Transfer Estonia code into new clean branch

RichardMN · Sep 16, 2021 · 1426e7a · 1426e7a
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Showing 25 changed files with 238 additions and 2 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -121,4 +121,4 @@ Encoding: UTF-8
 Language: en-gb
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
diff --git a/NAMESPACE b/NAMESPACE
@@ -10,6 +10,7 @@ export(Covid19DataHub)
 export(Cuba)
 export(DataClass)
 export(ECDC)
+export(Estonia)
 export(France)
 export(Germany)
 export(Google)
@@ -73,6 +74,7 @@ importFrom(dplyr,slice_tail)
 importFrom(dplyr,starts_with)
 importFrom(dplyr,summarise)
 importFrom(dplyr,tally)
+importFrom(dplyr,transmute)
 importFrom(dplyr,ungroup)
 importFrom(dplyr,vars)
 importFrom(httr,GET)

diff --git a/R/Estonia.R b/R/Estonia.R
@@ -0,0 +1,86 @@
+#' Estonia Class for downloading, cleaning and processing notification data
+#' @description Information for downloading, cleaning
+#'  and processing COVID-19 region data for Estonia
+#'
+# nolint start
+#' @source \url{https://www.terviseamet.ee/et/koroonaviirus/avaandmed}
+# nolint end
+#' @export
+#' @concept dataset
+#' @family subnational
+#' @examples
+#' \dontrun{
+#' region <- Estonia$new(verbose = TRUE, steps = TRUE, get = TRUE)
+#' region$return()
+#' }
+Estonia <- R6::R6Class("Estonia",
+  inherit = DataClass,
+  public = list(
+
+    # Core Attributes
+    #' @field origin name of origin to fetch data for
+    origin = "Estonia",
+    #' @field supported_levels A list of supported levels.
+    supported_levels = list("1"),
+    #' @field supported_region_names A list of region names in order of level.
+    supported_region_names = list("1" = "county"),
+    #' @field supported_region_codes A list of region codes in order of level.
+    supported_region_codes = list("1" = "iso_3166_2"),
+    #' @field common_data_urls List of named links to raw data.
+    # nolint start
+    common_data_urls = list(
+      "main" = "https://opendata.digilugu.ee/opendata_covid19_test_county_all.csv" # nolint
+    ),
+    # nolint end
+    #' @field source_data_cols existing columns within the raw data
+    source_data_cols = c("cases_new", "tested_new", "cases_total", "tested_total"),
+    #' @field source_text Plain text description of the source of the data
+    source_text = "Estonian Ministry of Social Affairs",
+    #' @field source_url Website address for explanation/introduction of the
+    #' data
+    source_url = "https://www.terviseamet.ee/et/koroonaviirus/avaandmed",
+
+
+    #' @description Set up a table of region codes for clean data
+    #' @importFrom tibble tibble
+    set_region_codes = function() {
+      self$codes_lookup$`1` <- tibble(
+        code = c("EE-37",
+          "EE-39", "EE-45", "EE-52", "EE-50", "EE-56", "EE-60", "EE-68",
+          "EE-64", "EE-71", "EE-74", "EE-79", "EE-81", "EE-84", "EE-87",
+          NA),
+        region = c("Harju", "Hiiu", "Ida-Viru", "J\u00e4rva",
+          "J\u00f5geva", "L\u00e4\u00e4ne", "L\u00e4\u00e4ne-Viru",
+          "P\u00e4rnu", "P\u00f5lva", "Rapla","Saare", "Tartu",
+          "Valga", "Viljandi", "V\u00f5ru", "Unknown")
+      )
+    },
+
+    #' @description Estonia specific state level data cleaning
+    #' @importFrom dplyr select mutate transmute
+    #' @importFrom tidyr pivot_wider
+    #' @importFrom rlang .data
+    #'
+    clean_common = function() {
+      self$data$clean <- self$data$raw[["main"]] %>%
+        pivot_wider(
+          id_cols = c("LastStatisticsDate","StatisticsDate","Country","CountryEHAK","County","CountyEHAK"),
+          names_from = ResultValue,
+          values_from = c("DailyTests","TotalTests","DailyCases","TotalCases")) %>%
+        select(-Country,-CountryEHAK) %>%
+        mutate(TestPositivity = ifelse((DailyTests_N+DailyTests_P)>0,
+                                       (DailyTests_P/(DailyTests_N+DailyTests_P)),
+                                       NA)) %>%
+      transmute(
+        level_1_region = gsub(" maakond","", .data$County),
+        level_1_region_code=gsub("00","EE-", .data$CountyEHAK),
+        date = .data$StatisticsDate,
+        cases_new = .data$DailyCases_P,
+        tested_new = .data$DailyTests_P + .data$DailyTests_N,
+        cases_total = .data$TotalCases_P,
+        tested_total = .data$TotalTests_P + .data$TotalTests_N,
+        test_positivity = .data$TestPositivity
+        ) 
+    }
+  )
+)
diff --git a/data/all_country_data.rda b/data/all_country_data.rda
diff --git a/man/Belgium.Rd b/man/Belgium.Rd
diff --git a/man/Brazil.Rd b/man/Brazil.Rd
diff --git a/man/Canada.Rd b/man/Canada.Rd
diff --git a/man/Colombia.Rd b/man/Colombia.Rd
diff --git a/man/Covid19DataHub.Rd b/man/Covid19DataHub.Rd
diff --git a/man/Cuba.Rd b/man/Cuba.Rd
diff --git a/man/Estonia.Rd b/man/Estonia.Rd
diff --git a/man/France.Rd b/man/France.Rd
diff --git a/man/Germany.Rd b/man/Germany.Rd
diff --git a/man/Google.Rd b/man/Google.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/JHU.Rd b/man/JHU.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