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.
You can install the current stable version of finbif from
CRAN,
install.packages("finbif")You can also install the latest development version of finbif from
GitHub,
remotes::install_github("luomus/finbif@dev")Read the online documentation for the current stable version of
finbif here, or the latest development
version of finbif here.
First load the finbif R package.
library(finbif)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("[email protected]")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).
Download occurrence data from FinBIF.
finbif_occurrence("Cygnus cygnus", n = 100)Data from FinBIF comes from many sources. For information on citing FinBIF itself and the contributed datasets please visit this link:
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
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.