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("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).
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.