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Download the FORCIS database

Source: R/download_forcis_db.R
download_forcis_db.Rd

Downloads the entire FORCIS database as a collection of five csv files from Zenodo (https://zenodo.org/doi/10.5281/zenodo.7390791). Additional files will be also downloaded.

Usage

download_forcis_db(
  path = ".",
  version = options()$forcis_version,
  check_for_update = options()$check_for_update,
  overwrite = FALSE,
  timeout = 60
)

Arguments

path

a character of length 1. The folder in which the FORCIS database will be saved. Note that a subdirectory will be created, e.g. forcis-db/version-99/ (with 99 the version number).

version

a character of length 1. The version number (with two numbers, e.g. 08 instead of 8) of the FORCIS database to use. Default is the latest version. Note that this argument can be handle with the global option forcis_version. For example, if user calls options(forcis_version = "07"), the version 07 will be used by default for the current R session. Note that it is recommended to use the latest version of the database.

check_for_update

a logical. If TRUE (default) the function will check if a newer version of the FORCIS database is available on Zenodo and will print an informative message. Note that this argument can be handle with the global option check_for_update. For example, if user calls options(check_for_update = FALSE), the message to download the latest version will be disabled for the current R session.

overwrite

a logical. If TRUE it will override the downloaded files of the FORCIS database. Default is FALSE.

timeout

an integer. The timeout for downloading files from Zenodo. Default is 60. This number can be increased for low Internet connection.

Value

No return value. The FORCIS files will be saved in the path folder.

Details

The FORCIS database is regularly updated. The global structure of the tables doesn’t change between versions but some bugs can be fixed and new records can be added. This is why it is recommended to use the latest version of the database. The package is designed to handle the versioning of the database on Zenodo and will inform the user if a new version is available each time he/she uses one of the read_*_data() functions.

For more information, please read the vignette available at https://frbcesab.github.io/forcis/articles/database-versions.html.

References

Chaabane S, De Garidel-Thoron T, Giraud X, et al. (2023) The FORCIS database: A global census of planktonic Foraminifera from ocean waters. Scientific Data, 10, 354. DOI: https://doi.org/10.1038/s41597-023-02264-2.

See also

read_plankton_nets_data() to import the FORCIS database.

Examples

if (FALSE) { # \dontrun{
# Attach the package ----
library("forcis")

# Folder in which the database will be saved ----
path_to_save_db <- "data"

# Download the database ----
download_forcis_db(path = path_to_save_db)

# Check the content of the folder ----
list.files(path_to_save_db, recursive = TRUE)
} # }