I am trying to retrieve multiple data txt files, that match a certain pattern, form multiple zipped files that I access through urls. I wrote a script that downloads the desired dataframe files from the url, saving them in a list, then rbinds all the dataframes together. I then sapply the function over a list of urls.
My desired end result is to have all the downloaded data form all urls in a single dataframe in the global environment in R.
Currently however, the individual files get downloaded into my working directory, which I don't want, and are not combined into a single dataframe. I'm wondering whether this problem stems from download.file, but I have been unable to find a solution or posts with similar issues.
# list of urls
url_df = data.frame(model = c("rcp26", "rcp45", "rcp85"),
url = c("https://b2share.eudat.eu/api/files/d4850267-3ce2-44f4-b5e3-8391a4f3dc27/LTER_site_data_from_EURO-CORDEX-RCMs_rel1.see_disclaimer.77c127c4-2ebe-453b-b5af-61858ff02e31.huss_historical_rcp26_day_txt.zip",
"https://b2share.eudat.eu/api/files/d4850267-3ce2-44f4-b5e3-8391a4f3dc27/LTER_site_data_from_EURO-CORDEX-RCMs_rel1.see_disclaimer.77c127c4-2ebe-453b-b5af-61858ff02e31.huss_historical_rcp45_day_txt.zip",
"https://b2share.eudat.eu/api/files/d4850267-3ce2-44f4-b5e3-8391a4f3dc27/LTER_site_data_from_EURO-CORDEX-RCMs_rel1.see_disclaimer.77c127c4-2ebe-453b-b5af-61858ff02e31.huss_historical_rcp85_day_txt.zip"))
# create empty dataframe where data will be saved
downloaded_data = data.frame()
# create function to retrieve desired files from a single url
get_data = function(url) {
temp <- tempfile() # create temp file
download.file(url,temp) # download file contained in the url
# get a list of the desired files
file.list <- grep("KNMI-RACMO22E.*txt|MPI-CSC-REMO.*txt|SMHI-RCA4.*txt", unzip(temp, list=TRUE)$Name, ignore.case=TRUE, value=TRUE)
data.list = lapply(unzip(temp, files=file.list), read.table, header=FALSE, comment.char = "", check.names = FALSE)
# bind the dataframes in the list into one single dataframe
bound_data = dplyr::bind_rows(data.list)
downloaded_data = rbind(downloaded_data, bound_data )
return(downloaded_data)
unlink(temp)
}
# apply function over the list of urls
sapply(url_df$url, get_data)
Any help would be greatly appreciated!
You can't refer to downloaded_data within the function -- the function will be applied to each URL separately, and then you can bind them together to create downloaded_data. There were also some changes to the unzipping and reading in of the data to make sure the files were actually being read in.
# list of urls
url_df = data.frame(model = c("rcp26", "rcp45", "rcp85"),
url = c("https://b2share.eudat.eu/api/files/d4850267-3ce2-44f4-b5e3-8391a4f3dc27/LTER_site_data_from_EURO-CORDEX-RCMs_rel1.see_disclaimer.77c127c4-2ebe-453b-b5af-61858ff02e31.huss_historical_rcp26_day_txt.zip",
"https://b2share.eudat.eu/api/files/d4850267-3ce2-44f4-b5e3-8391a4f3dc27/LTER_site_data_from_EURO-CORDEX-RCMs_rel1.see_disclaimer.77c127c4-2ebe-453b-b5af-61858ff02e31.huss_historical_rcp45_day_txt.zip",
"https://b2share.eudat.eu/api/files/d4850267-3ce2-44f4-b5e3-8391a4f3dc27/LTER_site_data_from_EURO-CORDEX-RCMs_rel1.see_disclaimer.77c127c4-2ebe-453b-b5af-61858ff02e31.huss_historical_rcp85_day_txt.zip"))
# create function to retrieve desired files from a single url
get_data = function(url) {
temp <- tempdir() # create temp file
download.file(url, file.path(temp, "downloaded.zip")) # download file contained in the url
downloaded_files <- unzip(file.path(temp, "downloaded.zip"), exdir = temp)
keep_files <- downloaded_files[grep("KNMI-RACMO22E.*txt|MPI-CSC-REMO.*txt|SMHI-RCA4.*txt",
downloaded_files)]
data.list <- lapply(keep_files, read.table, header=FALSE, comment.char = "", check.names = FALSE)
# bind the dataframes in the list into one single dataframe
bound_data = dplyr::bind_rows(data.list)
return(bound_data)
unlink(temp)
}
# apply function over the list of urls
downloaded_data <- dplyr::bind_rows(lapply(url_df$url, get_data))
dim(downloaded_data)
#> [1] 912962 7