These functions provide an R interface to list all files in a Zenodo record and to download one of those files (optionally reading it into R).
Usage
zenodo_file_list(record_id)
zenodo_download_file(
record_id = NULL,
file_name = NULL,
dest_file = NULL,
read_func = NULL,
delete_temp = TRUE,
unwrap_r = TRUE,
verbose = FALSE,
check_md5sum = TRUE,
timeout = 600L,
...
)Arguments
- record_id
Character or numeric. The Zenodo record ID (e.g.,
"1234567").- file_name
Character. The file key (or filename) as listed in the Zenodo record.
- dest_file
Character (optional). Local destination path to save the downloaded file. If
NULL(default), a temporary file is created and deleted ifread_funcis used.- read_func
Function (optional). A function to read or process the downloaded file (e.g.,
read.csv(),readr::read_csv(),readLines(),readxl::read_excel(), etc.). IfNULL, only the file path is returned.- delete_temp
Logical. Whether to delete temporary files after reading them with
read_func. Default isTRUE. Set toFALSEif you need the file to persist or if you're experiencing "resource busy" errors with complex read functions.- unwrap_r
Logical. If
read_funcreturns anPackedSpatRasterorPackedSpatVectorobject, this argument controls whether to unwrap packed objects usingterra::unwrap(). Default isTRUE.- verbose
Logical. Whether to print progress messages during download. Default is
FALSE.- check_md5sum
Logical. Whether to verify the MD5 checksum of the downloaded file against the checksum provided by Zenodo. Default is
TRUE. If the checksums do not match, an error is raised and the file is deleted. Set toFALSEto skip this verification step.- timeout
Numeric. Maximum time (in seconds) to wait for the download to complete. Default is
600Lseconds (10 minutes). Increase this value for larger files or slower connections.- ...
Additional arguments passed to
read_func.
Value
zenodo_file_listreturns atibblewith metadata for each file in the Zenodo record, including file key, filename, download link, and record-level metadata such as title, DOI, and creation dates.zenodo_download_file: Ifread_funcisNULL, returns the path to the downloaded file. Ifread_funcis provided, returns the output of that function.
Details
zenodo_file_list()lists all files and their metadata for a given Zenodo record.zenodo_download_file()downloads a specified file from a Zenodo record and can optionally read its contents into R using a user-supplied function.
Examples
require(ecokit)
ecokit::load_packages(terra, dplyr, fs)
files <- zenodo_file_list("6620748")
dplyr::glimpse(files)
#> Rows: 59
#> Columns: 12
#> $ title <chr> "Phanerozoic continental climate and Köppen–Geiger climate…
#> $ id_url <chr> "https://zenodo.org/api/records/6620748", "https://zenodo.…
#> $ created <dttm> 2022-06-07 15:21:05, 2022-06-07 15:21:05, 2022-06-07 15:2…
#> $ modified <dttm> 2024-07-16 15:44:29, 2024-07-16 15:44:29, 2024-07-16 15:4…
#> $ updated <dttm> 2024-07-16 15:44:29, 2024-07-16 15:44:29, 2024-07-16 15:4…
#> $ doi_version <chr> "10.5281/zenodo.6620748", "10.5281/zenodo.6620748", "10.52…
#> $ doi <chr> "10.5281/zenodo.6402040", "10.5281/zenodo.6402040", "10.52…
#> $ id <int> 6620748, 6620748, 6620748, 6620748, 6620748, 6620748, 6620…
#> $ key <chr> "40Ma_Pohletal2022_DIB_PhaneroContinentalClimate.nc", "0Ma…
#> $ size <int> 8261200, 14498683, 8261200, 14573851, 8261200, 14407735, 8…
#> $ checksum <chr> "md5:e9ca6e5e58b7b892c2dfd00fffdcc7af", "md5:65ee19cbf3da6…
#> $ link <chr> "https://zenodo.org/api/records/6620748/files/40Ma_Pohleta…
# --------------------------------------------
# Download as file only
pdf_file <- zenodo_download_file(
record_id = "1234567", file_name = "article.pdf")
print(pdf_file)
#> /tmp/Rtmph1PjGb/article260f6596d45d.pdf
ecokit::file_type(pdf_file)
#> [1] "PDF document, version 1.6"
try(fs::file_delete(pdf_file), silent = TRUE)
# --------------------------------------------
# Download and read NetCDF as SpatRaster
nc_file <- zenodo_download_file(
record_id = "6620748",
file_name = "100Ma_Pohletal2022_DIB_PhaneroContinentalClimate.nc",
read_func = terra::rast)
print(class(nc_file))
#> [1] "SpatRaster"
#> attr(,"package")
#> [1] "terra"
print(nc_file)
#> class : SpatRaster
#> size : 128, 128, 3 (nrow, ncol, nlyr)
#> resolution : 1.40625, 2.8125 (x, y)
#> extent : -90, 90, 0, 360 (xmin, xmax, ymin, ymax)
#> coord. ref. :
#> source(s) : memory
#> varname : topo (topography)
#> names : topo, koppen, area
#> unit : m above sea level, Koppen_Geiger classes (see associated data article), m2
terra::inMemory(nc_file)
#> [1] TRUE
# --------------------------------------------
# Download and read NetCDF as SpatRaster; using custom function
nc_file2 <- zenodo_download_file(
record_id = "6620748",
file_name = "100Ma_Pohletal2022_DIB_PhaneroContinentalClimate.nc",
read_func = function(x) { terra::rast(x) * 10 })
print(class(nc_file2))
#> [1] "SpatRaster"
#> attr(,"package")
#> [1] "terra"
print(nc_file2)
#> class : SpatRaster
#> size : 128, 128, 3 (nrow, ncol, nlyr)
#> resolution : 1.40625, 2.8125 (x, y)
#> extent : -90, 90, 0, 360 (xmin, xmax, ymin, ymax)
#> coord. ref. :
#> source(s) : memory
#> names : topo, koppen, area
#> min values : 200.00, 10, 5999121712
#> max values : 31916.11, 130, 488827875451
terra::inMemory(nc_file2)
#> [1] TRUE
# --------------------------------------------
terra::app(nc_file, "range")
#> class : SpatRaster
#> size : 128, 128, 2 (nrow, ncol, nlyr)
#> resolution : 1.40625, 2.8125 (x, y)
#> extent : -90, 90, 0, 360 (xmin, xmax, ymin, ymax)
#> coord. ref. :
#> source(s) : memory
#> names : lyr.1, lyr.2
#> min values : 1, 599912171
#> max values : 13, 48882787545
terra::app(nc_file2, "range")
#> class : SpatRaster
#> size : 128, 128, 2 (nrow, ncol, nlyr)
#> resolution : 1.40625, 2.8125 (x, y)
#> extent : -90, 90, 0, 360 (xmin, xmax, ymin, ymax)
#> coord. ref. :
#> source(s) : memory
#> names : lyr.1, lyr.2
#> min values : 10, 5999121712
#> max values : 130, 488827875451