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Moved old Switzerland code to SwitzerlandAlt, written functional 2-st…
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| #' Switzerland Class for downloading, cleaning and processing notification data | ||
| #' @description Information for downloading, cleaning | ||
| #' and processing COVID-19 region data for Switzerland | ||
| #' | ||
| #' @section Liechtenstein: | ||
| #' Liechtenstein is not a canton of Switzerland, but is presented in the | ||
| #' source data as a peer of Swiss cantons and assigned the two letter code | ||
| #' `FL`. `covidregionaldata` modifies this and presents the region code | ||
| #' for Liechtenstein as `FL-FL`, consistent with the Swiss ISO 3166-2 codes | ||
| #' which are of the form `CH-BE`, `CH-ZH`, `CH-VD`, ... | ||
| #' | ||
| #' If you do not wish to work with Liechtenstein | ||
| #' data, filter out on this code. Note that this is labelled as a ISO 3166-2 | ||
| #' code but Liechtenstein's real ISO 3166-2 codes refer to sub-national | ||
| #' regions. | ||
| #' | ||
| #' @section Additional data: | ||
| #' | ||
| #' In addition to the standard `covidregionaldata` columns provided, | ||
| #' the OpenDataZH source data provides other figures for ICU occupancy, | ||
| #' number of patients on ventilators, and the how many individuals are | ||
| #' isolated or quarantined. These columns are passed through unchanged. | ||
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| #' Further detail on them can be found at | ||
| # nolint start | ||
| #' \url{https://github.com/openZH/covid_19/#swiss-cantons-and-principality-of-liechtenstein-unified-dataset} | ||
| #' @source \url{https://github.com/openZH/covid_19/} | ||
| # nolint end | ||
| #' | ||
| #' @export | ||
| #' @concept dataset | ||
| #' @family subnational | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' region <- SwitzerlandAlt$new(verbose = TRUE, steps = TRUE, get = TRUE) | ||
| #' region$return() | ||
| #' } | ||
| SwitzerlandAlt <- R6::R6Class("SwitzerlandAlt", | ||
| inherit = DataClass, | ||
| public = list( | ||
|
|
||
| # Core Attributes | ||
| #' @field origin name of origin to fetch data for | ||
| origin = "Switzerland", | ||
| #' @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" = "canton"), | ||
| #' @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://github.com/openZH/covid_19/raw/master/COVID19_Fallzahlen_CH_total_v2.csv" | ||
| ), | ||
| # nolint end | ||
| #' @field source_data_cols existing columns within the raw data | ||
| source_data_cols = c( | ||
| "hosp_new", | ||
| "deaths_total", | ||
| "recovered_total", | ||
| "cases_total", | ||
| "tested_total" | ||
| ), | ||
| #' @field source_text Plain text description of the source of the data | ||
| source_text = "Open Data, Canton of Zurich", | ||
| #' @field source_url Website address for explanation/introduction of the | ||
| #' data | ||
| source_url = "https://github.com/openZH/covid_19/", | ||
|
|
||
| #' @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( | ||
| "CH-AG", "CH-AR", "CH-AI", "CH-BL", "CH-BS", | ||
| "CH-BE", "CH-FR", "CH-GE", "CH-GL", "CH-GR", "CH-JU", "CH-LU", | ||
| "CH-NE", "CH-NW", "CH-OW", "CH-SG", "CH-SH", "CH-SZ", "CH-SO", | ||
| "CH-TG", "CH-TI", "CH-UR", "CH-VS", "CH-VD", "CH-ZG", "CH-ZH", | ||
| "FL-FL" | ||
| ), | ||
| region = c( | ||
| "Aargau", "Appenzell Ausserrhoden", | ||
| "Appenzell Innerrhoden", "Basel-Landschaft", | ||
| "Basel-Stadt", "Bern", | ||
| "Fribourg", "Gen\u00e8ve", | ||
| "Glarus", "Grisons", | ||
| "Jura", "Luzern", "Neuch\u00e2tel", "Nidwalden", | ||
| "Obwalden", "St. Gallen", "Schaffhausen", | ||
| "Schwyz", "Solothurn", "Thurgau", "Ticino", | ||
| "Uri", "Valais", "Vaud", "Zug", | ||
| "Z\u00fcrich", "Liechtenstein" | ||
| ) | ||
| ) | ||
| }, | ||
|
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||
| #' @description Switzerland specific state level data cleaning | ||
| #' @importFrom dplyr select filter mutate left_join rename | ||
| #' @importFrom lubridate as_date ymd | ||
| #' @importFrom rlang .data | ||
| #' | ||
| clean_common = function() { | ||
| self$data$clean <- self$data$raw[["main"]] %>% | ||
| select(-time, -source) %>% | ||
| mutate( | ||
| level_1_region_code = if_else( | ||
| .data$abbreviation_canton_and_fl == "FL", | ||
| "FL-FL", | ||
| paste0("CH-", .data$abbreviation_canton_and_fl) | ||
| ), | ||
| date = as_date(ymd(.data$date)) | ||
| ) %>% | ||
| left_join( | ||
| self$codes_lookup$`1`, | ||
| by = c("level_1_region_code" = "code") | ||
| ) %>% | ||
| select(-abbreviation_canton_and_fl) %>% | ||
| rename( | ||
| level_1_region = .data$region, | ||
| cases_total = .data$ncumul_conf, | ||
| deaths_total = .data$ncumul_deceased, | ||
| hosp_new = .data$new_hosp, | ||
| recovered_total = .data$ncumul_released, | ||
| tested_total = .data$ncumul_tested | ||
| ) | ||
| } | ||
| ) | ||
| ) |