Download and parse NMD Biotic data to files

Downloads annual NMD Biotic data from the API and saves them as XML and/or RDS files on disk. Unlike downloadDatabase, this function does not write to a DuckDB database.

Usage

downloadDatabaseToFiles(
  years,
  dest,
  method = "compare",
  save = c("xml", "rds"),
  icesAreas = NULL,
  cruiseSeries = NULL,
  gearCodes = NULL
)

Arguments

years

Vector of integers specifying the years to be downloaded. The database reaches 1914:year(Sys.Date())

dest

Character string specifying the folder path where downloaded files should be saved. Subdirectories XMLfiles/ and Rdata/ are created automatically.

method

Character string controlling what to do when a file already exists. "compare" (default) re-downloads and overwrites; "keep" skips existing files.

save

Character vector of output formats. Can include "xml" (raw XML, always saved) and/or "rds" (parsed bioticToDatabase output as RDS).

icesAreas

ICES area shape st_polygon abject. Used for calculating the ICES area for a specific fishstation.

cruiseSeries

a data.table object of NMD cruise series list. Used to identify cruise series of a specific mission. See prepareCruiseSeriesList.

gearCodes

a data.table object of NMD gear code list. Used to make gearname and gearcategory columns. See prepareGearList.

Value

Called for its side effects: saves XML and/or RDS files to dest. Returns NULL invisibly.

Author

Ibrahim Umar, Mikko Vihtakari (Institute of Marine Research)