Add rvdss endpoint

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: epidatr
 Title: Client for Delphi's 'Epidata' API
-Version: 1.2.1
+Version: 1.2.2
 Authors@R: c(
     person("Logan", "Brooks", , "lcbrooks@andrew.cmu.edu", role = "aut"),
     person("Dmitry", "Shemetov", , "dshemeto@andrew.cmu.edu", role = "aut"),
@@ -68,7 +68,7 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Collate:
     'auth.R'
     'avail_endpoints.R'

NAMESPACE

@@ -38,6 +38,7 @@ export(pub_nidss_dengue)
 export(pub_nidss_flu)
 export(pub_nowcast)
 export(pub_paho_dengue)
+export(pub_rvdss)
 export(pub_wiki)
 export(pvt_cdc)
 export(pvt_dengue_sensors)

NEWS.md

@@ -1,5 +1,14 @@
-# epidatr 1.2.1
+# epidatr 1.3.0
+
+## Changes
+
+## Features
+
+- Add `rvdss` endpoint, which gives access to Canadian national, regional,
+  provincial, and lab-level respiratory disease data.
+
 ## Patches
+
 - Fix so that `covidcast_epidata()` will still print if fields are missing.
 
 # epidatr 1.2.0
@@ -14,10 +23,6 @@
 - `missing` doesn't count default values as non-missing. If a user doesn't pass `geo_values` or `time_values` (both of which default to `"*"` in `pub_covidcast`), or `dates` (in `pub_covid_hosp_state_timeseries`), the missing check fails. To avoid this, just don't check missingness of those two arguments.
 - `fetch_args_list` now has an `refresh_cache` argument, which is `FALSE` by default.
 
-# epidatr 1.1.1
-
-## Changes
-
 ## Features
 
 ## Patches

R/endpoints.R

@@ -2036,6 +2036,155 @@ pvt_quidel <- function(
   ) %>% fetch(fetch_args = fetch_args)
 }
 
+#' Canadian respiratory virus surveillance report
+#'
+#' @description
+#' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/rvdss.html>
+#'
+#' Data is weekly.
+#'
+#' @examples
+#' \dontrun{
+#' pub_rvdss(
+#'   geo_type = "province",
+#'   geo_values = c("yu", "on"),
+#'   time_values = epirange(20200601, 20200801)
+#' )
+#' pub_rvdss(
+#'   geo_type = "province",
+#'   geo_values = "*",
+#'   time_values = epirange(20200601, 20200801)
+#' )
+#' }
+#'
+#' @param geo_type string. The geographic resolution of the data. Levels available:
+#'    "nation", "region", "province", "lab".
+#' @param geo_values character. The geographies to return. Defaults to all
+#'  ("*") geographies within requested geographic resolution. "nation" and "province"
+#'  locations use standard 2-letter abbreviations (e.g. "on"). Available regions are
+#'  "atlantic", "bc", "on", "prairies", "qc", and "territories." "lab"s are full
+#'  facility names.
+#' @param time_values [`timeset`]. Dates to fetch. Defaults to all ("*") dates.
+#' @param ... not used for values, forces later arguments to bind by name
+#' @param as_of Date. Optionally, the as of date for the issues to fetch. If not
+#'   specified, the most recent data is returned. Mutually exclusive with
+#'   `issues` or `lag`.
+#' @param issues [`timeset`]. Optionally, the issue of the data to fetch. If not
+#'   specified, the most recent issue is returned. Mutually exclusive with
+#'   `as_of` or `lag`.
+#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
+#' @return [`tibble::tibble`]
+#'
+#' @seealso [pub_covidcast_meta()], [covidcast_epidata()], [epirange()]
+#' @keywords endpoint
+#' @export
+pub_rvdss <- function(
+    geo_type,
+    geo_values = "*",
+    time_values = "*",
+    ...,
+    as_of = NULL,
+    issues = NULL,
+    fetch_args = fetch_args_list()) {
+  rlang::check_dots_empty()
+
+  # Check parameters
+  if (missing(geo_type)) {
+    cli::cli_abort(
+      "`geo_type` is required",
+      class = "epidatr__pub_rvdss__missing_required_args"
+    )
+  }
+
+  if (sum(!is.null(issues), !is.null(as_of)) > 1) {
+    cli::cli_abort(
+      "`issues` and `as_of` are mutually exclusive",
+      class = "epidatr__pub_rvdss__too_many_issue_params"
+    )
+  }
+
+  assert_character_param("geo_type", geo_type, len = 1)
+  assert_timeset_param("time_values", time_values)
+  assert_character_param("geo_values", geo_values)
+  assert_date_param("as_of", as_of, len = 1, required = FALSE)
+  assert_timeset_param("issues", issues, required = FALSE)
+  time_values <- parse_timeset_input(time_values)
+  as_of <- parse_timeset_input(as_of)
+  issues <- parse_timeset_input(issues)
+
+  create_epidata_call(
+    "covidcast/",
+    list(
+      geo_type = geo_type,
+      geo_values = geo_values,
+      time_values = time_values,
+      as_of = as_of,
+      issues = issues
+    ),
+    list(
+      # descriptive fields
+      create_epidata_field_info(
+        "geo_type",
+        "categorical",
+        categories = c("nation", "region", "province", "lab")
+      ),
+      create_epidata_field_info("geo_value", "text"),
+      create_epidata_field_info("region", "text"),
+      create_epidata_field_info(
+        "time_type",
+        "categorical",
+        categories = c("week")
+      ),
+      create_epidata_field_info("epiweek", "epiweek"), # Stored as an int in YYYYWW format
+      create_epidata_field_info("time_value", "epiweek"), # Stored as a date
+      create_epidata_field_info("issue", "epiweek"), # Stored as a date
+      create_epidata_field_info("week", "int"),
+      create_epidata_field_info("weekorder", "int"),
+      create_epidata_field_info("year", "int"),
+
+      # value fields
+      create_epidata_field_info("adv_pct_positive", "float"),
+      create_epidata_field_info("adv_positive_tests", "float"),
+      create_epidata_field_info("adv_tests", "float"),
+      create_epidata_field_info("evrv_pct_positive", "float"),
+      create_epidata_field_info("evrv_positive_tests", "float"),
+      create_epidata_field_info("evrv_tests", "float"),
+      create_epidata_field_info("flu_pct_positive", "float"),
+      create_epidata_field_info("flu_positive_tests", "float"),
+      create_epidata_field_info("flu_tests", "float"),
+      create_epidata_field_info("flua_pct_positive", "float"),
+      create_epidata_field_info("flua_positive_tests", "float"),
+      create_epidata_field_info("flua_tests", "float"),
+      create_epidata_field_info("fluah1n1pdm09_positive_tests", "float"),
+      create_epidata_field_info("fluah3_positive_tests", "float"),
+      create_epidata_field_info("fluauns_positive_tests", "float"),
+      create_epidata_field_info("flub_pct_positive", "float"),
+      create_epidata_field_info("flub_positive_tests", "float"),
+      create_epidata_field_info("flub_tests", "float"),
+      create_epidata_field_info("hcov_pct_positive", "float"),
+      create_epidata_field_info("hcov_positive_tests", "float"),
+      create_epidata_field_info("hcov_tests", "float"),
+      create_epidata_field_info("hmpv_pct_positive", "float"),
+      create_epidata_field_info("hmpv_positive_tests", "float"),
+      create_epidata_field_info("hmpv_tests", "float"),
+      create_epidata_field_info("hpiv1_positive_tests", "float"),
+      create_epidata_field_info("hpiv2_positive_tests", "float"),
+      create_epidata_field_info("hpiv3_positive_tests", "float"),
+      create_epidata_field_info("hpiv4_positive_tests", "float"),
+      create_epidata_field_info("hpiv_pct_positive", "float"),
+      create_epidata_field_info("hpiv_positive_tests", "float"),
+      create_epidata_field_info("hpiv_tests", "float"),
+      create_epidata_field_info("hpivother_positive_tests", "float"),
+      create_epidata_field_info("rsv_pct_positive", "float"),
+      create_epidata_field_info("rsv_positive_tests", "float"),
+      create_epidata_field_info("rsv_tests", "float"),
+      create_epidata_field_info("sarscov2_pct_positive", "float"),
+      create_epidata_field_info("sarscov2_positive_tests", "float"),
+      create_epidata_field_info("sarscov2_tests", "float")
+    )
+  ) %>% fetch(fetch_args = fetch_args)
+}
+
 #' Influenza and dengue digital surveillance sensors
 #' @description
 #' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/sensors.html>

tests/testthat/test-endpoints.R

@@ -127,6 +127,12 @@ test_that("basic_epidata_call", {
     epiweeks = epirange(201201, 202001),
     fetch_args = fetch_args_list(dry_run = TRUE)
   ) %>% request_url())
+  expect_no_error(pub_rvdss(
+    geo_type = "nation",
+    time_values = epirange(20200601, 20200801),
+    geo_values = "ca",
+    fetch_args = fetch_args_list(dry_run = TRUE)
+  ) %>% request_url())
   expect_no_error(pvt_sensors(
     auth = "yourkey",
     names = "sar3",
@@ -325,6 +331,13 @@ test_that("endoints accept wildcard for date parameter", {
     epiweeks = "*",
     fetch_args = fetch_args_list(dry_run = TRUE)
   ))
+  expect_no_error(call <- pub_rvdss(
+    geo_type = "province",
+    time_values = "*",
+    geo_values = "*",
+    fetch_args = fetch_args_list(dry_run = TRUE)
+  ))
+
   expect_identical(call$params$epiweeks$from, 100001)
   expect_identical(call$params$epiweeks$to, 300001)