release candidate

.Rbuildignore

@@ -27,4 +27,4 @@ SMG.md
 ^.*.pdf$
 ^inst/paper$
 ^inst/examples$
-^\.devcontainer$
+^\.devcontainer$

.pre-commit-config.yaml

@@ -36,6 +36,7 @@ repos:
           .*\.RData|
           .*\.png|
           .*\.bib|
+          .*\.csv|
           cran-comments\.md
           )$
     -   id: lintr

NEWS.md

@@ -19,7 +19,7 @@ Thanks to @joseph-palmer, @RichardMN, and @kathsherratt for contributions toward
 ## Other changes
 
 * Testing of classes updated to allow for at least one of `common_data_urls` or `level_data_urls` to be present. The previous default which forced the presence of `common_data_urls` meant that several classes had to define an empty field (by @joseph-palmer).
-* Tests on data sets are now included as a method in `DataClass`. `test_regional-datasets` now calls the test function for all classes at each level. Data set specific tests (such as for NHS regions in the UK) are included as a `specific_tests` function within the country class, which is called by the parent (DataClass) `test` after performing standard checks. This allows all the code about a country to be defined in its own class. In addition, users can run tests interactively by calling the test method (e.g. `$test()`;) (by @joseph-palmer)
+* Tests on data sets are now included as a method in `DataClass`. `test_regional-datasets` now calls the test function for all classes at each level. Data set specific tests (such as for NHS regions in the UK) are included as a `specific_tests` function within the country class, which is called by the parent (DataClass) `test` after performing standard checks. This allows all the code about a country to be defined in its own class. In addition, users can run tests interactively by calling the test method (e.g. `$test()`) (by @joseph-palmer)
 * A function to create a template class and automatically add a github workflow file has been added. This makes adding a new data source for a country even easier as now you can call the function `make_new_data_source()` with the country / source name to add and it will set up the basic structure for you. There is also now a github check to make sure all new sources have a workflow set up (by @joseph-palmer).
 * Adds `source_` fields to all data sets to help users properly attribute their data sources (by @RichardMN).
 

R/Canada.R

@@ -42,7 +42,7 @@ Canada <- R6::R6Class("Canada",
     #' @field source_url Website address for explanation/introduction of the
     #' data
     source_url = "https://open.canada.ca/data/en/dataset/261c32ab-4cfd-4f81-9dea-7b64065690dc", # nolint
-  
+
     #' @description Set up a table of region codes for clean data
     #' @importFrom tibble tibble
     set_region_codes = function() {

R/Switzerland.R

@@ -106,7 +106,8 @@ Switzerland <- R6::R6Class("Switzerland",
           level_1_region_code = if_else(
             .data$abbreviation_canton_and_fl == "FL",
             "FL-FL",
-            paste0("CH-", .data$abbreviation_canton_and_fl)),
+            paste0("CH-", .data$abbreviation_canton_and_fl)
+          ),
           date = as_date(ymd(.data$date))
         ) %>%
         left_join(

R/UK.R

@@ -385,38 +385,43 @@ UK <- R6::R6Class("UK",
       # 1. Data from 7 April 2021 to now:
       # Data not always daily; set up to try urls for last 7 days
       try_date_seq <- seq.Date(self$release_date,
-                               by = -1, length.out = 7)
-      try_urls <- map_chr(try_date_seq,
-                          ~ paste0(
-                              self$data_urls[["nhs_recent_url"]],
-                              "/wp-content/uploads/sites/2/",
-                              year(.x), "/",
-                              ifelse(month(.x) < 10,
-                                     paste0(0, month(.x)),
-                                     month(.x)
-                              ),
-                              "/COVID-19-daily-admissions-and-beds-",
-                              gsub("-", "", as.character(.x)),
-                              ".xlsx")
-                          )
+        by = -1, length.out = 7
+      )
+      try_urls <- map_chr(
+        try_date_seq,
+        ~ paste0(
+          self$data_urls[["nhs_recent_url"]],
+          "/wp-content/uploads/sites/2/",
+          year(.x), "/",
+          ifelse(month(.x) < 10,
+            paste0(0, month(.x)),
+            month(.x)
+          ),
+          "/COVID-19-daily-admissions-and-beds-",
+          gsub("-", "", as.character(.x)),
+          ".xlsx"
+        )
+      )
 
       names(try_urls) <- try_date_seq
       # Check for working urls
-      url_status <- map_chr(try_urls,
-                        ~ GET(.x) %>%
-                          status_code())
+      url_status <- map_chr(
+        try_urls,
+        ~ GET(.x) %>%
+          status_code()
+      )
       # Keep latest working url
       url_status <- url_status[(url_status == 200)]
       names(url_status) <- as.Date(names(url_status))
       nhs_recent_url <- try_urls[as.character(max(names(url_status)))]
       # Get latest url download
       recent <- download_excel(nhs_recent_url,
-                               "nhs_recent.xlsx",
-                               verbose = self$verbose,
-                               transpose = TRUE,
-                               sheet = 1,
-                               range = cell_limits(c(28, 2), c(36, NA))
-        )
+        "nhs_recent.xlsx",
+        verbose = self$verbose,
+        transpose = TRUE,
+        sheet = 1,
+        range = cell_limits(c(28, 2), c(36, NA))
+      )
 
       # 2. Data for August 2020 to 7 April 2021
       archive <- download_excel(

R/shared-methods.R

@@ -510,7 +510,9 @@ DataClass <- R6::R6Class(
           "national", "regional"
         ),
         data_urls = paste(unlist(self$data_urls), collapse = ", "),
-        source_data_cols = paste(unlist(self$source_data_cols), collapse = ", "),
+        source_data_cols = paste(unlist(self$source_data_cols),
+          collapse = ", "
+        ),
         source_text = ifelse(is.null(self$source_text), NA, self$source_text),
         source_url = ifelse(is.null(self$source_url), NA, self$source_url)
       )

README.Rmd

@@ -15,7 +15,7 @@ knitr::opts_chunk$set(
 
 [![R-CMD-check](https://github.com/epiforecasts/covidregionaldata/workflows/R-CMD-check/badge.svg)](https://github.com/epiforecasts/covidregionaldata/actions) [![Codecov test coverage](https://codecov.io/gh/epiforecasts/covidregionaldata/branch/master/graph/badge.svg)](https://codecov.io/gh/epiforecasts/covidregionaldata?branch=master) [![Data status](https://img.shields.io/badge/Data-status-lightblue.svg?style=flat)](https://epiforecasts.io/covidregionaldata/articles/supported-countries.html) [![metacran downloads](http://cranlogs.r-pkg.org/badges/grand-total/covidregionaldata?color=ff69b4)](https://cran.r-project.org/package=covidregionaldata)
 
-[![MIT license](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/epiforecasts/covidregionaldata/blob/master/LICENSE.md/)   [![GitHub contributors](https://img.shields.io/github/contributors/epiforecasts/covidregionaldata)](https://github.com/epiforecasts/covidregionaldata/graphs/contributors)  [![PRs Welcome](https://img.shields.io/badge/PRs-welcome-yellow.svg)](https://makeapullrequest.com/) [![GitHub commits](https://img.shields.io/github/commits-since/epiforecasts/covidregionaldata/v0.9.2.svg?color=orange)](https://GitHub.com/epiforecasts/covidregionaldata/commit/master/) [![DOI](https://zenodo.org/badge/271601189.svg)](https://zenodo.org/badge/latestdoi/271601189) 
+[![MIT license](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/epiforecasts/covidregionaldata/blob/master/LICENSE.md/)   [![GitHub contributors](https://img.shields.io/github/contributors/epiforecasts/covidregionaldata)](https://github.com/epiforecasts/covidregionaldata/graphs/contributors)  [![PRs Welcome](https://img.shields.io/badge/PRs-welcome-yellow.svg)](https://makeapullrequest.com/) [![GitHub commits](https://img.shields.io/github/commits-since/epiforecasts/covidregionaldata/0.9.2.svg?color=orange)](https://GitHub.com/epiforecasts/covidregionaldata/commit/master/) [![DOI](https://zenodo.org/badge/271601189.svg)](https://zenodo.org/badge/latestdoi/271601189) 
 
 [![status](https://joss.theoj.org/papers/dd6f7acdae3b7136a3ac373ce9a0655c/status.svg)](https://joss.theoj.org/papers/dd6f7acdae3b7136a3ac373ce9a0655c)
 

README.md

@@ -16,7 +16,7 @@ contributors](https://img.shields.io/github/contributors/epiforecasts/covidregio
 [![PRs
 Welcome](https://img.shields.io/badge/PRs-welcome-yellow.svg)](https://makeapullrequest.com/)
 [![GitHub
-commits](https://img.shields.io/github/commits-since/epiforecasts/covidregionaldata/v0.9.2.svg?color=orange)](https://GitHub.com/epiforecasts/covidregionaldata/commit/master/)
+commits](https://img.shields.io/github/commits-since/epiforecasts/covidregionaldata/0.9.2.svg?color=orange)](https://GitHub.com/epiforecasts/covidregionaldata/commit/master/)
 [![DOI](https://zenodo.org/badge/271601189.svg)](https://zenodo.org/badge/latestdoi/271601189)
 
 [![status](https://joss.theoj.org/papers/dd6f7acdae3b7136a3ac373ce9a0655c/status.svg)](https://joss.theoj.org/papers/dd6f7acdae3b7136a3ac373ce9a0655c)
@@ -79,7 +79,7 @@ the temporary directory by default),
 
 ``` r
 start_using_memoise()
-#> Using a cache at: /tmp/RtmpB2UKDX
+#> Using a cache at: /tmp/RtmpMMiVQw
 ```
 
 To stop using `memoise` use,
@@ -104,7 +104,7 @@ the Google COVID-19 open data project), use:
 ``` r
 nots <- get_national_data()
 #> Downloading data from https://covid19.who.int/WHO-COVID-19-global-data.csv
-#> Rows: 129165 Columns: 8
+#> Rows: 129279 Columns: 8
 #> ── Column specification ────────────────────────────────────────────────────────
 #> Delimiter: ","
 #> chr  (3): Country_code, Country, WHO_region
@@ -116,7 +116,7 @@ nots <- get_national_data()
 #> Cleaning data
 #> Processing data
 nots
-#> # A tibble: 129,165 x 15
+#> # A tibble: 129,401 x 15
 #>    date       un_region who_region country        iso_code cases_new cases_total
 #>    <date>     <chr>     <chr>      <chr>          <chr>        <dbl>       <dbl>
 #>  1 2020-01-03 Asia      EMRO       Afghanistan    AF               0           0
@@ -129,7 +129,7 @@ nots
 #>  8 2020-01-03 Americas  AMRO       Antigua & Bar… AG               0           0
 #>  9 2020-01-03 Americas  AMRO       Argentina      AR               0           0
 #> 10 2020-01-03 Asia      EURO       Armenia        AM               0           0
-#> # … with 129,155 more rows, and 8 more variables: deaths_new <dbl>,
+#> # … with 129,391 more rows, and 8 more variables: deaths_new <dbl>,
 #> #   deaths_total <dbl>, recovered_new <dbl>, recovered_total <dbl>,
 #> #   hosp_new <dbl>, hosp_total <dbl>, tested_new <dbl>, tested_total <dbl>
 ```

inst/WORDLIST

@@ -1,100 +1,101 @@
+ac
 ACAPS
+afghanistan
+api
 APL
+apskritis
 Bundesland
+cloneable
 CMD
 CMMID
-COVID
-CSSE
-CoV
 Codecov
-Cota
-Covid
-DD
-DataClass
-ECDC
-Estados
-Github
-GoogleData
-Guidotti
-ICD
-INEGI
-IPC
-Inf
-Initalize
-JHU
-JRC
-Kreise
-Landkreis
-Linelist
-MX
-Meixco
-OSP
-OpenDataZH
-PHE
-PRs
-RVIM
-SARS
-SciELOPreprints
-SouthAfrica
-UCPM
-YYYY
-ac
-afghanistan
-api
-apskritis
-cloneable
 com
 conuntry
+Cota
+CoV
 covid
+Covid
+COVID
+covidregionaldata
+CSSE
+DataClass
 datahub
 dd
+DD
 documentaion
 doi
 ec
+ECDC
+Estados
 etc
 filepath
 fns
 geocode
 geocoding
 github
+Github
+GoogleData
+Guidotti
 hexsticker
+ICD
 inciteful
 inegi
+INEGI
+Inf
 initalize
+Initalize
+IPC
 iso
+JHU
 jrc
+JRC
 jure
+Kreise
+Landkreis
 linelist
+Linelist
 linelists
 ltla
 magrittr
 md
+Meixco
 memoise
 metacran
+MX
 nhs
 nhsregions
+OpenDataZH
 org
+OSP
 params
 paulcampbell
+PHE
+PRs
 quickstart
 rds
 recomended
 regioni
 reparameterise
+RVIM
+SARS
 savivaldybe
+SciELOPreprints
 seperate
 shapefiles
+SouthAfrica
 spi
 st
 subnationaldata
 supertracker
 testthat
 tibble
 tibbles
+UCPM
 uk
 urls
 useMemoise
 utla
 wikipedia
 yaml
 yyyy
+YYYY

tests/testthat/test-get_available_datasets.R

@@ -42,11 +42,13 @@ test_that(
 
 # test each column for na values
 for (name in colnames(data)) {
-  if (name %in% c("level_1_region",
-                  "level_2_region",
-                  "level_3_region",
-                  "source_text",
-                  "source_url")) {
+  if (name %in% c(
+    "level_1_region",
+    "level_2_region",
+    "level_3_region",
+    "source_text",
+    "source_url"
+  )) {
     next
   }
   test_that(