The URL for Johns Hopkins CSSE (Center for Systems Science and Engineering) COVID-19 GitHub website directs you to a master folder from which subfolders can be selected. In this example, I chose the csse_covid_19_data folder, then selected the csse_covid_19_daily_reports_us folder, then selected file 08-24-2020.csv. This is a URL version of the file; select Raw in the file header to obtain the comma-delimited file’s URL. Now we save the URL and the destination file names as variables url and destfile respectively, and use the download.file function in R to save the comma-delimited file to the default working directory.
url="https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_daily_reports_us/08-24-2020.csv"
destfile="Aug_24_2020_Daily.csv"
download.file(url,destfile,quiet=TRUE)The quiet argument suppresses some information about processing the request that I did not find particularly enlightening. You should open the file in your working directory in Excel or a text editor to make sure it imported correctly.
Suppose we wish to download data every day. It is not so difficult to modify the arguments in url and destfile, but we can automate it somewhat using a function with a single argument and the paste command (paste0 is used as well, just to show an alternative for pasting character strings with no delimiter between them).
COVIDDaily=function(datestring){
url=paste("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_daily_reports_us/",datestring,".csv",sep="")
destfile=paste0(datestring,"-Daily.csv")
download.file(url,destfile,quiet=TRUE)
}We can then call our function to retreive the next day’s data, and read the data into RStudio:
COVIDDaily("08-26-2020")
COVID_Aug_26=read.csv("08-26-2020-Daily.csv")