diff --git a/NAMESPACE b/NAMESPACE
index 5cdf4ccd..737bd862 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -99,6 +99,7 @@ importFrom(magrittr,"%>%")
importFrom(memoise,cache_filesystem)
importFrom(memoise,memoise)
importFrom(purrr,compact)
+importFrom(purrr,keep)
importFrom(purrr,map)
importFrom(purrr,map_chr)
importFrom(purrr,map_lgl)
diff --git a/NEWS.md b/NEWS.md
index 17b3e22f..39790cf5 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -5,10 +5,11 @@ This release is currently under development
## New data sets
* Support for level 1 region data in Estonia (thanks to @RichardMN). See `?Estonia` for details.
-* Support for level 1 region data in Vietnam (thanks to @biocyberman). See `?Vietname` for details.
+* Support for level 1 region data in Vietnam (thanks to @biocyberman). See `?Vietnam` for details.
## Other changes
+* Change the data source for Switzerland to draw data from the Swiss Federal Office of Public Health (FOPH)
* Updated the package logo to include the newly supported data sets.
## Bug fixes
diff --git a/R/Switzerland.R b/R/Switzerland.R
index bc296b90..a5d43415 100644
--- a/R/Switzerland.R
+++ b/R/Switzerland.R
@@ -2,31 +2,6 @@
#' @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.
-
-#' 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
@@ -48,12 +23,12 @@ Switzerland <- R6::R6Class("Switzerland",
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
+ #' @field common_data_urls List of named links to raw data. This url links
+ #' to a JSON file which provides the addresses for the most recently-updated
+ #' CSV files, which are then downloaded.
common_data_urls = list(
- "main" = "https://github.com/openZH/covid_19/raw/master/COVID19_Fallzahlen_CH_total_v2.csv"
+ "main" = "https://www.covid19.admin.ch/api/data/context"
),
- # nolint end
#' @field source_data_cols existing columns within the raw data
source_data_cols = c(
"hosp_new",
@@ -63,10 +38,10 @@ Switzerland <- R6::R6Class("Switzerland",
"tested_total"
),
#' @field source_text Plain text description of the source of the data
- source_text = "Open Data, Canton of Zurich",
+ source_text = "Swiss Federal Office of Public Health FOPH",
#' @field source_url Website address for explanation/introduction of the
#' data
- source_url = "https://github.com/openZH/covid_19/",
+ source_url = "https://www.covid19.admin.ch/en/overview",
#' @description Set up a table of region codes for clean data
#' @importFrom tibble tibble
@@ -94,19 +69,71 @@ Switzerland <- R6::R6Class("Switzerland",
)
},
+ #' @description Download function to get raw data. Downloads
+ #' the updated list of CSV files using `download_JSON`, filters
+ #' that to identify the required CSV files, then uses the parent
+ #' method `download` to download the CSV files.
+ #' @importFrom purrr keep
+ download = function() {
+ message_verbose(
+ self$verbose,
+ paste0("Downloading updated URLs from ", self$common_data_urls$main))
+
+ super$download_JSON()
+
+ self$data_urls <-
+ self$data$raw$main$data$sources$individual$csv$daily %>%
+ keep(names(.) %in% c("cases", "test", "death", "hosp"))
+
+ super$download()
+ },
+
#' @description Switzerland specific state level data cleaning
- #' @importFrom dplyr select filter mutate left_join rename
+ #' @importFrom dplyr select filter mutate left_join rename full_join
#' @importFrom lubridate as_date ymd
#' @importFrom rlang .data
#'
clean_common = function() {
- self$data$clean <- self$data$raw[["main"]] %>%
- select(-time, -source) %>%
+ cases <- self$data$raw$cases %>%
+ filter(geoRegion != "CH", geoRegion != "CHFL", datum_unit == "day") %>%
+ select(geoRegion, datum, entries, sumTotal) %>%
+ rename(level_1_region_code = geoRegion,
+ date = datum,
+ cases_new = entries,
+ cases_total = sumTotal)
+ hosp <- self$data$raw$hosp %>%
+ filter(geoRegion != "CH", geoRegion != "CHFL", datum_unit == "day") %>%
+ select(geoRegion, datum, entries, sumTotal) %>%
+ rename(level_1_region_code = geoRegion,
+ date = datum,
+ hosp_new = entries,
+ hosp_total = sumTotal)
+ deaths <- self$data$raw$death %>%
+ filter(geoRegion != "CH", geoRegion != "CHFL", datum_unit == "day") %>%
+ select(geoRegion, datum, entries, sumTotal) %>%
+ rename(level_1_region_code = geoRegion,
+ date = datum,
+ deaths_new = entries,
+ deaths_total = sumTotal)
+ tests <- self$data$raw$test %>%
+ filter(geoRegion != "CH", geoRegion != "CHFL", datum_unit == "day") %>%
+ # note that the data has entries_pos and entries_neg and we're
+ # currently not using it.
+ select(geoRegion, datum, entries, sumTotal) %>%
+ rename(level_1_region_code = geoRegion,
+ date = datum,
+ tested_new = entries,
+ tested_total = sumTotal)
+
+ self$data$clean <-
+ full_join(cases, deaths, by = c("date", "level_1_region_code")) %>%
+ full_join(hosp, by = c("date", "level_1_region_code")) %>%
+ full_join(tests, by = c("date", "level_1_region_code")) %>%
mutate(
level_1_region_code = if_else(
- .data$abbreviation_canton_and_fl == "FL",
+ .data$level_1_region_code == "FL",
"FL-FL",
- paste0("CH-", .data$abbreviation_canton_and_fl)
+ paste0("CH-", .data$level_1_region_code)
),
date = as_date(ymd(.data$date))
) %>%
@@ -114,15 +141,7 @@ Switzerland <- R6::R6Class("Switzerland",
self$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$ncumul_tested
- )
+ rename(level_1_region = region)
}
)
)
diff --git a/data/all_country_data.rda b/data/all_country_data.rda
index 0d177cf3..5e83bf89 100644
Binary files a/data/all_country_data.rda and b/data/all_country_data.rda differ
diff --git a/inst/WORDLIST b/inst/WORDLIST
index e3fb521e..4423c8e6 100644
--- a/inst/WORDLIST
+++ b/inst/WORDLIST
@@ -48,6 +48,7 @@ filepath
flavio
Flavio
fns
+FOPH
fromJSON
gb
geocode
diff --git a/man/Switzerland.Rd b/man/Switzerland.Rd
index c5ab1201..3f942b05 100644
--- a/man/Switzerland.Rd
+++ b/man/Switzerland.Rd
@@ -3,38 +3,10 @@
\name{Switzerland}
\alias{Switzerland}
\title{Switzerland Class for downloading, cleaning and processing notification data}
-\source{
-\url{https://github.com/openZH/covid_19/}
-}
\description{
Information for downloading, cleaning
and processing COVID-19 region data for Switzerland
}
-\section{Liechtenstein}{
-
-Liechtenstein is not a canton of Switzerland, but is presented in the
-source data as a peer of Swiss cantons and assigned the two letter code
-\code{FL}. \code{covidregionaldata} modifies this and presents the region code
-for Liechtenstein as \code{FL-FL}, consistent with the Swiss ISO 3166-2 codes
-which are of the form \code{CH-BE}, \code{CH-ZH}, \code{CH-VD}, ...
-
-If you do not wish to work with Liechtenstein
-data, filter out on this code. Note that this is labelled as a ISO 3166-2
-code but Liechtenstein's real ISO 3166-2 codes refer to sub-national
-regions.
-}
-
-\section{Additional data}{
-
-
-In addition to the standard \code{covidregionaldata} columns provided,
-the OpenDataZH source data provides other figures for ICU occupancy,
-number of patients on ventilators, and the how many individuals are
-isolated or quarantined. These columns are passed through unchanged.
-Further detail on them can be found at
-\url{https://github.com/openZH/covid_19/#swiss-cantons-and-principality-of-liechtenstein-unified-dataset}
-}
-
\examples{
\dontrun{
region <- Switzerland$new(verbose = TRUE, steps = TRUE, get = TRUE)
@@ -80,7 +52,9 @@ Subnational data sources
\item{\code{supported_region_codes}}{A list of region codes in order of level.}
-\item{\code{common_data_urls}}{List of named links to raw data.}
+\item{\code{common_data_urls}}{List of named links to raw data. This url links
+to a JSON file which provides the addresses for the most recently-updated
+CSV files, which are then downloaded.}
\item{\code{source_data_cols}}{existing columns within the raw data}
@@ -95,6 +69,7 @@ data}
\subsection{Public methods}{
\itemize{
\item \href{#method-set_region_codes}{\code{Switzerland$set_region_codes()}}
+\item \href{#method-download}{\code{Switzerland$download()}}
\item \href{#method-clean_common}{\code{Switzerland$clean_common()}}
\item \href{#method-clone}{\code{Switzerland$clone()}}
}
@@ -104,7 +79,6 @@ data}
\itemize{
\item \out{<span class="pkg-link" data-pkg="covidregionaldata" data-topic="DataClass" data-id="available_regions">}\href{../../covidregionaldata/html/DataClass.html#method-available_regions}{\code{covidregionaldata::DataClass$available_regions()}}\out{</span>}
\item \out{<span class="pkg-link" data-pkg="covidregionaldata" data-topic="DataClass" data-id="clean">}\href{../../covidregionaldata/html/DataClass.html#method-clean}{\code{covidregionaldata::DataClass$clean()}}\out{</span>}
-\item \out{<span class="pkg-link" data-pkg="covidregionaldata" data-topic="DataClass" data-id="download">}\href{../../covidregionaldata/html/DataClass.html#method-download}{\code{covidregionaldata::DataClass$download()}}\out{</span>}
\item \out{<span class="pkg-link" data-pkg="covidregionaldata" data-topic="DataClass" data-id="download_JSON">}\href{../../covidregionaldata/html/DataClass.html#method-download_JSON}{\code{covidregionaldata::DataClass$download_JSON()}}\out{</span>}
\item \out{<span class="pkg-link" data-pkg="covidregionaldata" data-topic="DataClass" data-id="filter">}\href{../../covidregionaldata/html/DataClass.html#method-filter}{\code{covidregionaldata::DataClass$filter()}}\out{</span>}
\item \out{<span class="pkg-link" data-pkg="covidregionaldata" data-topic="DataClass" data-id="get">}\href{../../covidregionaldata/html/DataClass.html#method-get}{\code{covidregionaldata::DataClass$get()}}\out{</span>}
@@ -125,6 +99,19 @@ Set up a table of region codes for clean data
\if{html}{\out{<div class="r">}}\preformatted{Switzerland$set_region_codes()}\if{html}{\out{</div>}}
}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-download"></a>}}
+\if{latex}{\out{\hypertarget{method-download}{}}}
+\subsection{Method \code{download()}}{
+Download function to get raw data. Downloads
+the updated list of CSV files using \code{download_JSON}, filters
+that to identify the required CSV files, then uses the parent
+method \code{download} to download the CSV files.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{Switzerland$download()}\if{html}{\out{</div>}}
+}
+
}
\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-clean_common"></a>}}
diff --git a/tests/testthat/custom_data/Switzerland_level_1.rds b/tests/testthat/custom_data/Switzerland_level_1.rds
index 0206b40f..0c0fc1be 100644
Binary files a/tests/testthat/custom_data/Switzerland_level_1.rds and b/tests/testthat/custom_data/Switzerland_level_1.rds differ