Extract FLUXNET data from downloaded zip files

Extracts data from zip files downloaded by flux_download() with options to extract only subsets of the files they contain.

Usage

flux_extract(
  zip_dir = "fluxnet",
  output_dir = fs::path(zip_dir, "unzipped"),
  site_ids = "all",
  networks = c("AMF", "CNF", "EUF", "FLX", "ICOS", "JPF", "KOF", "SAEON", "TERN"),
  resolutions = c("y", "m", "w", "d", "h"),
  extract_varinfo = TRUE,
  extract_txt = FALSE,
  overwrite = FALSE
)

Arguments

zip_dir

The directory with the zip files

output_dir

The directory to unzip files to. Within this directory, data files will be nested by site.

site_ids

A character vector of site IDs (e.g. c("AR-TF2", "CA-Ca2")) can be supplied to only unzip data for certain sites. If "all" (default), all zip files found in zip_dir will be unzipped.

networks

A character vector indicating which networks to extract files from. Multiple values may be provided. Defaults to all networks.

resolutions

A character vector indicating which time resolutions to extract. Options are yearly ("y"), monthly ("m"), daily ("d"), and hourly/half-hourly ("h"). Multiple options may be passed with all of them as default.

extract_varinfo

Logical; extract the BIF and BIFVARINFO files containing variable information in the BADM Interchange Format? Defaults to TRUE.

extract_txt

Logical; extract the README.txt and DATA_POLICY_LICENSE_AND_INSTRUCTIONS.txt files? Defaults to FALSE.

overwrite

Logical; should existing extracted files be overwritten (TRUE) or ignored (FALSE)?

Value

Invisbly returns a dataframe of file paths and error messages if there are any errors generated by unzipping.