Download and parse NMD data for the BioticExplorer database

Downloads annual NMD data from the API and writes them as a DuckDB database

Usage

downloadDatabase(
  years,
  connection,
  icesAreas = NULL,
  cruiseSeries = NULL,
  gearCodes = NULL,
  taxaList = NULL,
  overwrite = FALSE
)

Arguments

years

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

connection

Object defining the duckdb connection. Typically made within compileDatabase.

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.

taxaList

a data.table object of NMD taxa reference data. Written to the taxaindex DuckDB table. See prepareTaxaList.

overwrite

Logical indicating whether requested years and reference tables already present in the duckdb database should be downloaded again and replaced. Existing annual rows are deleted transactionally before replacement, so they are not duplicated.

Value

Called for its side effects: appends parsed Biotic data to the DuckDB database. Returns NULL invisibly.

Details

The function writes the taxa reference list to the database, downloads NMD data from the API per year, saves these in temp files, reformats them for the DuckDB and writes them into the database.

Author

Ibrahim Umar, Mikko Vihtakari (Institute of Marine Research)