cases_med_history <- clean_case_med_history(cases = cases)
+#' language_tokens <- get_language_tokens(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   language = "english_us"
+#' )
+#'
+#' cases_med_history <- clean_case_med_history(
+#'   cases = cases,
+#'   language_tokens = language_tokens
+#' )
 #' }
-clean_case_med_history <- function(cases) {
+clean_case_med_history <- function(cases,
+                                   language_tokens) {
 
   cases_dateranges_history_clean <- dplyr::filter(
     .data = cases,
@@ -54,14 +67,9 @@ clean_case_med_history <- function(cases) {
     tolower
   )
 
-  cases_dateranges_history_clean <- dplyr::mutate(
-    .data = cases_dateranges_history_clean,
-    dateranges_typeid = sub(".*TYPE_", "", dateranges_typeid)
-  )
-
-  cases_dateranges_history_clean <- dplyr::mutate(
-    .data = cases_dateranges_history_clean,
-    dateranges_centername = sub(".*NAME_", "", dateranges_centername)
+  cases_dateranges_history_clean <- translate_categories(
+    data = cases_dateranges_history_clean,
+    language_tokens = language_tokens
   )
 
   cases_dateranges_history_clean <- dplyr::mutate_at(
diff --git a/man/clean_case_med_history.Rd b/man/clean_case_med_history.Rd
index bf1fa66..120ce53 100644
--- a/man/clean_case_med_history.Rd
+++ b/man/clean_case_med_history.Rd
@@ -4,11 +4,14 @@
 \alias{clean_case_med_history}
 \title{Extracts and cleans medical history from case data}
 \usage{
-clean_case_med_history(cases)
+clean_case_med_history(cases, language_tokens)
 }
 \arguments{
 \item{cases}{A tibble with case data. Case data is returned by
 \code{\link[=get_cases]{get_cases()}}.}
+
+\item{language_tokens}{A tibble of language tokens returned by
+\code{\link[=get_language_tokens]{get_language_tokens()}} to translate the string tokens in the data.}
 }
 \value{
 A tibble with information on isolation and hospitalization history.
@@ -31,6 +34,16 @@ cases <- get_cases(
   outbreak_id = outbreak_id
 )
 
-cases_med_history <- clean_case_med_history(cases = cases)
+language_tokens <- get_language_tokens(
+  url = url,
+  username = username,
+  password = password,
+  language = "english_us"
+)
+
+cases_med_history <- clean_case_med_history(
+  cases = cases,
+  language_tokens = language_tokens
+)
 }
 }
diff --git a/tests/testthat/test-clean_case_med_history.R b/tests/testthat/test-clean_case_med_history.R
index 895dcd0..55cd50d 100644
--- a/tests/testthat/test-clean_case_med_history.R
+++ b/tests/testthat/test-clean_case_med_history.R
@@ -1,13 +1,24 @@
 test_that("clean_case_med_history works as expected", {
   skip("get_cases requires API call")
 
-  res <- get_cases(
+  cases <- get_cases(
     url = url,
     username = username,
     password = password,
     outbreak_id = outbreak_id
   )
-  res <- clean_case_med_history(cases = res)
+
+  language_tokens <- get_language_tokens(
+    url = url,
+    username = username,
+    password = password,
+    language = "english_us"
+  )
+
+  res <- clean_case_med_history(
+    cases = cases,
+    language_tokens = language_tokens
+  )
 
   expect_s3_class(res, "tbl_df")
   expect_s3_class(res, "data.frame")

From 7ed2c2544f4bb49de56b963572cc9ada1ea50116 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 6 Apr 2023 16:04:11 +0100
Subject: [PATCH 186/203] added translation function to clean_case_vax_history

---
 R/clean_case_vax_history.R                   | 28 +++++++++++++-------
 man/clean_case_vax_history.Rd                | 17 ++++++++++--
 tests/testthat/test-clean_case_vax_history.R | 15 +++++++++--
 3 files changed, 46 insertions(+), 14 deletions(-)

diff --git a/R/clean_case_vax_history.R b/R/clean_case_vax_history.R
index d70f9c8..3c30f58 100644
--- a/R/clean_case_vax_history.R
+++ b/R/clean_case_vax_history.R
@@ -4,6 +4,8 @@
 #' complete, from case data. Case data is returned from [`get_cases()`].
 #'
 #' @param cases A tibble with address information from cases data.
+#' @param language_tokens A tibble of language tokens returned by
+#' [`get_language_tokens()`] to translate the string tokens in the data.
 #'
 #' @return A tibble with cleaned and un-nested vaccination history data.
 #' @export
@@ -22,9 +24,20 @@
 #'   outbreak_id = outbreak_id
 #' )
 #'
-#' vax_history <- clean_case_vax_history(cases = cases)
+#' language_tokens <- get_language_tokens(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   language = "english_us"
+#' )
+#'
+#' vax_history <- clean_case_vax_history(
+#'   cases = cases,
+#'   language_tokens = language_tokens
+#' )
 #' }
-clean_case_vax_history <- function(cases) {
+clean_case_vax_history <- function(cases,
+                                   language_tokens) {
 
   cases_vacc_history_clean <- dplyr::filter(
     .data = cases,
@@ -59,14 +72,9 @@ clean_case_vax_history <- function(cases) {
     .fn = tolower
   )
 
-  cases_vacc_history_clean <- dplyr::mutate(
-    .data = cases_vacc_history_clean,
-    vaccinesreceived_vaccine = sub(".*VACCINE_", "", vaccinesreceived_vaccine)
-  )
-
-  cases_vacc_history_clean <- dplyr::mutate(
-    .data = cases_vacc_history_clean,
-    vaccinesreceived_status = sub(".*STATUS_", "", vaccinesreceived_status)
+  cases_vacc_history_clean <- translate_categories(
+    data = cases_vacc_history_clean,
+    language_tokens = language_tokens
   )
 
   cases_vacc_history_clean <- dplyr::mutate(
diff --git a/man/clean_case_vax_history.Rd b/man/clean_case_vax_history.Rd
index 95f6570..710d73d 100644
--- a/man/clean_case_vax_history.Rd
+++ b/man/clean_case_vax_history.Rd
@@ -4,10 +4,13 @@
 \alias{clean_case_vax_history}
 \title{Cleans vaccination data from case data}
 \usage{
-clean_case_vax_history(cases)
+clean_case_vax_history(cases, language_tokens)
 }
 \arguments{
 \item{cases}{A tibble with address information from cases data.}
+
+\item{language_tokens}{A tibble of language tokens returned by
+\code{\link[=get_language_tokens]{get_language_tokens()}} to translate the string tokens in the data.}
 }
 \value{
 A tibble with cleaned and un-nested vaccination history data.
@@ -30,6 +33,16 @@ cases <- get_cases(
   outbreak_id = outbreak_id
 )
 
-vax_history <- clean_case_vax_history(cases = cases)
+language_tokens <- get_language_tokens(
+  url = url,
+  username = username,
+  password = password,
+  language = "english_us"
+)
+
+vax_history <- clean_case_vax_history(
+  cases = cases,
+  language_tokens = language_tokens
+)
 }
 }
diff --git a/tests/testthat/test-clean_case_vax_history.R b/tests/testthat/test-clean_case_vax_history.R
index c2b9fc2..6372f45 100644
--- a/tests/testthat/test-clean_case_vax_history.R
+++ b/tests/testthat/test-clean_case_vax_history.R
@@ -1,13 +1,24 @@
 test_that("clean_case_vax_history works as expected", {
   skip("get_cases requires API call")
 
-  res <- get_cases(
+  cases <- get_cases(
     url = url,
     username = username,
     password = password,
     outbreak_id = outbreak_id
   )
-  res <- clean_case_vax_history(cases = res)
+
+  language_tokens <- get_language_tokens(
+    url = url,
+    username = username,
+    password = password,
+    language = "english_us"
+  )
+
+  res <- clean_case_vax_history(
+    cases = cases,
+    language_tokens = language_tokens
+  )
 
   expect_s3_class(res, "tbl_df")
   expect_s3_class(res, "data.frame")

From 4e27174ef2ccc3dfaab4a5995a111a2e19e5767a Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 6 Apr 2023 16:33:22 +0100
Subject: [PATCH 187/203] used translation function in clean_cases

---
 R/clean_cases.R                   | 64 +++++++++++++++++++++++--------
 man/clean_cases.Rd                | 42 +++++++++++++++++---
 tests/testthat/test-clean_cases.R | 23 +++++++++--
 3 files changed, 103 insertions(+), 26 deletions(-)

diff --git a/R/clean_cases.R b/R/clean_cases.R
index 1f00853..27932ed 100644
--- a/R/clean_cases.R
+++ b/R/clean_cases.R
@@ -4,6 +4,10 @@
 #' [`get_cases()`].
 #'
 #' @param cases A `tibble` containing the case data.
+#' @param locations_clean A tibble with cleaned locations data. Locations data
+#' is returned by [`get_locations()`] and cleaned by [`clean_locations()`].
+#' @param language_tokens A tibble of language tokens returned by
+#' [`get_language_tokens()`] to translate the string tokens in the data.
 #'
 #' @return A `tibble` containing the cleaned case data.
 #' @export
@@ -22,22 +26,48 @@
 #'   outbreak_id = outbreak_id
 #' )
 #'
+#' language_tokens <- get_language_tokens(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   language = "english_us"
+#' )
+#'
+#' locations <- get_locations(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
+#' locations_clean <- clean_locations(locations = locations)
+#'
 #' # other cleaned data required for `clean_cases()`
-#' cases_vacc_history_clean <- clean_case_vax_history(cases = cases)
-#' cases_address_history_clean <- clean_case_address_history(cases = cases)
-#' cases_dateranges_history_clean <- clean_case_med_history(cases = cases)
+#' cases_vacc_history_clean <- clean_case_vax_history(
+#'   cases = cases,
+#'   language_tokens = language_tokens
+#' )
+#' cases_address_history_clean <- clean_case_address_history(
+#'   cases = cases,
+#'   locations_clean = locations_clean,
+#'   language_tokens = language_tokens
+#' )
+#' cases_dateranges_history_clean <- clean_case_med_history(
+#'   cases = cases,
+#'   language_tokens = language_tokens
+#' )
 #'
 #' cases_clean <- clean_cases(
 #'   cases = cases,
 #'   cases_address_history_clean = cases_address_history_clean,
 #'   cases_vacc_history_clean = cases_vacc_history_clean,
-#'   cases_dateranges_history_clean = cases_dateranges_history_clean
+#'   cases_dateranges_history_clean = cases_dateranges_history_clean,
+#'   language_tokens = language_tokens
 #' )
 #' }
 clean_cases <- function(cases,
                         cases_address_history_clean,
                         cases_vacc_history_clean,
-                        cases_dateranges_history_clean) {
+                        cases_dateranges_history_clean,
+                        language_tokens) {
 
   # Remove all deleted records
   cases_clean <- dplyr::filter(
@@ -100,35 +130,35 @@ clean_cases <- function(cases,
     datetime_created_at = as.POSIXct(datetime_created_at,format="%Y-%m-%dT%H:%M")
   )
 
-  #  truncate responses of categorical vars so easier to read
-  cases_clean <- dplyr::mutate(
+  # translate responses of categorical vars so easier to read
+  cases_clean <- translate_categories(
+    data = cases_clean,
+    language_tokens = language_tokens
+  )
+
+  cases_clean <- dplyr::rename(
     .data = cases_clean,
-    classification = sub(".*CLASSIFICATION_", "", classification),
-    gender = sub(".*GENDER_", "", gender),
-    occupation = sub(".*OCCUPATION_", "", occupation),
-    outcome = sub(".*OUTCOME_", "", outcome_id),
-    pregnancy_status = sub(".*STATUS_", "", pregnancy_status),
-    risk_level = sub(".*LEVEL_", "", risk_level)
+    outcome = "outcome_id"
   )
 
   cases_clean <- dplyr::mutate(
     .data = cases_clean,
-    isolated = dplyr::case_when(id %in% cases_dateranges_history_clean$id[cases_dateranges_history_clean$dateranges_typeid == "ISOLATION"] ~ TRUE, TRUE ~ FALSE)
+    isolated = dplyr::case_when(id %in% cases_dateranges_history_clean$id[cases_dateranges_history_clean$dateranges_typeid == "Isolation"] ~ TRUE, TRUE ~ FALSE)
   )
 
   cases_clean <- dplyr::mutate(
     .data = cases_clean,
-    hospitalized = dplyr::case_when(id %in% cases_dateranges_history_clean$id[cases_dateranges_history_clean$dateranges_typeid == "HOSPITALIZATION"] ~ TRUE, TRUE ~ FALSE)
+    hospitalized = dplyr::case_when(id %in% cases_dateranges_history_clean$id[cases_dateranges_history_clean$dateranges_typeid == "Hospitalization"] ~ TRUE, TRUE ~ FALSE)
   )
 
   cases_clean <- dplyr::mutate(
     .data = cases_clean,
-    icu = dplyr::case_when(id %in% cases_dateranges_history_clean$id[cases_dateranges_history_clean$dateranges_typeid == "ICU_ADMISSION"] ~ TRUE, TRUE ~ FALSE)
+    icu = dplyr::case_when(id %in% cases_dateranges_history_clean$id[cases_dateranges_history_clean$dateranges_typeid == "ICU Admission"] ~ TRUE, TRUE ~ FALSE)
   )
 
   cases_address_history_clean <- dplyr::filter(
     .data = cases_address_history_clean,
-    addresses_typeid == "USUAL_PLACE_OF_RESIDENCE"
+    addresses_typeid == "Current address"
   )
 
   # join in current address from address history, only current place of residence
diff --git a/man/clean_cases.Rd b/man/clean_cases.Rd
index 96b9a54..4e86764 100644
--- a/man/clean_cases.Rd
+++ b/man/clean_cases.Rd
@@ -8,11 +8,18 @@ clean_cases(
   cases,
   cases_address_history_clean,
   cases_vacc_history_clean,
-  cases_dateranges_history_clean
+  cases_dateranges_history_clean,
+  language_tokens
 )
 }
 \arguments{
 \item{cases}{A \code{tibble} containing the case data.}
+
+\item{language_tokens}{A tibble of language tokens returned by
+\code{\link[=get_language_tokens]{get_language_tokens()}} to translate the string tokens in the data.}
+
+\item{locations_clean}{A tibble with cleaned locations data. Locations data
+is returned by \code{\link[=get_locations]{get_locations()}} and cleaned by \code{\link[=clean_locations]{clean_locations()}}.}
 }
 \value{
 A \code{tibble} containing the cleaned case data.
@@ -35,16 +42,41 @@ cases <- get_cases(
   outbreak_id = outbreak_id
 )
 
+language_tokens <- get_language_tokens(
+  url = url,
+  username = username,
+  password = password,
+  language = "english_us"
+)
+
+locations <- get_locations(
+  url = url,
+  username = username,
+  password = password
+)
+locations_clean <- clean_locations(locations = locations)
+
 # other cleaned data required for `clean_cases()`
-cases_vacc_history_clean <- clean_case_vax_history(cases = cases)
-cases_address_history_clean <- clean_case_address_history(cases = cases)
-cases_dateranges_history_clean <- clean_case_med_history(cases = cases)
+cases_vacc_history_clean <- clean_case_vax_history(
+  cases = cases,
+  language_tokens = language_tokens
+)
+cases_address_history_clean <- clean_case_address_history(
+  cases = cases,
+  locations_clean = locations_clean,
+  language_tokens = language_tokens
+)
+cases_dateranges_history_clean <- clean_case_med_history(
+  cases = cases,
+  language_tokens = language_tokens
+)
 
 cases_clean <- clean_cases(
   cases = cases,
   cases_address_history_clean = cases_address_history_clean,
   cases_vacc_history_clean = cases_vacc_history_clean,
-  cases_dateranges_history_clean = cases_dateranges_history_clean
+  cases_dateranges_history_clean = cases_dateranges_history_clean,
+  language_tokens = language_tokens
 )
 }
 }
diff --git a/tests/testthat/test-clean_cases.R b/tests/testthat/test-clean_cases.R
index a98f56b..8a7445d 100644
--- a/tests/testthat/test-clean_cases.R
+++ b/tests/testthat/test-clean_cases.R
@@ -8,6 +8,13 @@ test_that("clean_cases works as expected", {
     outbreak_id = outbreak_id
   )
 
+  language_tokens <- get_language_tokens(
+    url = url,
+    username = username,
+    password = password,
+    language = "english_us"
+  )
+
   locations <- get_locations(
     url = url,
     username = username,
@@ -16,18 +23,26 @@ test_that("clean_cases works as expected", {
 
   locations_clean <- clean_locations(locations = locations)
 
-  cases_vacc_history_clean <- clean_case_vax_history(cases = cases)
+  cases_vacc_history_clean <- clean_case_vax_history(
+    cases = cases,
+    language_tokens = language_tokens
+  )
   cases_address_history_clean <- clean_case_address_history(
     cases = cases,
-    locations_clean = locations_clean
+    locations_clean = locations_clean,
+    language_tokens = language_tokens
+  )
+  cases_dateranges_history_clean <- clean_case_med_history(
+    cases = cases,
+    language_tokens = language_tokens
   )
-  cases_dateranges_history_clean <- clean_case_med_history(cases = cases)
 
   res <- clean_cases(
     cases = cases,
     cases_address_history_clean = cases_address_history_clean,
     cases_vacc_history_clean = cases_vacc_history_clean,
-    cases_dateranges_history_clean = cases_dateranges_history_clean
+    cases_dateranges_history_clean = cases_dateranges_history_clean,
+    language_tokens = language_tokens
   )
 
   expect_s3_class(res, "tbl_df")

From 5bdef5442dcb1840c4e27fa65ca2c35fbad28da7 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 6 Apr 2023 16:50:39 +0100
Subject: [PATCH 188/203] used translation function in
 clean_contact_address_history

---
 R/clean_contact_address_history.R             | 21 ++++++++++++++-----
 man/clean_contact_address_history.Rd          | 15 +++++++++++--
 .../test-clean_contact_address_history.R      | 12 +++++++++--
 3 files changed, 39 insertions(+), 9 deletions(-)

diff --git a/R/clean_contact_address_history.R b/R/clean_contact_address_history.R
index 15222b2..754cae6 100644
--- a/R/clean_contact_address_history.R
+++ b/R/clean_contact_address_history.R
@@ -8,6 +8,8 @@
 #' [`get_contacts()`].
 #' @param locations_clean A tibble with cleaned locations data. Locations data
 #' is returned by [`get_locations()`] and cleaned by [`clean_locations()`].
+#' @param language_tokens A tibble of language tokens returned by
+#' [`get_language_tokens()`] to translate the string tokens in the data.
 #'
 #' @return A tibble with address information from contacts data.
 #' @export
@@ -33,13 +35,22 @@
 #' )
 #' locations_clean <- clean_locations(locations = locations)
 #'
+#' language_tokens <- get_language_tokens(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   language = "english_us"
+#' )
+#'
 #' contact_address_history <- clean_contact_address_history(
 #'   contacts = contacts,
-#'   locations_clean = locations_clean
+#'   locations_clean = locations_clean,
+#'   language_tokens = language_tokens
 #' )
 #' }
 clean_contact_address_history <- function(contacts,
-                                          locations_clean) {
+                                          locations_clean,
+                                          language_tokens) {
 
   contacts_address_history_clean <- dplyr::filter(
     .data = contacts,
@@ -67,9 +78,9 @@ clean_contact_address_history <- function(contacts,
     purrr::negate(is.list)
   )
 
-  contacts_address_history_clean <- dplyr::mutate(
-    .data = contacts_address_history_clean,
-    addresses_typeid = sub(".*TYPE_", "", addresses_typeid)
+  contacts_address_history_clean <- translate_categories(
+    data = contacts_address_history_clean,
+    language_tokens = language_tokens
   )
 
   contacts_address_history_clean <- dplyr::left_join(
diff --git a/man/clean_contact_address_history.Rd b/man/clean_contact_address_history.Rd
index 1209f5a..16b3c8e 100644
--- a/man/clean_contact_address_history.Rd
+++ b/man/clean_contact_address_history.Rd
@@ -4,7 +4,7 @@
 \alias{clean_contact_address_history}
 \title{Extracts address information from contact data}
 \usage{
-clean_contact_address_history(contacts, locations_clean)
+clean_contact_address_history(contacts, locations_clean, language_tokens)
 }
 \arguments{
 \item{contacts}{A tibble with contacts data. Contacts data is returned by
@@ -12,6 +12,9 @@ clean_contact_address_history(contacts, locations_clean)
 
 \item{locations_clean}{A tibble with cleaned locations data. Locations data
 is returned by \code{\link[=get_locations]{get_locations()}} and cleaned by \code{\link[=clean_locations]{clean_locations()}}.}
+
+\item{language_tokens}{A tibble of language tokens returned by
+\code{\link[=get_language_tokens]{get_language_tokens()}} to translate the string tokens in the data.}
 }
 \value{
 A tibble with address information from contacts data.
@@ -42,9 +45,17 @@ locations <- get_locations(
 )
 locations_clean <- clean_locations(locations = locations)
 
+language_tokens <- get_language_tokens(
+  url = url,
+  username = username,
+  password = password,
+  language = "english_us"
+)
+
 contact_address_history <- clean_contact_address_history(
   contacts = contacts,
-  locations_clean = locations_clean
+  locations_clean = locations_clean,
+  language_tokens = language_tokens
 )
 }
 }
diff --git a/tests/testthat/test-clean_contact_address_history.R b/tests/testthat/test-clean_contact_address_history.R
index 50930ab..d5786f0 100644
--- a/tests/testthat/test-clean_contact_address_history.R
+++ b/tests/testthat/test-clean_contact_address_history.R
@@ -15,14 +15,22 @@ test_that("clean_contact_address_history works as expected", {
   )
   locations_clean <- clean_locations(locations = locations)
 
+  language_tokens <- get_language_tokens(
+    url = url,
+    username = username,
+    password = password,
+    language = "english_us"
+  )
+
   res <- clean_contact_address_history(
     contacts = contacts,
-    locations_clean = locations_clean
+    locations_clean = locations_clean,
+    language_tokens = language_tokens
   )
 
   expect_s3_class(res, "tbl_df")
   expect_s3_class(res, "data.frame")
-  expect_identical(dim(res), c(15L, 13L))
+  expect_identical(dim(res), c(16L, 13L))
   expect_true(
     all(c(
       "id", "addresses_locationid", "addresses_typeid", "lat", "long",

From c9460d5cf4fa7a4d3fb0a51fe1a4dee8f6b32573 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 6 Apr 2023 16:56:49 +0100
Subject: [PATCH 189/203] used translation function in
 clean_contact_vax_history

---
 R/clean_contact_vax_history.R                 | 28 ++++++++++++-------
 man/clean_contact_vax_history.Rd              | 17 +++++++++--
 .../testthat/test-clean_contact_vax_history.R | 12 +++++++-
 3 files changed, 44 insertions(+), 13 deletions(-)

diff --git a/R/clean_contact_vax_history.R b/R/clean_contact_vax_history.R
index 32ea9da..3125dfc 100644
--- a/R/clean_contact_vax_history.R
+++ b/R/clean_contact_vax_history.R
@@ -5,6 +5,8 @@
 #' [`get_contacts()`].
 #'
 #' @param contacts A tibble with address information from contact data.
+#' @param language_tokens A tibble of language tokens returned by
+#' [`get_language_tokens()`] to translate the string tokens in the data.
 #'
 #' @return A tibble with cleaned and un-nested vaccination history data.
 #' @export
@@ -23,9 +25,20 @@
 #'   outbreak_id = outbreak_id
 #' )
 #'
-#' vax_history <- clean_contact_vax_history(contacts = contacts)
+#' language_tokens <- get_language_tokens(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   language = "english_us"
+#' )
+#'
+#' vax_history <- clean_contact_vax_history(
+#'   contacts = contacts,
+#'   language_tokens = language_tokens
+#' )
 #' }
-clean_contact_vax_history <- function(contacts) {
+clean_contact_vax_history <- function(contacts,
+                                      language_tokens) {
 
   contacts_vax_history_clean <- dplyr::filter(
     .data = contacts,
@@ -58,14 +71,9 @@ clean_contact_vax_history <- function(contacts) {
     .funs = tolower
   )
 
-  contacts_vax_history_clean <- dplyr::mutate(
-    .data = contacts_vax_history_clean,
-    vaccinesreceived_vaccine = sub(".*VACCINE_", "", vaccinesreceived_vaccine)
-  )
-
-  contacts_vax_history_clean <- dplyr::mutate(
-    .data = contacts_vax_history_clean,
-    vaccinesreceived_status = sub(".*STATUS_", "", vaccinesreceived_status)
+  contacts_vax_history_clean <- translate_categories(
+    data = contacts_vax_history_clean,
+    language_tokens = language_tokens
   )
 
   contacts_vax_history_clean <- dplyr::mutate_at(
diff --git a/man/clean_contact_vax_history.Rd b/man/clean_contact_vax_history.Rd
index a24cd21..c7e49f3 100644
--- a/man/clean_contact_vax_history.Rd
+++ b/man/clean_contact_vax_history.Rd
@@ -4,10 +4,13 @@
 \alias{clean_contact_vax_history}
 \title{Cleans vaccination data from contact data}
 \usage{
-clean_contact_vax_history(contacts)
+clean_contact_vax_history(contacts, language_tokens)
 }
 \arguments{
 \item{contacts}{A tibble with address information from contact data.}
+
+\item{language_tokens}{A tibble of language tokens returned by
+\code{\link[=get_language_tokens]{get_language_tokens()}} to translate the string tokens in the data.}
 }
 \value{
 A tibble with cleaned and un-nested vaccination history data.
@@ -31,6 +34,16 @@ contacts <- get_contacts(
   outbreak_id = outbreak_id
 )
 
-vax_history <- clean_contact_vax_history(contacts = contacts)
+language_tokens <- get_language_tokens(
+  url = url,
+  username = username,
+  password = password,
+  language = "english_us"
+)
+
+vax_history <- clean_contact_vax_history(
+  contacts = contacts,
+  language_tokens = language_tokens
+)
 }
 }
diff --git a/tests/testthat/test-clean_contact_vax_history.R b/tests/testthat/test-clean_contact_vax_history.R
index 3b53f8e..a632cbf 100644
--- a/tests/testthat/test-clean_contact_vax_history.R
+++ b/tests/testthat/test-clean_contact_vax_history.R
@@ -8,7 +8,17 @@ test_that("clean_contact_vax_history works as expected", {
     outbreak_id = outbreak_id
   )
 
-  res <- clean_contact_vax_history(contacts = contacts)
+  language_tokens <- get_language_tokens(
+    url = url,
+    username = username,
+    password = password,
+    language = "english_us"
+  )
+
+  res <- clean_contact_vax_history(
+    contacts = contacts,
+    language_tokens = language_tokens
+  )
 
   expect_s3_class(res, "tbl_df")
   expect_s3_class(res, "data.frame")

From 3316a804c0d2a6c71016e8eb25ea7128fa1e0f7c Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 6 Apr 2023 17:03:48 +0100
Subject: [PATCH 190/203] used translation function in
 clean_contacts_of_contacts_address_history

---
 ...ean_contacts_of_contacts_address_history.R | 21 ++++++++++++++-----
 ...an_contacts_of_contacts_address_history.Rd | 16 ++++++++++++--
 ...ean_contacts_of_contacts_address_history.R | 10 ++++++++-
 3 files changed, 39 insertions(+), 8 deletions(-)

diff --git a/R/clean_contacts_of_contacts_address_history.R b/R/clean_contacts_of_contacts_address_history.R
index b749a71..8bca0d2 100644
--- a/R/clean_contacts_of_contacts_address_history.R
+++ b/R/clean_contacts_of_contacts_address_history.R
@@ -8,6 +8,8 @@
 #' Contacts of contacts data is returned by [`get_contacts_of_contacts()`].
 #' @param locations_clean A `tibble` with cleaned location data. Location data
 #' is returned by [`get_locations()`] and cleaned by [`clean_locations()`].
+#' @param language_tokens A tibble of language tokens returned by
+#' [`get_language_tokens()`] to translate the string tokens in the data.
 #'
 #' @return A `tibble` with address information from contacts of contacts data.
 #' @export
@@ -33,13 +35,22 @@
 #' )
 #' locations_clean <- clean_locations(locations = locations)
 #'
+#' language_tokens <- get_language_tokens(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   language = "english_us"
+#' )
+#'
 #' contact_of_contacts_add_hist <- clean_contacts_of_contacts_address_history(
 #'   contacts_of_contacts = contacts_of_contacts,
-#'   locations_clean = locations_clean
+#'   locations_clean = locations_clean,
+#'   language_tokens = language_tokens
 #' )
 #' }
 clean_contacts_of_contacts_address_history <- function(contacts_of_contacts,
-                                                       locations_clean) {
+                                                       locations_clean,
+                                                       language_tokens) {
 
   coc_add_hist <- dplyr::filter(
     .data = contacts_of_contacts,
@@ -67,9 +78,9 @@ clean_contacts_of_contacts_address_history <- function(contacts_of_contacts,
     .predicate = purrr::negate(is.list)
   )
 
-  coc_add_hist <- dplyr::mutate(
-    .data = coc_add_hist,
-    addresses_typeid = sub(".*TYPE_", "", addresses_typeid)
+  coc_add_hist <- translate_categories(
+    data = coc_add_hist,
+    language_tokens = language_tokens
   )
 
   coc_add_hist <- dplyr::left_join(
diff --git a/man/clean_contacts_of_contacts_address_history.Rd b/man/clean_contacts_of_contacts_address_history.Rd
index 2896a5f..92b1a46 100644
--- a/man/clean_contacts_of_contacts_address_history.Rd
+++ b/man/clean_contacts_of_contacts_address_history.Rd
@@ -6,7 +6,8 @@
 \usage{
 clean_contacts_of_contacts_address_history(
   contacts_of_contacts,
-  locations_clean
+  locations_clean,
+  language_tokens
 )
 }
 \arguments{
@@ -15,6 +16,9 @@ Contacts of contacts data is returned by \code{\link[=get_contacts_of_contacts]{
 
 \item{locations_clean}{A \code{tibble} with cleaned location data. Location data
 is returned by \code{\link[=get_locations]{get_locations()}} and cleaned by \code{\link[=clean_locations]{clean_locations()}}.}
+
+\item{language_tokens}{A tibble of language tokens returned by
+\code{\link[=get_language_tokens]{get_language_tokens()}} to translate the string tokens in the data.}
 }
 \value{
 A \code{tibble} with address information from contacts of contacts data.
@@ -45,9 +49,17 @@ locations <- get_locations(
 )
 locations_clean <- clean_locations(locations = locations)
 
+language_tokens <- get_language_tokens(
+  url = url,
+  username = username,
+  password = password,
+  language = "english_us"
+)
+
 contact_of_contacts_add_hist <- clean_contacts_of_contacts_address_history(
   contacts_of_contacts = contacts_of_contacts,
-  locations_clean = locations_clean
+  locations_clean = locations_clean,
+  language_tokens = language_tokens
 )
 }
 }
diff --git a/tests/testthat/test-clean_contacts_of_contacts_address_history.R b/tests/testthat/test-clean_contacts_of_contacts_address_history.R
index c8a0589..0314c4e 100644
--- a/tests/testthat/test-clean_contacts_of_contacts_address_history.R
+++ b/tests/testthat/test-clean_contacts_of_contacts_address_history.R
@@ -15,9 +15,17 @@ test_that("clean_contacts_of_contacts_address_history works as expected", {
   )
   locations_clean <- clean_locations(locations = locations)
 
+  language_tokens <- get_language_tokens(
+    url = url,
+    username = username,
+    password = password,
+    language = "english_us"
+  )
+
   res <- clean_contacts_of_contacts_address_history(
     contacts_of_contacts = contacts_of_contacts,
-    locations_clean = locations_clean
+    locations_clean = locations_clean,
+    language_tokens = language_tokens
   )
 
   expect_s3_class(res, "tbl_df")

From fe7009dc36ac8dc9b636b9e9e40325ec2fe1cf17 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 6 Apr 2023 17:11:14 +0100
Subject: [PATCH 191/203] used translation function in
 clean_contacts_of_contacts_vax_history

---
 R/clean_contacts_of_contacts_vax_history.R    | 26 ++++++++++++-------
 man/clean_contacts_of_contacts_vax_history.Rd | 15 +++++++++--
 ...t-clean_contacts_of_contacts_vax_history.R | 10 ++++++-
 3 files changed, 38 insertions(+), 13 deletions(-)

diff --git a/R/clean_contacts_of_contacts_vax_history.R b/R/clean_contacts_of_contacts_vax_history.R
index 44e75c7..10c8244 100644
--- a/R/clean_contacts_of_contacts_vax_history.R
+++ b/R/clean_contacts_of_contacts_vax_history.R
@@ -6,6 +6,8 @@
 #'
 #' @param contacts_of_contacts A `tibble` with address information from contacts
 #' of contacts data.
+#' @param language_tokens A tibble of language tokens returned by
+#' [`get_language_tokens()`] to translate the string tokens in the data.
 #'
 #' @return A `tibble` with cleaned and un-nested vaccination history data.
 #' @export
@@ -24,11 +26,20 @@
 #'   outbreak_id = outbreak_id
 #' )
 #'
+#' language_tokens <- get_language_tokens(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   language = "english_us"
+#' )
+#'
 #' vax_history <- clean_contacts_of_contacts_vax_history(
-#'   contacts_of_contacts = contacts_of_contacts
+#'   contacts_of_contacts = contacts_of_contacts,
+#'   language_tokens = language_tokens
 #' )
 #' }
-clean_contacts_of_contacts_vax_history <- function(contacts_of_contacts) {
+clean_contacts_of_contacts_vax_history <- function(contacts_of_contacts,
+                                                   language_tokens) {
 
   coc_vacc_hist <- dplyr::filter(
     .data = contacts_of_contacts,
@@ -47,14 +58,9 @@ clean_contacts_of_contacts_vax_history <- function(contacts_of_contacts) {
     tolower
   )
 
-  coc_vacc_hist <- dplyr::mutate(
-    .data = coc_vacc_hist,
-    vaccinesreceived_vaccine = sub(".*VACCINE_", "", vaccinesreceived_vaccine)
-  )
-
-  coc_vacc_hist <- dplyr::mutate(
-    .data = coc_vacc_hist,
-    vaccinesreceived_status = sub(".*STATUS_", "", vaccinesreceived_status)
+  coc_vacc_hist <- translate_categories(
+    data = coc_vacc_hist,
+    language_tokens = language_tokens
   )
 
   coc_vacc_hist <- dplyr::mutate_at(
diff --git a/man/clean_contacts_of_contacts_vax_history.Rd b/man/clean_contacts_of_contacts_vax_history.Rd
index 43cb262..fd355e1 100644
--- a/man/clean_contacts_of_contacts_vax_history.Rd
+++ b/man/clean_contacts_of_contacts_vax_history.Rd
@@ -4,11 +4,14 @@
 \alias{clean_contacts_of_contacts_vax_history}
 \title{Cleans vaccination data from contacts of contacts data}
 \usage{
-clean_contacts_of_contacts_vax_history(contacts_of_contacts)
+clean_contacts_of_contacts_vax_history(contacts_of_contacts, language_tokens)
 }
 \arguments{
 \item{contacts_of_contacts}{A \code{tibble} with address information from contacts
 of contacts data.}
+
+\item{language_tokens}{A tibble of language tokens returned by
+\code{\link[=get_language_tokens]{get_language_tokens()}} to translate the string tokens in the data.}
 }
 \value{
 A \code{tibble} with cleaned and un-nested vaccination history data.
@@ -32,8 +35,16 @@ contacts_of_contacts <- get_contacts_of_contacts(
   outbreak_id = outbreak_id
 )
 
+language_tokens <- get_language_tokens(
+  url = url,
+  username = username,
+  password = password,
+  language = "english_us"
+)
+
 vax_history <- clean_contacts_of_contacts_vax_history(
-  contacts_of_contacts = contacts_of_contacts
+  contacts_of_contacts = contacts_of_contacts,
+  language_tokens = language_tokens
 )
 }
 }
diff --git a/tests/testthat/test-clean_contacts_of_contacts_vax_history.R b/tests/testthat/test-clean_contacts_of_contacts_vax_history.R
index e537ec7..425c116 100644
--- a/tests/testthat/test-clean_contacts_of_contacts_vax_history.R
+++ b/tests/testthat/test-clean_contacts_of_contacts_vax_history.R
@@ -8,8 +8,16 @@ test_that("clean_contacts_of_contacts_vax_history works as expected", {
     outbreak_id = outbreak_id
   )
 
+  language_tokens <- get_language_tokens(
+    url = url,
+    username = username,
+    password = password,
+    language = "english_us"
+  )
+
   res <- clean_contacts_of_contacts_vax_history(
-    contacts_of_contacts = contacts_of_contacts
+    contacts_of_contacts = contacts_of_contacts,
+    language_tokens = language_tokens
   )
 
   expect_s3_class(res, "tbl_df")

From ae4a7e58d38818fa9511253ccb31d6b58da1c9ec Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 6 Apr 2023 17:17:57 +0100
Subject: [PATCH 192/203] removing extra #' in clean_case_vax_history

---
 R/clean_case_vax_history.R    | 2 +-
 man/clean_case_vax_history.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/clean_case_vax_history.R b/R/clean_case_vax_history.R
index 3c30f58..9201fbb 100644
--- a/R/clean_case_vax_history.R
+++ b/R/clean_case_vax_history.R
@@ -11,7 +11,7 @@
 #' @export
 #'
 #' @examples
-#' #' \dontrun{
+#' \dontrun{
 #' url <- "https://MyGoDataServer.com/"
 #' username <- "myemail@email.com"
 #' password <- "mypassword"
diff --git a/man/clean_case_vax_history.Rd b/man/clean_case_vax_history.Rd
index 710d73d..5b3121e 100644
--- a/man/clean_case_vax_history.Rd
+++ b/man/clean_case_vax_history.Rd
@@ -20,7 +20,7 @@ Cleans and un-nests vaccination history, where vaccination is
 complete, from case data. Case data is returned from \code{\link[=get_cases]{get_cases()}}.
 }
 \examples{
-#' \dontrun{
+\dontrun{
 url <- "https://MyGoDataServer.com/"
 username <- "myemail@email.com"
 password <- "mypassword"

From 77c0665a5e6b8b24295e8769cec6b21eb88a5571 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Thu, 6 Apr 2023 17:36:53 +0100
Subject: [PATCH 193/203] used translation function in
 clean_contacts_of_contacts (function fails)

---
 R/clean_contacts_of_contacts.R    | 47 ++++++++++++++++---------------
 man/clean_contacts_of_contacts.Rd | 30 ++++++++++++++------
 2 files changed, 47 insertions(+), 30 deletions(-)

diff --git a/R/clean_contacts_of_contacts.R b/R/clean_contacts_of_contacts.R
index c9c6444..1c25de8 100644
--- a/R/clean_contacts_of_contacts.R
+++ b/R/clean_contacts_of_contacts.R
@@ -11,16 +11,18 @@
 #' @param contacts_of_contacts_vacc_history_clean A `tibble` containing the
 #' cleaned vaccination history from contacts of contacts (data is cleaned by
 #' [`clean_contacts_of_contacts_vax_history()`]).
+#' @param language_tokens A tibble of language tokens returned by
+#' [`get_language_tokens()`] to translate the string tokens in the data.
 #'
 #' @return A `tibble` containing the cleaned contacts of contacts data.
 #' @export
 #'
 #' @examples
 #' \dontrun{
-#'   url <- "https://MyGoDataServer.com/"
-#'   username <- "myemail@email.com"
-#'   password <- "mypassword"
-#'   outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 #'
 #' contacts_of_contacts <- get_contacts_of_contacts(
 #'   url = url,
@@ -37,24 +39,35 @@
 #'
 #' locations_clean <- clean_locations(locations = locations)
 #'
+#' language_tokens <- get_language_tokens(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   language = "english_us"
+#' )
+#'
 #' contacts_of_contacts_address_history_clean <- clean_contacts_of_contacts_address_history(
 #'   contacts_of_contacts = contacts_of_contacts,
-#'   locations_clean = locations_clean
+#'   locations_clean = locations_clean,
+#'   language_tokens = language_tokens
 #' )
 #'
 #' contacts_of_contacts_vacc_history_clean <- clean_contacts_of_contacts_vax_history(
-#'   contacts_of_contacts = contacts_of_contacts
+#'   contacts_of_contacts = contacts_of_contacts,
+#'   language_tokens = language_tokens
 #' )
 #'
 #' contacts_of_contacts_clean <- clean_contacts_of_contacts(
 #'   contacts_of_contacts = contacts_of_contacts,
 #'   contacts_of_contacts_address_history_clean = contacts_of_contacts_address_history_clean,
-#'   contacts_of_contacts_vacc_history_clean = contacts_of_contacts_vacc_history_clean
+#'   contacts_of_contacts_vacc_history_clean = contacts_of_contacts_vacc_history_clean,
+#'   language_tokens = language_tokens
 #' )
 #' }
 clean_contacts_of_contacts <- function(contacts_of_contacts,
                                        contacts_of_contacts_address_history_clean,
-                                       contacts_of_contacts_vacc_history_clean) {
+                                       contacts_of_contacts_vacc_history_clean,
+                                       language_tokens) {
 
   # Remove all deleted records
   coc_clean <- dplyr::filter(
@@ -103,24 +116,14 @@ clean_contacts_of_contacts <- function(contacts_of_contacts,
   )
 
   #  truncate responses of categorical vars so easier to read
-  coc_clean <- dplyr::mutate(
-    .data = coc_clean,
-    classification = sub(".*CLASSIFICATION_", "", classification),
-    gender = sub(".*GENDER_", "", gender),
-    occupation = sub(".*OCCUPATION_", "", occupation),
-    outcome = sub(".*OUTCOME_", "", outcome_id),
-    pregnancy_status = sub(".*STATUS_", "", pregnancy_status),
-    risk_level = sub(".*LEVEL_", "", risk_level),
-    relationship_certainty_level = sub(".*LEVEL_", "", relationship_certainty_level_id),
-    relationship_exposure_type = sub(".*TYPE_", "", relationship_exposure_type_id),
-    relationship_context_of_transmission = sub(".*TRANSMISSION_", "", relationship_social_relationship_type_id),
-    relationship_exposure_frequency = sub(".*FREQUENCY_", "", relationship_exposure_frequency_id),
-    relationship_exposure_duration = sub(".*DURATION_", "", relationship_exposure_duration_id)
+  coc_clean <- translate_categories(
+    data = coc_clean,
+    language_tokens = language_tokens
   )
 
   contacts_of_contacts_address_history_clean <- dplyr::filter(
     .data = contacts_of_contacts_address_history_clean,
-    addresses_typeid == "USUAL_PLACE_OF_RESIDENCE"
+    addresses_typeid == "Current address"
   )
 
   # join in current address from address history, only current place of
diff --git a/man/clean_contacts_of_contacts.Rd b/man/clean_contacts_of_contacts.Rd
index 2cada00..1b31a65 100644
--- a/man/clean_contacts_of_contacts.Rd
+++ b/man/clean_contacts_of_contacts.Rd
@@ -7,7 +7,8 @@
 clean_contacts_of_contacts(
   contacts_of_contacts,
   contacts_of_contacts_address_history_clean,
-  contacts_of_contacts_vacc_history_clean
+  contacts_of_contacts_vacc_history_clean,
+  language_tokens
 )
 }
 \arguments{
@@ -21,6 +22,9 @@ cleaned address history data from contacts of contacts (data is cleaned by
 \item{contacts_of_contacts_vacc_history_clean}{A \code{tibble} containing the
 cleaned vaccination history from contacts of contacts (data is cleaned by
 \code{\link[=clean_contacts_of_contacts_vax_history]{clean_contacts_of_contacts_vax_history()}}).}
+
+\item{language_tokens}{A tibble of language tokens returned by
+\code{\link[=get_language_tokens]{get_language_tokens()}} to translate the string tokens in the data.}
 }
 \value{
 A \code{tibble} containing the cleaned contacts of contacts data.
@@ -31,10 +35,10 @@ contacts data is returned by \code{\link[=get_contacts_of_contacts]{get_contacts
 }
 \examples{
 \dontrun{
-  url <- "https://MyGoDataServer.com/"
-  username <- "myemail@email.com"
-  password <- "mypassword"
-  outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 
 contacts_of_contacts <- get_contacts_of_contacts(
   url = url,
@@ -51,19 +55,29 @@ locations <- get_locations(
 
 locations_clean <- clean_locations(locations = locations)
 
+language_tokens <- get_language_tokens(
+  url = url,
+  username = username,
+  password = password,
+  language = "english_us"
+)
+
 contacts_of_contacts_address_history_clean <- clean_contacts_of_contacts_address_history(
   contacts_of_contacts = contacts_of_contacts,
-  locations_clean = locations_clean
+  locations_clean = locations_clean,
+  language_tokens = language_tokens
 )
 
 contacts_of_contacts_vacc_history_clean <- clean_contacts_of_contacts_vax_history(
-  contacts_of_contacts = contacts_of_contacts
+  contacts_of_contacts = contacts_of_contacts,
+  language_tokens = language_tokens
 )
 
 contacts_of_contacts_clean <- clean_contacts_of_contacts(
   contacts_of_contacts = contacts_of_contacts,
   contacts_of_contacts_address_history_clean = contacts_of_contacts_address_history_clean,
-  contacts_of_contacts_vacc_history_clean = contacts_of_contacts_vacc_history_clean
+  contacts_of_contacts_vacc_history_clean = contacts_of_contacts_vacc_history_clean,
+  language_tokens = language_tokens
 )
 }
 }

From 3e4d5020b95854d092a40fba61b929e05b11d7cd Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 14 Apr 2023 11:48:03 +0100
Subject: [PATCH 194/203] added janitor as package dependency

---
 DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ef8a27d..d45210b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -28,7 +28,8 @@ Imports:
     stringr,
     tibble,
     tidyr,
-    urltools
+    urltools,
+    janitor
 Suggests:
     devtools,
     testthat (>= 3.0.0)

From dedc9dfb59520988b39ca665c61f269a41413bad Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 14 Apr 2023 12:20:14 +0100
Subject: [PATCH 195/203] used translation function in clean_contacts

---
 R/clean_contacts.R | 141 ++++++++++++++++++++++++++-------------------
 1 file changed, 81 insertions(+), 60 deletions(-)

diff --git a/R/clean_contacts.R b/R/clean_contacts.R
index d2907d8..5e8bd37 100644
--- a/R/clean_contacts.R
+++ b/R/clean_contacts.R
@@ -19,57 +19,79 @@
 #'
 #' @examples
 #' \dontrun{
-#'   url <- "https://MyGoDataServer.com/"
-#'   username <- "myemail@email.com"
-#'   password <- "mypassword"
-#'   outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+#' url <- "https://MyGoDataServer.com/"
+#' username <- "myemail@email.com"
+#' password <- "mypassword"
+#' outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 #'
-#'   contacts <- get_contacts(
-#'     url = url,
-#'     username = username,
-#'     password = password,
-#'     outbreak_id = outbreak_id
-#'   )
+#' contacts <- get_contacts(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
 #'
-#'   locations <- get_locations(
-#'     url = url,
-#'     username = username,
-#'     password = password
-#'   )
+#' locations <- get_locations(
+#'   url = url,
+#'   username = username,
+#'   password = password
+#' )
 #'
-#'   locations_clean <- clean_locations(locations = locations)
+#' locations_clean <- clean_locations(locations = locations)
 #'
-#'   # other cleaned data required for `clean_contacts()`
-#'   contacts_vacc_history_clean <- clean_contact_vax_history(contacts = contacts)
-#'   contacts_address_history_clean <- clean_contact_address_history(
-#'     contacts = contacts,
-#'     locations_clean = locations_clean
-#'   )
+#' language_tokens <- get_language_tokens(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   language = "english_us"
+#' )
 #'
-#'   cases <- get_cases(
-#'     url = url,
-#'     username = username,
-#'     password = password,
-#'     outbreak_id = outbreak_id
-#'   )
-#'   cases_address_history_clean <- clean_case_address_history(cases = cases)
-#'   cases_vacc_history_clean <- clean_case_vax_history(cases = cases)
-#'   cases_dateranges_history_clean <- clean_case_med_history(cases = cases)
+#' # other cleaned data required for `clean_contacts()`
+#' contacts_vacc_history_clean <- clean_contact_vax_history(
+#'   contacts = contacts,
+#'   language_tokens = language_tokens
+#' )
+#' contacts_address_history_clean <- clean_contact_address_history(
+#'   contacts = contacts,
+#'   locations_clean = locations_clean,
+#'   language_tokens = language_tokens
+#' )
 #'
-#'   cases_clean <- clean_cases(
-#'     cases = cases,
-#'     cases_address_history_clean = cases_address_history_clean,
-#'     cases_vacc_history_clean = cases_vacc_history_clean,
-#'     cases_dateranges_history_clean = cases_dateranges_history_clean
-#'   )
-#'   contacts_becoming_cases <- cases_from_contacts(cases_clean = cases_clean)
+#' cases <- get_cases(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   outbreak_id = outbreak_id
+#' )
+#' cases_address_history_clean <- clean_case_address_history(
+#'   cases = cases,
+#'   locations_clean = locations_clean,
+#'   language_tokens = language_tokens
+#' )
+#' cases_vacc_history_clean <- clean_case_vax_history(
+#'   cases = cases,
+#'   language_tokens = language_tokens
+#' )
+#' cases_dateranges_history_clean <- clean_case_med_history(
+#'   cases = cases,
+#'   language_tokens = language_tokens
+#' )
 #'
-#'   contacts_clean <- clean_contacts(
-#'     contacts = contacts,
-#'     contacts_address_history_clean = cases_address_history_clean,
-#'     contacts_vacc_history_clean = cases_vacc_history_clean,
-#'     contacts_becoming_cases = contacts_becoming_cases
-#'   )
+#' cases_clean <- clean_cases(
+#'   cases = cases,
+#'   cases_address_history_clean = cases_address_history_clean,
+#'   cases_vacc_history_clean = cases_vacc_history_clean,
+#'   cases_dateranges_history_clean = cases_dateranges_history_clean,
+#'   language_tokens = language_tokens
+#' )
+#' contacts_becoming_cases <- cases_from_contacts(cases_clean = cases_clean)
+#'
+#' contacts_clean <- clean_contacts(
+#'   contacts = contacts,
+#'   contacts_address_history_clean = cases_address_history_clean,
+#'   contacts_vacc_history_clean = cases_vacc_history_clean,
+#'   contacts_becoming_cases = contacts_becoming_cases
+#' )
 #' }
 clean_contacts <- function(contacts,
                            contacts_address_history_clean,
@@ -145,26 +167,25 @@ clean_contacts <- function(contacts,
     datetime_created_at = as.POSIXct(datetime_created_at, format = "%Y-%m-%dT%H:%M")
   )
 
-  #  truncate responses of categorical vars so easier to read
-  contacts_clean <- dplyr::mutate(
+  # translate responses of categorical vars so easier to read
+  contacts_clean <- translate_categories(
+    data = contacts_clean,
+    language_tokens = language_tokens
+  )
+
+  contacts_clean <- dplyr::rename(
     .data = contacts_clean,
-    classification = sub(".*CLASSIFICATION_", "", classification),
-    gender = sub(".*GENDER_", "", gender),
-    occupation = sub(".*OCCUPATION_", "", occupation),
-    outcome = sub(".*OUTCOME_", "", outcome_id),
-    pregnancy_status = sub(".*STATUS_", "", pregnancy_status),
-    risk_level = sub(".*LEVEL_", "", risk_level),
-    follow_up_status = sub(".*TYPE_", "", follow_up_status),
-    relationship_certainty_level = sub(".*LEVEL_", "", relationship_certainty_level_id),
-    relationship_exposure_type = sub(".*TYPE_", "", relationship_exposure_type_id),
-    relationship_context_of_transmission = sub(".*TRANSMISSION_", "", relationship_social_relationship_type_id),
-    relationship_exposure_frequency = sub(".*FREQUENCY_", "", relationship_exposure_frequency_id),
-    relationship_exposure_duration = sub(".*DURATION_", "", relationship_exposure_duration_id)
+    outcome = "outcome_id",
+    relationship_certainty_level = "relationship_certainty_level_id",
+    relationship_exposure_type = "relationship_exposure_type_id",
+    relationship_context_of_transmission = "relationship_social_relationship_type_id",
+    relationship_exposure_frequency = "relationship_exposure_frequency_id",
+    relationship_exposure_duration = "relationship_exposure_duration_id"
   )
 
   contacts_address_history_clean <- dplyr::filter(
     .data = contacts_address_history_clean,
-    addresses_typeid == "USUAL_PLACE_OF_RESIDENCE"
+    addresses_typeid == "Current address"
   )
 
   # join in current address from address history, only current place of residence
@@ -177,7 +198,7 @@ clean_contacts <- function(contacts,
   # join in info from vacc block
   contacts_clean <- dplyr::mutate(
     .data = contacts_clean,
-    vaccinated = case_when(id %in% contacts_vacc_history_clean$id[contacts_vacc_history_clean$vaccinesreceived_status == "VACCINATED"] ~ TRUE, TRUE ~ FALSE)
+    vaccinated = case_when(id %in% contacts_vacc_history_clean$id[contacts_vacc_history_clean$vaccinesreceived_status == "Vaccinated"] ~ TRUE, TRUE ~ FALSE)
   )
 
   # force NA ages to appear as NA, not as 0 like sometimes occurs

From dd93982af4d15fbc396be0c273dafbfdad0b03df Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 14 Apr 2023 12:20:28 +0100
Subject: [PATCH 196/203] added test for clean_contacts

---
 tests/testthat/test-clean_contacts.R | 104 +++++++++++++++++++++++++++
 1 file changed, 104 insertions(+)
 create mode 100644 tests/testthat/test-clean_contacts.R

diff --git a/tests/testthat/test-clean_contacts.R b/tests/testthat/test-clean_contacts.R
new file mode 100644
index 0000000..d3e1d5f
--- /dev/null
+++ b/tests/testthat/test-clean_contacts.R
@@ -0,0 +1,104 @@
+test_that("clean_contacts works as expected", {
+  skip("get_contacts requires API call")
+
+  contacts <- get_contacts(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+
+  locations <- get_locations(
+    url = url,
+    username = username,
+    password = password
+  )
+
+  locations_clean <- clean_locations(locations = locations)
+
+  language_tokens <- get_language_tokens(
+    url = url,
+    username = username,
+    password = password,
+    language = "english_us"
+  )
+
+  # other cleaned data required for `clean_contacts()`
+  contacts_vacc_history_clean <- clean_contact_vax_history(
+    contacts = contacts,
+    language_tokens = language_tokens
+  )
+  contacts_address_history_clean <- clean_contact_address_history(
+    contacts = contacts,
+    locations_clean = locations_clean,
+    language_tokens = language_tokens
+  )
+
+  cases <- get_cases(
+    url = url,
+    username = username,
+    password = password,
+    outbreak_id = outbreak_id
+  )
+  cases_address_history_clean <- clean_case_address_history(
+    cases = cases,
+    locations_clean = locations_clean,
+    language_tokens = language_tokens
+  )
+  cases_vacc_history_clean <- clean_case_vax_history(
+    cases = cases,
+    language_tokens = language_tokens
+  )
+  cases_dateranges_history_clean <- clean_case_med_history(
+    cases = cases,
+    language_tokens = language_tokens
+  )
+
+  cases_clean <- clean_cases(
+    cases = cases,
+    cases_address_history_clean = cases_address_history_clean,
+    cases_vacc_history_clean = cases_vacc_history_clean,
+    cases_dateranges_history_clean = cases_dateranges_history_clean,
+    language_tokens = language_tokens
+  )
+  contacts_becoming_cases <- cases_from_contacts(cases_clean = cases_clean)
+
+  res <- clean_contacts(
+    contacts = contacts,
+    contacts_address_history_clean = cases_address_history_clean,
+    contacts_vacc_history_clean = cases_vacc_history_clean,
+    contacts_becoming_cases = contacts_becoming_cases
+  )
+
+  expect_s3_class(res, "tbl_df")
+  expect_s3_class(res, "data.frame")
+  expect_identical(dim(res), c(19L, 48L))
+  expect_true(
+    all(c(
+      "id", "visual_id", "classification", "follow_up_status", "first_name",
+      "middle_name", "last_name", "gender", "age", "age_class", "occupation",
+      "pregnancy_status", "date_of_reporting", "date_of_last_contact",
+      "date_of_burial", "date_of_follow_up_start", "date_of_follow_up_end",
+      "was_case", "risk_level", "risk_reason", "safe_burial",
+      "transfer_refused", "responsible_user_id", "follow_up_team_id",
+      "admin_0_name", "admin_1_name", "admin_2_name", "lat", "long", "address",
+      "postal_code", "city", "telephone", "email", "vaccinated", "outcome",
+      "date_of_outcome", "relationship_exposure_type",
+      "relationship_context_of_transmission", "relationship_exposure_duration",
+      "relationship_exposure_frequency", "relationship_certainty_level",
+      "relationship_cluster_id", "location_id", "created_by",
+      "datetime_created_at", "updated_by", "datetime_updated_at"
+    ) %in% colnames(res))
+  )
+
+  expect_identical(
+    unname(sapply(res[1, ], function(x) class(x)[1])),
+    c(
+      rep("character", 8), "numeric", "factor", "character", "character",
+      rep("Date", 5), "logical", "character", "character", "logical", "logical",
+      rep("character", 5), "numeric", "numeric", rep("character", 5), "logical",
+      "character", "Date", rep("character", 5), "logical", "character",
+      "character", "POSIXct", "character", "POSIXct"
+    )
+  )
+})

From 31734f813e3358333273aa5de67a5f616122112b Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 14 Apr 2023 13:58:27 +0100
Subject: [PATCH 197/203] updated clean_events function and test

---
 R/clean_events.R                   |  2 +-
 tests/testthat/test-clean_events.R | 33 ++++++++++++++++++++++--------
 2 files changed, 26 insertions(+), 9 deletions(-)

diff --git a/R/clean_events.R b/R/clean_events.R
index 7bd02fa..1288477 100644
--- a/R/clean_events.R
+++ b/R/clean_events.R
@@ -96,7 +96,7 @@ clean_events <- function(events,
     "date", # dates
     "date_of_reporting", # dates
     "description",
-    "responsible_user_id", # assigned contact tracer
+    "responsible_user", # assigned contact tracer
     matches("^admin_.*name$"),
     lat = "address_geo_location_lat", # address
     long = "address_geo_location_lng", # address
diff --git a/tests/testthat/test-clean_events.R b/tests/testthat/test-clean_events.R
index 90cd59c..96b71e4 100644
--- a/tests/testthat/test-clean_events.R
+++ b/tests/testthat/test-clean_events.R
@@ -1,28 +1,45 @@
 test_that("clean_events works as expected", {
   skip("get_events requires API call")
 
-  res <- get_events(
+  events <- get_events(
     url = url,
     username = username,
     password = password,
     outbreak_id = outbreak_id
   )
-  res <- clean_events(events = res)
+
+  locations <- get_locations(
+    url = url,
+    username = username,
+    password = password
+  )
+  locations_clean <- clean_locations(locations = locations)
+
+  res <- clean_events(
+    events = events,
+    locations_clean = locations_clean
+  )
 
   expect_s3_class(res, "tbl_df")
   expect_s3_class(res, "data.frame")
-  expect_identical(dim(res), c(3L, 15L))
+  expect_identical(dim(res), c(3L, 21L))
   expect_true(
     all(c(
-      "id", "name", "user_ids_1", "user_ids_2", "user_ids_3", "user_ids_4",
-      "user_ids_5", "location_ids_1", "location_ids_2", "location_ids_3",
-      "location_ids_4", "created_by", "datetime_created_at", "updated_by",
+      "id", "name", "date", "date_of_reporting", "description",
+      "responsible_user", "admin_0_name", "admin_1_name", "admin_2_name", "lat",
+      "long", "address", "postal_code", "city", "telephone", "email",
+      "location_id", "created_by", "datetime_created_at", "updated_by",
       "datetime_updated_at"
     ) %in% colnames(res))
   )
 
   expect_identical(
-    unname(sapply(res[1, ], class)),
-    rep("character", 15)
+    unname(sapply(res[1, ], function(x) class(x)[1])),
+    c(
+      "character", "character", "character", "Date", "logical", "logical",
+      "character", "character", "character", "numeric", "numeric", "logical",
+      "logical", "logical", "logical", "logical", "character", "character",
+      "POSIXct", "character", "POSIXct"
+    )
   )
 })

From 00762473e217367ddc8a40547ef4161967a0322d Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 14 Apr 2023 14:22:56 +0100
Subject: [PATCH 198/203] used translation function for clean_followups and
 updated test

---
 R/clean_followups.R                   | 29 ++++++++++++++++++++-------
 tests/testthat/test-clean_followups.R | 12 +++++++++--
 2 files changed, 32 insertions(+), 9 deletions(-)

diff --git a/R/clean_followups.R b/R/clean_followups.R
index 056d604..1be33d5 100644
--- a/R/clean_followups.R
+++ b/R/clean_followups.R
@@ -41,18 +41,28 @@
 #'
 #' locations_clean <- clean_locations(locations = locations)
 #'
+#' language_tokens <- get_language_tokens(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   language = "english_us"
+#' )
+#'
 #' contacts_address_history_clean <- clean_contact_address_history(
 #'   contacts = contacts,
-#'   locations_clean = locations_clean
+#'   locations_clean = locations_clean,
+#'   language_tokens = language_tokens
 #' )
 #'
 #' followups_clean <- clean_followups(
 #'   followups = followups,
-#'   contacts_address_history_clean = contacts_address_history_clean
+#'   contacts_address_history_clean = contacts_address_history_clean,
+#'   language_tokens = language_tokens
 #' )
 #' }
 clean_followups <- function(followups,
-                            contacts_address_history_clean) {
+                            contacts_address_history_clean,
+                            language_tokens) {
 
   # Remove all deleted records
   followups_clean <- dplyr::filter(
@@ -105,15 +115,20 @@ clean_followups <- function(followups,
     datetime_created_at = as.POSIXct(datetime_created_at, format = "%Y-%m-%dT%H:%M")
   )
 
-  #  truncate responses of categorical vars so easier to read
-  followups_clean <- dplyr::mutate(
+  # translate responses of categorical vars so easier to read
+  followups_clean <- translate_categories(
+    data = followups_clean,
+    language_tokens = language_tokens
+  )
+
+  followups_clean <- dplyr::rename(
     .data = followups_clean,
-    followup_status = sub(".*TYPE_", "", status_id)
+    followup_status = "status_id"
   )
 
   contacts_address_history_clean <- dplyr::filter(
     .data = contacts_address_history_clean,
-    addresses_typeid == "USUAL_PLACE_OF_RESIDENCE"
+    addresses_typeid == "Current address"
   )
 
   followups_clean <- dplyr::left_join(
diff --git a/tests/testthat/test-clean_followups.R b/tests/testthat/test-clean_followups.R
index 630f7d4..85724d5 100644
--- a/tests/testthat/test-clean_followups.R
+++ b/tests/testthat/test-clean_followups.R
@@ -23,9 +23,17 @@ test_that("clean_followups works as expected", {
 
   locations_clean <- clean_locations(locations = locations)
 
+  language_tokens <- get_language_tokens(
+    url = url,
+    username = username,
+    password = password,
+    language = "english_us"
+  )
+
   contacts_address_history_clean <- clean_contact_address_history(
     contacts = contacts,
-    locations_clean = locations_clean
+    locations_clean = locations_clean,
+    language_tokens = language_tokens
   )
 
   res <- clean_followups(
@@ -35,7 +43,7 @@ test_that("clean_followups works as expected", {
 
   expect_s3_class(res, "tbl_df")
   expect_s3_class(res, "data.frame")
-  expect_identical(dim(res), c(49L, 24L))
+  expect_identical(dim(res), c(172L, 24L))
   expect_true(
     all(c(
       "id", "contact_id", "contact_visual_id", "date", "followup_number",

From 2569f9f78008f7ff1e815adcf77a7f71827e0f8a Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 14 Apr 2023 14:30:29 +0100
Subject: [PATCH 199/203] used translation function in clean_locations and
 updated test

---
 R/clean_locations.R                   | 21 +++++++++++++++++----
 tests/testthat/test-clean_locations.R | 12 ++++++++++--
 2 files changed, 27 insertions(+), 6 deletions(-)

diff --git a/R/clean_locations.R b/R/clean_locations.R
index 1c5afba..49bf1f3 100644
--- a/R/clean_locations.R
+++ b/R/clean_locations.R
@@ -21,9 +21,17 @@
 #'   password = password
 #' )
 #'
-#' clean_locations(locations = locations)
+#' language_tokens <- get_language_tokens(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   language = "english_us"
+#' )
+#'
+#' clean_locations(locations = locations, language_tokens = language_tokens)
 #' }
-clean_locations <- function(locations) {
+clean_locations <- function(locations,
+                            language_tokens) {
 
   # filter out delete and inactive (or NA) values
   clean_locations <- dplyr::filter(
@@ -35,10 +43,15 @@ clean_locations <- function(locations) {
     .data$active == TRUE | is.na(.data$active)
   )
 
+  clean_locations <- translate_categories(
+    data = clean_locations,
+    language_tokens = language_tokens
+  )
+
   # add admin-level column
-  clean_locations <- dplyr::mutate(
+  clean_locations <- dplyr::rename(
     .data = clean_locations,
-    admin_level = sub(".*LEVEL_", "", .data$geographicalLevelId)
+    admin_level = "geographicalLevelId"
   )
 
   # select columns
diff --git a/tests/testthat/test-clean_locations.R b/tests/testthat/test-clean_locations.R
index 9e6648c..95b6824 100644
--- a/tests/testthat/test-clean_locations.R
+++ b/tests/testthat/test-clean_locations.R
@@ -1,12 +1,20 @@
 test_that("clean_locations works as expected", {
   skip("get_locations requires API call")
 
-  res <- get_locations(
+  locations <- get_locations(
     url = url,
     username = username,
     password = password
   )
-  res <- clean_locations(locations = res)
+
+  language_tokens <- get_language_tokens(
+    url = url,
+    username = username,
+    password = password,
+    language = "english_us"
+  )
+
+  res <- clean_locations(locations = locations, language_tokens = language_tokens)
 
   expect_s3_class(res, "tbl_df")
   expect_s3_class(res, "data.frame")

From ac142b39784010eedf03b3c8f28e050fd2f7b46b Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 14 Apr 2023 14:38:39 +0100
Subject: [PATCH 200/203] used translation function in clean_relationships and
 updated test

---
 R/clean_relationships.R                   | 24 ++++++++++++++++-------
 tests/testthat/test-clean_relationships.R | 15 ++++++++++++--
 2 files changed, 30 insertions(+), 9 deletions(-)

diff --git a/R/clean_relationships.R b/R/clean_relationships.R
index c0cc883..afbe7d5 100644
--- a/R/clean_relationships.R
+++ b/R/clean_relationships.R
@@ -23,9 +23,20 @@
 #'   outbreak_id = outbreak_id
 #' )
 #'
-#' clean_relationships <- clean_relationships(relationships)
+#' language_tokens <- get_language_tokens(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   language = "english_us"
+#' )
+#'
+#' clean_relationships <- clean_relationships(
+#'   relationships,
+#'   language_tokens = language_tokens
+#' )
 #' }
-clean_relationships <- function(relationships) {
+clean_relationships <- function(relationships,
+                                language_tokens) {
 
   # Remove all deleted records
   clean_relationships <- dplyr::filter(
@@ -77,11 +88,10 @@ clean_relationships <- function(relationships) {
     )
   )
 
-  #  truncate responses of categorical vars so easier to read
-  clean_relationships <- dplyr::mutate(
-    .data = clean_relationships,
-    source_person_type = sub(".*TYPE_", "", source_person_type),
-    target_person_type = sub(".*TYPE_", "", target_person_type)
+  # translate responses of categorical vars so easier to read
+  clean_relationships <- translate_categories(
+    data = clean_relationships,
+    language_tokens = language_tokens
   )
 
   # organize order of vars, only bring in what we need, take away confusing vars
diff --git a/tests/testthat/test-clean_relationships.R b/tests/testthat/test-clean_relationships.R
index 6fff74c..3fcac36 100644
--- a/tests/testthat/test-clean_relationships.R
+++ b/tests/testthat/test-clean_relationships.R
@@ -7,11 +7,22 @@ test_that("clean_relationships works as expected", {
     password = password,
     outbreak_id = outbreak_id
   )
-  res <- clean_relationships(relationships = relationships)
+
+  language_tokens <- get_language_tokens(
+    url = url,
+    username = username,
+    password = password,
+    language = "english_us"
+  )
+
+  res <- clean_relationships(
+    relationships = relationships,
+    language_tokens = language_tokens
+  )
 
   expect_s3_class(res, "tbl_df")
   expect_s3_class(res, "data.frame")
-  expect_identical(dim(res), c(28L, 11L))
+  expect_identical(dim(res), c(29L, 11L))
   expect_true(
     all(c(
       "id", "source_person_id", "source_person_visual_id", "target_person_id",

From fdcb33ad48798c13128ac5bfe8de4c5bde015fe7 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 14 Apr 2023 16:00:19 +0100
Subject: [PATCH 201/203] updated clean_teams test

---
 tests/testthat/test-clean_teams.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-clean_teams.R b/tests/testthat/test-clean_teams.R
index ff8a10f..5ca4029 100644
--- a/tests/testthat/test-clean_teams.R
+++ b/tests/testthat/test-clean_teams.R
@@ -6,7 +6,7 @@ test_that("clean_teams works as expected", {
 
   expect_s3_class(res, "tbl_df")
   expect_s3_class(res, "data.frame")
-  expect_identical(dim(res), c(4L, 15L))
+  expect_identical(dim(res), c(5L, 15L))
   expect_true(
     all(c(
       "id", "name", "user_ids_1", "user_ids_2", "user_ids_3", "user_ids_4",

From 5bb71f6bac8d1eb8e12e855a6772103c0260a698 Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 14 Apr 2023 16:05:44 +0100
Subject: [PATCH 202/203] used translation function in clean_users and updated
 test

---
 R/clean_users.R                   | 20 ++++++++++++++------
 tests/testthat/test-clean_users.R | 10 +++++++++-
 2 files changed, 23 insertions(+), 7 deletions(-)

diff --git a/R/clean_users.R b/R/clean_users.R
index cca13d3..7bc15c9 100644
--- a/R/clean_users.R
+++ b/R/clean_users.R
@@ -21,9 +21,17 @@
 #'   password = password
 #' )
 #'
-#' clean_users <- clean_users(users)
+#' language_tokens <- get_language_tokens(
+#'   url = url,
+#'   username = username,
+#'   password = password,
+#'   language = "english_us"
+#' )
+#'
+#' clean_users <- clean_users(users = users, language_tokens = language_tokens)
 #' }
-clean_users <- function(users) {
+clean_users <- function(users,
+                        language_tokens) {
 
   # standardize column name syntax
   clean_users <- janitor::clean_names(users)
@@ -43,10 +51,10 @@ clean_users <- function(users) {
 
   clean_users <- tidyr::unnest_wider(clean_users, "role_ids", names_sep = "_")
 
-  #  truncate responses of categorical vars so easier to read
-  clean_users <- dplyr::mutate(
-    clean_users,
-    institution_name = sub(".*NAME_", "", .data$institution_name)
+  # translate responses of categorical vars so easier to read
+  clean_users <- translate_categories(
+    data = clean_users,
+    language_tokens = language_tokens
   )
 
   # organize order of vars, only bring in what we need, take away confusing vars
diff --git a/tests/testthat/test-clean_users.R b/tests/testthat/test-clean_users.R
index 876963a..338b16c 100644
--- a/tests/testthat/test-clean_users.R
+++ b/tests/testthat/test-clean_users.R
@@ -2,7 +2,15 @@ test_that("clean_users works as expected", {
   skip("get_users requires API call")
 
   users <- get_users(url = url, username = username, password = password)
-  res <- clean_users(users = users)
+
+  language_tokens <- get_language_tokens(
+    url = url,
+    username = username,
+    password = password,
+    language = "english_us"
+  )
+
+  res <- clean_users(users = users, language_tokens = language_tokens)
 
   expect_s3_class(res, "tbl_df")
   expect_s3_class(res, "data.frame")

From f6daa6f47397d84087c200bbd8bf3bcc28ed72bd Mon Sep 17 00:00:00 2001
From: Joshua Lambert <joshua.lambert@lshtm.ac.uk>
Date: Fri, 14 Apr 2023 16:06:34 +0100
Subject: [PATCH 203/203] updated examples in documentation

---
 man/clean_contacts.Rd      | 110 ++++++++++++++++++++++---------------
 man/clean_followups.Rd     |  15 ++++-
 man/clean_locations.Rd     |  11 +++-
 man/clean_relationships.Rd |  14 ++++-
 man/clean_users.Rd         |  11 +++-
 5 files changed, 108 insertions(+), 53 deletions(-)

diff --git a/man/clean_contacts.Rd b/man/clean_contacts.Rd
index 02de61c..a5d5f90 100644
--- a/man/clean_contacts.Rd
+++ b/man/clean_contacts.Rd
@@ -35,56 +35,78 @@ Cleans and un-nests contact data. Contact data is returned by
 }
 \examples{
 \dontrun{
-  url <- "https://MyGoDataServer.com/"
-  username <- "myemail@email.com"
-  password <- "mypassword"
-  outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
+url <- "https://MyGoDataServer.com/"
+username <- "myemail@email.com"
+password <- "mypassword"
+outbreak_id <- "3b5554d7-2c19-41d0-b9af-475ad25a382b"
 
-  contacts <- get_contacts(
-    url = url,
-    username = username,
-    password = password,
-    outbreak_id = outbreak_id
-  )
+contacts <- get_contacts(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+
+locations <- get_locations(
+  url = url,
+  username = username,
+  password = password
+)
 
-  locations <- get_locations(
-    url = url,
-    username = username,
-    password = password
-  )
+locations_clean <- clean_locations(locations = locations)
 
-  locations_clean <- clean_locations(locations = locations)
+language_tokens <- get_language_tokens(
+  url = url,
+  username = username,
+  password = password,
+  language = "english_us"
+)
 
-  # other cleaned data required for `clean_contacts()`
-  contacts_vacc_history_clean <- clean_contact_vax_history(contacts = contacts)
-  contacts_address_history_clean <- clean_contact_address_history(
-    contacts = contacts,
-    locations_clean = locations_clean
-  )
+# other cleaned data required for `clean_contacts()`
+contacts_vacc_history_clean <- clean_contact_vax_history(
+  contacts = contacts,
+  language_tokens = language_tokens
+)
+contacts_address_history_clean <- clean_contact_address_history(
+  contacts = contacts,
+  locations_clean = locations_clean,
+  language_tokens = language_tokens
+)
 
-  cases <- get_cases(
-    url = url,
-    username = username,
-    password = password,
-    outbreak_id = outbreak_id
-  )
-  cases_address_history_clean <- clean_case_address_history(cases = cases)
-  cases_vacc_history_clean <- clean_case_vax_history(cases = cases)
-  cases_dateranges_history_clean <- clean_case_med_history(cases = cases)
+cases <- get_cases(
+  url = url,
+  username = username,
+  password = password,
+  outbreak_id = outbreak_id
+)
+cases_address_history_clean <- clean_case_address_history(
+  cases = cases,
+  locations_clean = locations_clean,
+  language_tokens = language_tokens
+)
+cases_vacc_history_clean <- clean_case_vax_history(
+  cases = cases,
+  language_tokens = language_tokens
+)
+cases_dateranges_history_clean <- clean_case_med_history(
+  cases = cases,
+  language_tokens = language_tokens
+)
 
-  cases_clean <- clean_cases(
-    cases = cases,
-    cases_address_history_clean = cases_address_history_clean,
-    cases_vacc_history_clean = cases_vacc_history_clean,
-    cases_dateranges_history_clean = cases_dateranges_history_clean
-  )
-  contacts_becoming_cases <- cases_from_contacts(cases_clean = cases_clean)
+cases_clean <- clean_cases(
+  cases = cases,
+  cases_address_history_clean = cases_address_history_clean,
+  cases_vacc_history_clean = cases_vacc_history_clean,
+  cases_dateranges_history_clean = cases_dateranges_history_clean,
+  language_tokens = language_tokens
+)
+contacts_becoming_cases <- cases_from_contacts(cases_clean = cases_clean)
 
-  contacts_clean <- clean_contacts(
-    contacts = contacts,
-    contacts_address_history_clean = cases_address_history_clean,
-    contacts_vacc_history_clean = cases_vacc_history_clean,
-    contacts_becoming_cases = contacts_becoming_cases
-  )
+contacts_clean <- clean_contacts(
+  contacts = contacts,
+  contacts_address_history_clean = cases_address_history_clean,
+  contacts_vacc_history_clean = cases_vacc_history_clean,
+  contacts_becoming_cases = contacts_becoming_cases
+)
 }
 }
diff --git a/man/clean_followups.Rd b/man/clean_followups.Rd
index 074c21d..a4d3745 100644
--- a/man/clean_followups.Rd
+++ b/man/clean_followups.Rd
@@ -4,7 +4,7 @@
 \alias{clean_followups}
 \title{Clean followup data}
 \usage{
-clean_followups(followups, contacts_address_history_clean)
+clean_followups(followups, contacts_address_history_clean, language_tokens)
 }
 \arguments{
 \item{followups}{A \code{tibble} with events data. Followup data is returned by
@@ -50,14 +50,23 @@ locations <- get_locations(
 
 locations_clean <- clean_locations(locations = locations)
 
+language_tokens <- get_language_tokens(
+  url = url,
+  username = username,
+  password = password,
+  language = "english_us"
+)
+
 contacts_address_history_clean <- clean_contact_address_history(
   contacts = contacts,
-  locations_clean = locations_clean
+  locations_clean = locations_clean,
+  language_tokens = language_tokens
 )
 
 followups_clean <- clean_followups(
   followups = followups,
-  contacts_address_history_clean = contacts_address_history_clean
+  contacts_address_history_clean = contacts_address_history_clean,
+  language_tokens = language_tokens
 )
 }
 }
diff --git a/man/clean_locations.Rd b/man/clean_locations.Rd
index 0e2578b..3752796 100644
--- a/man/clean_locations.Rd
+++ b/man/clean_locations.Rd
@@ -4,7 +4,7 @@
 \alias{clean_locations}
 \title{Cleans location data}
 \usage{
-clean_locations(locations)
+clean_locations(locations, language_tokens)
 }
 \arguments{
 \item{locations}{A \code{\link{tibble}} containing locations data. This is the data
@@ -29,6 +29,13 @@ locations <- get_locations(
   password = password
 )
 
-clean_locations(locations = locations)
+language_tokens <- get_language_tokens(
+  url = url,
+  username = username,
+  password = password,
+  language = "english_us"
+)
+
+clean_locations(locations = locations, language_tokens = language_tokens)
 }
 }
diff --git a/man/clean_relationships.Rd b/man/clean_relationships.Rd
index e834893..cedab1a 100644
--- a/man/clean_relationships.Rd
+++ b/man/clean_relationships.Rd
@@ -4,7 +4,7 @@
 \alias{clean_relationships}
 \title{Cleans relationship data}
 \usage{
-clean_relationships(relationships)
+clean_relationships(relationships, language_tokens)
 }
 \arguments{
 \item{relationships}{A \code{tibble} of relationship data. Relationship data is
@@ -31,6 +31,16 @@ relationships <- get_relationships(
   outbreak_id = outbreak_id
 )
 
-clean_relationships <- clean_relationships(relationships)
+language_tokens <- get_language_tokens(
+  url = url,
+  username = username,
+  password = password,
+  language = "english_us"
+)
+
+clean_relationships <- clean_relationships(
+  relationships,
+  language_tokens = language_tokens
+)
 }
 }
diff --git a/man/clean_users.Rd b/man/clean_users.Rd
index d06731b..8c9d11f 100644
--- a/man/clean_users.Rd
+++ b/man/clean_users.Rd
@@ -4,7 +4,7 @@
 \alias{clean_users}
 \title{Cleans users data}
 \usage{
-clean_users(users)
+clean_users(users, language_tokens)
 }
 \arguments{
 \item{users}{A \code{tibble} containing users data. Users data is returned by
@@ -29,6 +29,13 @@ users <- get_users(
   password = password
 )
 
-clean_users <- clean_users(users)
+language_tokens <- get_language_tokens(
+  url = url,
+  username = username,
+  password = password,
+  language = "english_us"
+)
+
+clean_users <- clean_users(users = users, language_tokens = language_tokens)
 }
 }