View source: R/compileDatabase.R
compileDatabase | R Documentation |
Downloads, formulates and indexes IMR Biotic database into a format used by BioticExplorer
compileDatabase(
years = 1900:data.table::year(Sys.time()),
dbPath = "~/IMR_biotic_BES_database",
dbIndexFile = file.path(dbPath, "dbIndex.rda"),
dbName = NULL,
overwrite = FALSE
)
years |
Vector of integers specifying the years to be downloaded. The database reaches 1914:year(Sys.Date()) |
dbPath |
Character string specifying the folder where the duckdb and dbIndex files should be saved. |
dbIndexFile |
Character string specifying the file path where the index of the database should be saved. Must include |
dbName |
Character string or |
overwrite |
Logical indicating whether existing information in the duckdb database ( |
Runs the prepareCruiseSeriesList
, prepareGearList
, downloadDatabase
and indexDatabase
functions, and saves the results into a duckdb. Be aware that running these functions requires access to the IMR intranet and reasonably stable internet. It is advisable to run the function in a separate R session or in a screen session in the terminal on Unix machines, as downloading the database takes several hours and requires a stable internet connection. If the connection is unstable, the function may return an error. In such cases, ensure that the connection is stable and rerun the function. The function should continue downloading from where it left off.
Mikko Vihtakari, Ibrahim Umar (Institute of Marine Research)
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