Render documentation, generate available datasets file, lint

epiforecasts · seabbs · Jul 1, 2021 · Jun 24, 2021 · Jun 24, 2021 · Jun 26, 2021
commit 1de2205233b0d741360b7e637dc3997aac491bf0
diff --git a/R/Canada.R b/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() {

diff --git a/R/Colombia.R b/R/Colombia.R
@@ -35,10 +35,10 @@ Colombia <- R6::R6Class("Colombia",
     #' @field source_data_cols existing columns within the raw data
     source_data_cols = c("cases_total"),
     #' @field source_text Plain text description of the source of the data
-    source_text = "Daniel Cárdenas",
+    source_text = "Daniel C\u00e1rdenas",
     #' @field source_url Website address for explanation/introduction of the
     #' data
-    source_url = "https://github.com/danielcs88/colombia_covid-19/", 
+    source_url = "https://github.com/danielcs88/colombia_covid-19/",
 
     #' @description Set up a table of region codes for clean data
     #' @importFrom tibble tibble

diff --git a/R/Cuba.R b/R/Cuba.R
@@ -38,7 +38,7 @@ Cuba <- R6::R6Class("Cuba",
     source_text = "COVID19 Cuba Data team",
     #' @field source_url Website address for explanation/introduction of the
     #' data
-    source_url = "https://covid19cubadata.github.io/#cuba", 
+    source_url = "https://covid19cubadata.github.io/#cuba",
 
 
     #' @description Set up a table of region codes for clean data

diff --git a/R/Germany.R b/R/Germany.R
@@ -40,7 +40,7 @@ Germany <- R6::R6Class("Germany",
     source_text = "Robert Koch-Institut (RKI)",
     #' @field source_url Website address for explanation/introduction of the
     #' data
-    source_url = "https://hub.arcgis.com/datasets/dd4580c810204019a7b8eb3e0b329dd6_0/explore",
+    source_url = "https://hub.arcgis.com/datasets/dd4580c810204019a7b8eb3e0b329dd6_0/explore", # nolint
 
 
     #' @description Set up a table of region codes for clean data

diff --git a/R/Lithuania.R b/R/Lithuania.R
@@ -158,7 +158,7 @@ Lithuania <- R6::R6Class("Lithuania",
     source_text = "Lithuanian Statistics Department",
     #' @field source_url Website address for explanation/introduction of the
     #' data
-    source_url = "https://hub.arcgis.com/datasets/d49a63c934be4f65a93b6273785a8449_0/about",
+    source_url = "https://hub.arcgis.com/datasets/d49a63c934be4f65a93b6273785a8449_0/about", # nolint
 
     # Additional attributes specific to the Lithuania functionality
     #' @field death_definition which criteria of deaths attributed to

diff --git a/R/Netherlands.R b/R/Netherlands.R
@@ -40,7 +40,7 @@ Netherlands <- R6::R6Class("Netherlands",
     #' @field source_data_cols existing columns within the raw data
     source_data_cols = c("cases_new", "deaths_new", "hosp_new"),
     #' @field source_text Plain text description of the source of the data
-    source_text = "National Institute for Public Health and the Environment (RIVM), Netherlands",
+    source_text = "National Institute for Public Health and the Environment (RIVM), Netherlands", # nolint
     #' @field source_url Website address for explanation/introduction of the
     #' data
     source_url = "https://data.rivm.nl/covid-19/",

diff --git a/R/SouthAfrica.R b/R/SouthAfrica.R
@@ -35,7 +35,7 @@ SouthAfrica <- R6::R6Class("SouthAfrica",
     #' @field source_data_cols existing columns within the raw data
     source_data_cols = c("cases_new", "deaths_new", "recovered_new"),
     #' @field source_text Plain text description of the source of the data
-    source_text = "Data Science for Social Impact research group, University of Pretoria",
+    source_text = "Data Science for Social Impact research group, University of Pretoria", # nolint
     #' @field source_url Website address for explanation/introduction of the
     #' data
     source_url = "https://github.com/dsfsi/covid19za",

diff --git a/data/all_country_data.rda b/data/all_country_data.rda
diff --git a/man/France.Rd b/man/France.Rd
diff --git a/man/Germany.Rd b/man/Germany.Rd
diff --git a/man/India.Rd b/man/India.Rd
diff --git a/man/Italy.Rd b/man/Italy.Rd
diff --git a/man/Lithuania.Rd b/man/Lithuania.Rd
diff --git a/man/Mexico.Rd b/man/Mexico.Rd
diff --git a/man/Netherlands.Rd b/man/Netherlands.Rd
diff --git a/man/SouthAfrica.Rd b/man/SouthAfrica.Rd
diff --git a/man/Switzerland.Rd b/man/Switzerland.Rd
diff --git a/man/UK.Rd b/man/UK.Rd
diff --git a/man/USA.Rd b/man/USA.Rd
diff --git a/man/all_country_data.Rd b/man/all_country_data.Rd
diff --git a/tests/testthat/custom_data/Switzerland_level_1.rds b/tests/testthat/custom_data/Switzerland_level_1.rds
diff --git a/tests/testthat/test-DataClass.R b/tests/testthat/test-DataClass.R
@@ -114,7 +114,7 @@ test_that("DataClass returns a summary", {
     names(sum),
     c(
       "origin", "class", "level_1_region", "level_2_region", "level_3_region",
-      "type", "data_urls", "source_data_cols"
+      "type", "data_urls", "source_data_cols", "source_text", "source_url"
     )
   )
   expect_true(sum$class[1] == "D")

diff --git a/tests/testthat/test-get_available_datasets.R b/tests/testthat/test-get_available_datasets.R
@@ -9,7 +9,8 @@ test_that(
     expected_names <- c(
       "origin", "class", "level_1_region",
       "level_2_region", "level_3_region", "type",
-      "data_urls", "source_data_cols"
+      "data_urls", "source_data_cols",
+      "source_text", "source_url"
     )
     expect_identical(colnames(data), expected_names)
   }
@@ -41,7 +42,11 @@ 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")) {
+  if (name %in% c("level_1_region",
+                  "level_2_region",
+                  "level_3_region",
+                  "source_text",
+                  "source_url")) {
     next
   }
   test_that(