finbif

R interface for the Finnish Biodiversity Information Facility (FinBIF) API

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 3 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
○
Committers with academic emails
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (20.9%) to scientific vocabulary

Keywords

api biodiversity biodiversity-informatics biodiversity-information finbif finbif-access occurrences r-package r-programming rstats species specimens taxon taxonomy web-services

Last synced: 6 months ago · JSON representation ·

Repository

R interface for the Finnish Biodiversity Information Facility (FinBIF) API

Basic Info

Host: GitHub
Owner: luomus
License: other
Language: R
Default Branch: main
Homepage: https://luomus.github.io/finbif/
Size: 73.4 MB

Statistics

Stars: 7
Watchers: 1
Forks: 1
Open Issues: 0
Releases: 30

Topics

api biodiversity biodiversity-informatics biodiversity-information finbif finbif-access occurrences r-package r-programming rstats species specimens taxon taxonomy web-services

Created over 6 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation Codeowners Codemeta Zenodo

README.Rmd

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

branch <- system2("git", c("rev-parse", "--abbrev-ref", "HEAD"), TRUE)
```
# FinBIF R package 


[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![License](https://img.shields.io/badge/license-MIT-brightgreen.svg?style=flat)](https://opensource.org/license/mit-0)
[![CRAN status](https://www.r-pkg.org/badges/version-last-release/finbif)](https://cran.r-project.org/package=finbif)
[![r-universe](https://luomus.r-universe.dev/badges/finbif)](https://luomus.r-universe.dev)
[![CRAN downloads](https://cranlogs.r-pkg.org/badges/grand-total/finbif?color=brightgreen)](https://cran.r-project.org/package=finbif)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3612814.svg)](https://doi.org/10.5281/zenodo.3612814)
[![Build Status](https://github.com/luomus/finbif/actions/workflows/check-standard.yml/badge.svg?branch=`r branch`)](https://github.com/luomus/finbif/actions)
[![codecov](https://codecov.io/gh/luomus/finbif/branch/`r branch`/graph/badge.svg)](https://app.codecov.io/github/luomus/finbif/branch/`r branch`)


The `finbif` R package is a programmatic interface to the
[Finnish Biodiversity Information Facility (FinBIF) API](https://api.laji.fi).
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](https://cran.r-project.org),
```{r install_cran, eval = FALSE}
install.packages("finbif")
```

You can also install the latest development version of `finbif` from
[GitHub](https://github.com),
```{r install_gh, eval = FALSE}
remotes::install_github("luomus/finbif@dev")
```

## Documentation
Read the online documentation for the current stable version of
`finbif` [here](https://luomus.github.io/finbif/), or the latest development
version of `finbif` [here](https://finbif-docs-dev.netlify.app).

## Getting a FinBIF access token
First load the `finbif` R package.
```{r setup}
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`.
```{r request-token, eval = FALSE}
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,
```{r set-token, eval = FALSE}
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](https://rviews.rstudio.com/2017/04/19/r-for-enterprise-understanding-r-s-startup/)
 for details). 

## Usage
Download occurrence data from FinBIF.
```{r occurrence, eval = FALSE}
finbif_occurrence("Cygnus cygnus", n = 100)
```

## Citation
```{r citation, results = "asis", echo = FALSE}
print(citation("finbif"), bibtex = FALSE)
```

----

## Contributing
Development is a community effort, and we encourage participation. Please read
[the contribution guide](https://github.com/luomus/finbif/blob/main/CONTRIBUTING.md)
for details.

Please note that the 'finbif' project is released with a
[Contributor Code of Conduct](https://github.com/luomus/finbif/blob/main/CODE_OF_CONDUCT.md).
By contributing to this project, you agree to abide by its terms.

Owner

Name: Luomus
Login: luomus
Kind: organization
Email: helpdesk@laji.fi
Location: Helsinki, Finland

Website: https://laji.fi
Repositories: 17
Profile: https://github.com/luomus

Finnish Museum of Natural History Luomus & Finnish Biodiversity Information Facility

Citation (CITATION.cff)

# YAML 1.2
---
version: "0.9.11"
date-released: 2025-08-22
title: finbif
abstract: |
    "The `finbif` R package is a programmatic interface to the [Finnish
    Biodiversity Information Facility (FinBIF) API](https://api.laji.fi). 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."
authors:
  -
    affiliation: "Finnish Museum of Natural History - Luomus"
    family-names: Morris
    given-names: "William K."
    orcid: "https://orcid.org/0000-0002-8686-4154"
cff-version: "1.2.0"
doi: "10.5281/zenodo.3612814"
keywords:
  - api
  - biodiversity
  - "biodiversity-informatics"
  - "biodiversity-information"
  - finbif
  - "finbif-access"
  - occurrences
  - "r-package"
  - "r-programming"
  - rstats
  - species
  - specimens
  - taxon
  - taxonomy
  - "web-services"
license: MIT
url: "https://luomus.github.io/finbif/"
repository-code: "https://github.com/luomus/finbif"
preferred-citation:
  authors:
    - family-names: Morris
      given-names: William K.
      orcid: "https://orcid.org/0000-0002-8686-4154"
  title: Introduction to the finbif package
  type: manual
  year: 2025
  doi: "10.5281/zenodo.3612814"
  notes: "R package version 0.9.11"
  url: "https://luomus.github.io/finbif/articles/finbif.html"
message: "If you use this software, please cite it using these metadata."
...

CodeMeta (codemeta.json)

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GitHub Events

Total

Create event: 2
Release event: 3
Issues event: 13
Watch event: 3
Issue comment event: 3
Push event: 23

Last Year

Create event: 2
Release event: 3
Issues event: 13
Watch event: 3
Issue comment event: 3
Push event: 23

Committers

Last synced: over 1 year ago

All Time

Total Commits: 1,923
Total Committers: 1
Avg Commits per committer: 1,923.0
Development Distribution Score (DDS): 0.0

Past Year

Commits: 199
Committers: 1
Avg Commits per committer: 199.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
wkmor1	w**i@m**l	1,923

Committer Domains (Top 20 + Academic)

mmorris.email: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 8
Total pull requests: 0
Average time to close issues: 18 days
Average time to close pull requests: N/A
Total issue authors: 4
Total pull request authors: 0
Average comments per issue: 0.88
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 5
Pull requests: 0
Average time to close issues: about 1 month
Average time to close pull requests: N/A
Issue authors: 2
Pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

wkmor1 (8)
jennybc (1)
HenrikBengtsson (1)
rduflot (1)

Pull Request Authors

Top Labels

Issue Labels

documentation (2) bug (1)

Pull Request Labels

Dependencies

DESCRIPTION cran

R >= 3.5.0 depends
digest * imports
graphics * imports
httr * imports
jsonlite * imports
lubridate * imports
lutz * imports
methods * imports
tools * imports
utils * imports
data.table * suggests
dplyr * suggests
future * suggests
grDevices * suggests
knitr * suggests
readODS * suggests
readxl * suggests
rmarkdown * suggests
testthat >= 2.1.0 suggests
tidyr * suggests
vcr * suggests
webfakes * suggests

.github/workflows/check-standard.yaml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/upload-artifact v3 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite

.github/workflows/test-coverage.yaml actions

actions/cache v3 composite
actions/checkout v3 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

finbif

Science Score: 67.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

Citation (CITATION.cff)

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies