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Download FishBase and SeaLifeBase Data

Source: R/fishbase_data.R
download_fishbase_data.Rd

This function downloads the tables of a FishBase and/or SeaLifeBase release (the static snapshots of the database tables used by the rfishbase package, as parquet files) to data_dir, so they can be used offline. By default it downloads the tables the package uses (species, estimate, families, synonyms, stocks and faoareas: about 15 MB for each database); a complete release takes about 140 MB for FishBase and 110 MB for SeaLifeBase.

Usage

download_fishbase_data(
  server = c("fishbase", "sealifebase"),
  version = "latest",
  tables = "needed",
  data_dir = fao_data_dir(),
  overwrite = FALSE,
  quiet = FALSE
)

Arguments

server

"fishbase", "sealifebase" or both (default).

version

The release to download, e.g. "26.06". Default is "latest".

tables

"needed" (default) for the tables the package uses, "all" for every table, or table names, e.g. c("species", "estimate").

data_dir

The directory where the data is saved. Default is fao_data_dir().

overwrite

A logical value. If TRUE, tables already downloaded are downloaded again. Default is FALSE.

quiet

A logical value. If TRUE, progress messages are not printed. Default is FALSE.

Value

Invisibly, a data frame with one row per table: server, version, table, size and status ("downloaded", "already downloaded" or "failed").

Details

Downloading beforehand is optional: functions that use FishBase data, such as fishbase_match(), look online for the newest release first and download the tables they need. When the computer is offline they use the newest release downloaded here, and when nothing has been downloaded, fishbase_match() uses the table built into the package. Tables already downloaded are skipped, so an interrupted download can be resumed by running the function again.

Reading the tables needs the nanoparquet package (install.packages("nanoparquet")). FishBase and SeaLifeBase data are licensed CC BY-NC 4.0 by the FishBase team: they can be used with attribution, but not commercially.

References

Froese, R. and Pauly, D. (Eds.) FishBase. World Wide Web electronic publication. https://www.fishbase.se

Palomares, M.L.D. and Pauly, D. (Eds.) SeaLifeBase. World Wide Web electronic publication. https://www.sealifebase.se

Boettiger, C., Lang, D.T. and Wainwright, P.C. (2012). rfishbase: exploring, manipulating and visualizing FishBase data from R. Journal of Fish Biology 81(6): 2030-2039. doi:10.1111/j.1095-8649.2012.03464.x . Source code: https://github.com/ropensci/rfishbase

Examples

if (FALSE) { # \dontrun{
check_fishbase_update()
download_fishbase_data()                          # the tables the package uses
download_fishbase_data(tables = "all")            # every table of FishBase and SeaLifeBase
download_fishbase_data("fishbase", tables = c("species", "estimate"))
} # }