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FinBIF R package

The finbif R package is a programmatic interface to the Finnish Biodiversity Information Facility (FinBIF) API. FinBIF aggregates Finnish biodiversity data from multiple sources in a single open access portal for researchers, citizen scientists, industry and government. FinBIF allows users of biodiversity information to find, access, combine and visualise data on Finnish plants, animals and microorganisms. The finbif R package makes the publicly available data in FinBIF easily accessible to programmers. Biodiversity information is available on taxonomy and taxon occurrence. Occurrence data can be filtered by taxon, time, location and other variables. The data accessed are conveniently preformatted for subsequent analyses.

Installation

You can install the current stable version of finbif from CRAN,

You can also install the latest development version of finbif from GitHub,

remotes::install_github("luomus/finbif@dev")

Documentation

Read the online documentation for the current stable version of finbif here, or the latest development version of finbif here.

Getting a FinBIF access token

First load the finbif R package.

To use the FinBIF API you must first request and set a personal access token. You can request an API token to be sent to your email address with the function finbif_get_token.

finbif_request_token("your@email.com")

Copy the access token that was sent to your email and set it as the environment variable FINBIF_ACCESS_TOKEN either for the current session,

Sys.setenv(
  FINBIF_ACCESS_TOKEN = "xtmSOIxjPwq0pOMB1WvcZgFLU9QBklauOlonWl8K5oaLIx8RniJLrvcJU4v9H7Et"
)
# Note: the above is not a real access token. Do not try using it.

, or by adding it to a Renviron startup file (see here for details).

Usage

Download occurrence data from FinBIF.

finbif_occurrence("Cygnus cygnus", n = 100)

Citation

Data from FinBIF comes from many sources. For information on citing FinBIF itself and the contributed datasets please visit this link:

https://laji.fi/en/about/2986

To cite the finbif R package in publications please use:

Morris, William K. (2024). Introduction to the finbif package. R package version 0.9.9, https://doi.org/10.5281/zenodo.3612814

Contributing

Development is a community effort, and we encourage participation. Please read the contribution guide for details.

Please note that the ‘finbif’ project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.