In waldronlab/chasingcovid: Data Repository for the Chasing Covid Cohort

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Last run: r date()

library(chasingcovid)

Data Access

Get rid of %X to get rid of time of day:

fname <- file.path("..", "inst", "extdata", paste0("public_", format(Sys.time(), "%Y-%m-%d_%X"), ".csv"))
dat1 <- getData(url = "https://www.dropbox.com/s/pa9oiozesrpeug2/fakec3data_small.csv?dl=1",
  file = fname,
  key = "demokeyvalue")
getwd()
dir()

Try printing an environment variable - should appear in vignette but not GHA logs:

print(Sys.getenv("DROPBOX_TESTURL"))

dat2 <- getData(url = Sys.getenv("DROPBOX_TESTURL"), 
                file = "testfile2.csv",
                key = Sys.getenv("MD5_TESTKEY"))
identical(dat1, dat2)

List data files

See listing of data files on GitHub at https://github.com/waldronlab/chasingcovid/tree/main/inst/extdata.

baseurl <- "https://raw.githubusercontent.com/waldronlab/chasingcovid/main/inst/extdata/"
csvfiles <- dir(file.path("..", "inst", "extdata"), 
                   pattern=glob2rx("public*.csv"))
csvurls <- paste0(baseurl, csvfiles)
filetab <- data.frame(file = sub("\\.csv", "", csvfiles), csv = csvurls)