Download Johns Hopkins University CSSE data on Covid-19 — download_jhu_csse_covid19

Downloads Johns Hopkins University CSSE data on the spread of the SARS-CoV-2 virus and the Covid-19 pandemic (https://github.com/CSSEGISandData/COVID-19). The data for confirmed cases, reported deaths and recoveries are merged into one data frame, converted to long format and joined with ISO3c (ISO 3166-1 alpha-3) country codes based on the countrycode package. Please note: JHU stopped updating the data on March 10, 2023.

download_jhu_csse_covid19_data(
  type = "country",
  silent = FALSE,
  cached = FALSE
)

Arguments

type

type	The type of data that you want to retrieve. Can be any subset of "country": Data at the country level (the default). "country_region": Data at the country region level (only available for Australia, Canada, China and some oversea areas). "us_county": Data at the U.S. county level.
silent	Whether you want the function to send some status messages to the console. Might be informative as downloading will take some time and thus defaults to `TRUE`.
cached	Whether you want to download the cached version of the data from the tidycovid19 Github repository instead of retrieving the data from the authorative source. Downloading the cached version is faster and the cache is updated daily. Defaults to `FALSE`.

The type of data that you want to retrieve. Can be any subset of

"country": Data at the country level (the default).
"country_region": Data at the country region level (only available for Australia, Canada, China and some oversea areas).
"us_county": Data at the U.S. county level.

silent

Whether you want the function to send some status messages to the console. Might be informative as downloading will take some time and thus defaults to TRUE.

cached

Whether you want to download the cached version of the data from the tidycovid19 Github repository instead of retrieving the data from the authorative source. Downloading the cached version is faster and the cache is updated daily. Defaults to FALSE.

Value

If only one type was selected, a data frame containing the data. Otherwise, a list containing the desired data frames ordered as in type.

Examples

df <- download_jhu_csse_covid19_data(silent = TRUE, cached = TRUE)
df %>%
  dplyr::group_by(country) %>%
  dplyr::summarise(confirmed_cases = max(confirmed, na.rm = TRUE)) %>%
  dplyr::arrange(-confirmed_cases) %>%
  dplyr::top_n(10)
#> Selecting by confirmed_cases
#> # A tibble: 10 × 2
#>    country        confirmed_cases
#>    <chr>                    <dbl>
#>  1 US                   103802702
#>  2 India                 44690738
#>  3 France                39866718
#>  4 Germany               38249060
#>  5 Brazil                37081209
#>  6 Japan                 33320438
#>  7 Korea, South          30615522
#>  8 Italy                 25603510
#>  9 United Kingdom        24658705
#> 10 Russia                22075858

df <- download_jhu_csse_covid19_data(
  type = "us_county", silent = TRUE, cached = TRUE
)
df %>%
  dplyr::filter(!is.na(state)) %>%
  dplyr::group_by(state) %>%
  dplyr::summarise(deaths = max(deaths, na.rm = TRUE)) %>%
  dplyr::arrange(-deaths) %>%
  dplyr::top_n(10)
#> Selecting by deaths
#> # A tibble: 10 × 2
#>    state        deaths
#>    <chr>         <dbl>
#>  1 California    35545
#>  2 Florida       25840
#>  3 Arizona       18846
#>  4 Illinois      15289
#>  5 New York      14219
#>  6 Texas         11623
#>  7 Nevada         9313
#>  8 Michigan       9107
#>  9 Puerto Rico    5823
#> 10 Pennsylvania   5549