data-raw/ECDC.R

In eebrown/data2019nCoV: Data on the COVID-19 Outbreak

# ECDC.R

# Retrieved from https://covid.ourworldindata.org/data/ecdc/full_data.csv
# https://ourworldindata.org/coronavirus-source-data

library(tidyr)
library(plyr)
library(countrycode)

update_data_ecdc <- function() {

	download.file("https://covid.ourworldindata.org/data/ecdc/full_data.csv",
		          destfile = "data-raw/full_data.csv")
	ECDC_owid <- read.csv("data-raw/full_data.csv")

	ECDC_owid$date <- as.Date(ECDC_owid$date)

	usethis::use_data(ECDC_owid, overwrite = TRUE)

	ECDC_owid$location <- tolower(countrycode(ECDC_owid$location, 
		                              origin="country.name", destination="genc3c",
		                              custom_match=c(International="international", 
		                              	Timor="TLS", Kosovo="Kosovo", 
		                              	World="global")))

	cases <- pivot_wider(ECDC_owid, names_from = location, 
		                 values_from = total_cases, 
		                 id_cols = date, names_prefix = "cases_")

	deaths <- pivot_wider(ECDC_owid, names_from = location, 
		                  values_from = total_deaths, 
		                  id_cols = date, names_prefix = "deaths_")

	sarscov2_ecdc_2019 <- merge(cases, deaths, by = "date")

	usethis::use_data(sarscov2_ecdc_2019, overwrite = TRUE)

}

save(sarscov2_ecdc_2019, file = "sarscov2_who_2019.RData", version = 2)