Data

Tools

Indexes

Applications

Experiments

Open Sustainable Technology

forcis

Provide an interface to the FORCIS database that includes data on living planktonic foraminifera diversity and distribution in the global oceans from 1910 until 2018 collected using plankton tows, continuous plankton recorder, sediment traps and plankton pump from the global ocean.
https://github.com/ropensci/forcis

Category: Biosphere
Sub Category: Marine Life and Fishery

Keywords from Contributors

optimize archiving measur transforms animals conversion generic observation projection compose

Last synced: about 5 hours ago
JSON representation

Repository metadata

Handle the FORCIS foraminifera database

README.Rmd 

          ---
output: github_document
---




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







forcis 
=========================================================


[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/660_status.svg)](https://github.com/ropensci/software-review/issues/660)
[![CRAN status](https://www.r-pkg.org/badges/version/forcis)](https://CRAN.R-project.org/package=forcis)
[![License: GPL (>= 2)](https://img.shields.io/badge/License-GPL%20%28%3E%3D%202%29-blue.svg)](https://choosealicense.com/licenses/gpl-2.0/)
[![R CMD Check](https://github.com/ropensci/forcis/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/forcis/actions/workflows/R-CMD-check.yaml)
[![codecov](https://codecov.io/gh/ropensci/forcis/branch/main/graph/badge.svg)](https://app.codecov.io/gh/ropensci/forcis)
[![JOSS](https://joss.theoj.org/papers/10.21105/joss.09217/status.svg)](https://doi.org/10.21105/joss.09217)
[![DOI](https://zenodo.org/badge/428715013.svg)](https://doi.org/10.5281/zenodo.15470664)



## Table of contents



  • Overview

  • Installation

  • Documentation

  • Citation

  • Contributing

  • Acknowledgments

  • References





## Overview

The goal of the R package `forcis` is to provide an interface to the [FORCIS database](https://zenodo.org/doi/10.5281/zenodo.7390791) on global foraminifera distribution (Chaabane _et al._ 2023). This database includes data on living planktonic foraminifera diversity and distribution in the global oceans from 1910 until 2018 collected using plankton tows, continuous plankton recorder, sediment traps and plankton pump from the global ocean.

![Figure 1: Recommended workflow and main features of `forcis`](man/figures/workflow.png)




This package has been developed for researchers interested in working with the FORCIS database, even without advanced R skills. It provides basic functions to facilitate the handling of this large database, including functions to download, select, filter, homogenize, and visualize the data. It also enables users to explore the spatial distribution and temporal evolution of planktonic foraminifera.


![Figure 2: Overview of visualizations available in `forcis`](man/figures/visualization.png)

## Installation

You can install the development version from [GitHub](https://github.com/) with:

```{r eval=FALSE}
## Install < remotes > package (if not already installed) ----
if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}

## Install dev version of < forcis > from GitHub ----
remotes::install_github("ropensci/forcis")
```

**N.B.** The `forcis` package depends on the [`sf`](https://r-spatial.github.io/sf/) package which requires some spatial system libraries (GDAL and PROJ). Please read [this page](https://github.com/r-spatial/sf?tab=readme-ov-file#installing) if you have any trouble to install `forcis`.


Finally you can attach the package `forcis` with:

```{r eval=FALSE}
library("forcis")
```


## Documentation

`forcis` provides five vignettes to learn more about the package:

- the [Get started](https://docs.ropensci.org/forcis/articles/forcis.html) vignette describes the core features of the package
- the [Database versions](https://docs.ropensci.org/forcis/articles/database-versions.html) vignette provides information on how to deal with the versioning of the database
- the [Select and filter data](https://docs.ropensci.org/forcis/articles/select-and-filter-data.html) vignette shows examples to handle the FORCIS data
- the [Data conversion](https://docs.ropensci.org/forcis/articles/data-conversion.html) vignette describes the conversion functions available in `forcis` to compute abundances, concentrations, and frequencies
- the [Data visualization](https://docs.ropensci.org/forcis/articles/data-visualization.html) vignette describes the plotting functions available in `forcis`




## Citation

Please cite this package as: 

> Casajus N, Chaabane S, de Garidel-Thoron T, Giraud X & Greco M  (2025) forcis: An R package for accessing, handling and analysing the FORCIS database. **Journal of Open Source Software**, 10(114), 9217. DOI: [10.21105/joss.09217](https://doi.org/10.21105/joss.09217).

You can also run:

```{r eval = FALSE}
citation("forcis")
```



## Contributing

All types of contributions are encouraged and valued. For more information, check out our [Contributor Guidelines](https://github.com/ropensci/forcis/blob/main/CONTRIBUTING.md).

Please note that this package is released with a [Contributor
Code of Conduct](https://ropensci.org/code-of-conduct/). 
By contributing to this project, you agree to abide by its terms.



## Acknowledgments

This package has been developed for the [FRB-CESAB](https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/) working group [FORCIS](https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/forcis/) that aims to understand the importance of the main stressors such as temperature and ocean acidification that govern foraminifera species distribution and calcification processes, with focus on present and near-future ocean impacts. 

We want to thanks Khalil Hammami ([@khammami](https://github.com/khammami)) for his valuable contribution to this package.



## References

Chaabane S, De Garidel-Thoron T, Giraud X, Schiebel R, Beaugrand G, Brummer G-J, Casajus N, Greco M, Grigoratou M, Howa H, Jonkers L, Kucera M, Kuroyanagi A, Meilland J, Monteiro F, Mortyn G, Almogi-Labin A, Asahi H, Avnaim-Katav S, Bassinot F, Davis CV, Field DB, Hernández-Almeida I, Herut B, Hosie G, Howard W, Jentzen A, Johns DG, Keigwin L, Kitchener J, Kohfeld KE, Lessa DVO, Manno C, Marchant M, Ofstad S, Ortiz JD, Post A, Rigual-Hernandez A, Rillo MC, Robinson K, Sagawa T, Sierro F, Takahashi KT, Torfstein A, Venancio I, Yamasaki M & Ziveri P (2023) The FORCIS database: A global census of planktonic Foraminifera from ocean waters. **Scientific Data**, 10, 354.
DOI: [10.1038/s41597-023-02264-2](https://doi.org/10.1038/s41597-023-02264-2).

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "forcis" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'forcis: Handle the FORCIS Foraminifera Database'
version: 1.0.1
doi: 10.21105/joss.09217
identifiers:
- type: doi
  value: 10.32614/CRAN.package.forcis
abstract: Provides an interface to the 'FORCIS' database (Chaabane et al. (2024) <https://doi.org/10.5281/zenodo.7390791>)
  on global foraminifera distribution. This package allows to download and to handle
  'FORCIS' data. It is part of the FRB-CESAB working group FORCIS. <https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/forcis/>.
authors:
- family-names: Casajus
  given-names: Nicolas
  email: nicolas.casajus@fondationbiodiversite.fr
  orcid: https://orcid.org/0000-0002-5537-5294
- family-names: Greco
  given-names: Mattia
  email: mattia_greco@outlook.com
  orcid: https://orcid.org/0000-0003-2416-6235
- family-names: Chaabane
  given-names: Sonia
  email: sonia.chaabane@gmail.com
  orcid: https://orcid.org/0000-0002-4653-8610
- family-names: Giraud
  given-names: Xavier
  email: giraud@cerege.fr
  orcid: https://orcid.org/0000-0001-5067-8176
- family-names: Garidel-Thoron
  given-names: Thibault
  name-particle: de
  email: garidel@cerege.fr
  orcid: https://orcid.org/0000-0001-8983-9571
preferred-citation:
  type: article
  title: 'forcis: An R package for accessing, handling and analysing the FORCIS database'
  authors:
  - name: Casajus Nicolas
  - name: Chaabane Sonia
  - name: Giraud Xavier
  - name: de Garidel-Thoron Thibault
  - name: Greco Mattia
  journal: Journal of Open Source Software
  volume: '10'
  doi: 10.21105/joss.09217
  year: '2025'
  start: '9217'
repository: https://CRAN.R-project.org/package=forcis
repository-code: https://github.com/ropensci/forcis
url: https://docs.ropensci.org/forcis/
contact:
- family-names: Casajus
  given-names: Nicolas
  email: nicolas.casajus@fondationbiodiversite.fr
  orcid: https://orcid.org/0000-0002-5537-5294
references:
- type: article
  title: 'The FORCIS database: A global census of planktonic Foraminifera from ocean
    waters'
  authors:
  - name: Chaabane Sonia
  - name: De Garidel-Thoron Thibault
  - name: Giraud Xavier
  - name: Schiebel Ralf
  - name: Beaugrand Gregory
  - name: Brummer Geert-Jan
  - name: Casajus Nicolas
  - name: Greco Mattia
  - name: Grigoratou Maria
  - name: Howa Hélène
  - name: Jonkers Lukas
  - name: Kucera Michal
  - name: Kuroyanagi Azumi
  - name: Meilland Julie
  - name: Monteiro Fanny
  - name: Mortyn Graham
  - name: Almogi-Labin Ahuva
  - name: Asahi Hirofumi
  - name: Avnaim-Katav Simona
  - name: Bassinot Franck
  - name: Davis Catherine V.
  - name: Field David B.
  - name: Hernández-Almeida Iván
  - name: Herut Barak
  - name: Hosie Graham
  - name: Howard Will
  - name: Jentzen Anna
  - name: Johns David G.
  - name: Keigwin Lloyd
  - name: Kitchener John
  - name: Kohfeld Karen E.
  - name: Lessa Douglas V. O.
  - name: Manno Clara
  - name: Marchant Margarita
  - name: Ofstad Siri
  - name: Ortiz Joseph D.
  - name: Post Alexandra
  - name: Rigual-Hernandez Andres
  - name: Rillo Marina C.
  - name: Robinson Karen
  - name: Sagawa Takuya
  - name: Sierro Francisco
  - name: Takahashi Kunio T.
  - name: Torfstein Adi
  - name: Venancio Igor
  - name: Yamasaki Makoto
  - name: Ziveri Patrizia
  journal: Scientific Data
  volume: '10'
  doi: 10.1038/s41597-023-02264-2
  year: '2023'
  start: '354'
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
  version: '>= 4.1.0'
- type: software
  title: ggplot2
  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
  notes: Imports
  url: https://ggplot2.tidyverse.org
  repository: https://CRAN.R-project.org/package=ggplot2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Chang
    given-names: Winston
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Henry
    given-names: Lionel
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Takahashi
    given-names: Kohske
  - family-names: Wilke
    given-names: Claus
    orcid: https://orcid.org/0000-0002-7470-9261
  - family-names: Woo
    given-names: Kara
    orcid: https://orcid.org/0000-0002-5125-4188
  - family-names: Yutani
    given-names: Hiroaki
    orcid: https://orcid.org/0000-0002-3385-7233
  - family-names: Dunnington
    given-names: Dewey
    orcid: https://orcid.org/0000-0002-9415-4582
  - family-names: Brand
    given-names: Teun
    name-particle: van den
    orcid: https://orcid.org/0000-0002-9335-7468
  year: '2025'
  doi: 10.32614/CRAN.package.ggplot2
- type: software
  title: httr2
  abstract: 'httr2: Perform HTTP Requests and Process the Responses'
  notes: Imports
  url: https://httr2.r-lib.org
  repository: https://CRAN.R-project.org/package=httr2
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.httr2
- type: software
  title: rlang
  abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
  notes: Imports
  url: https://rlang.r-lib.org
  repository: https://CRAN.R-project.org/package=rlang
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.rlang
- type: software
  title: sf
  abstract: 'sf: Simple Features for R'
  notes: Imports
  url: https://r-spatial.github.io/sf/
  repository: https://CRAN.R-project.org/package=sf
  authors:
  - family-names: Pebesma
    given-names: Edzer
    email: edzer.pebesma@uni-muenster.de
    orcid: https://orcid.org/0000-0001-8049-7069
  year: '2025'
  doi: 10.32614/CRAN.package.sf
- type: software
  title: tibble
  abstract: 'tibble: Simple Data Frames'
  notes: Imports
  url: https://tibble.tidyverse.org/
  repository: https://CRAN.R-project.org/package=tibble
  authors:
  - family-names: Müller
    given-names: Kirill
    email: kirill@cynkra.com
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2025'
  doi: 10.32614/CRAN.package.tibble
- type: software
  title: tidyr
  abstract: 'tidyr: Tidy Messy Data'
  notes: Imports
  url: https://tidyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=tidyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
  - family-names: Girlich
    given-names: Maximilian
  year: '2025'
  doi: 10.32614/CRAN.package.tidyr
- type: software
  title: utils
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
- type: software
  title: vroom
  abstract: 'vroom: Read and Write Rectangular Text Data Quickly'
  notes: Imports
  url: https://vroom.r-lib.org
  repository: https://CRAN.R-project.org/package=vroom
  authors:
  - family-names: Hester
    given-names: Jim
    orcid: https://orcid.org/0000-0002-2739-7082
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Bryan
    given-names: Jennifer
    email: jenny@posit.co
    orcid: https://orcid.org/0000-0002-6983-2759
  year: '2025'
  doi: 10.32614/CRAN.package.vroom
- type: software
  title: fs
  abstract: 'fs: Cross-Platform File System Operations Based on ''libuv'''
  notes: Suggests
  url: https://fs.r-lib.org
  repository: https://CRAN.R-project.org/package=fs
  authors:
  - family-names: Hester
    given-names: Jim
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Csárdi
    given-names: Gábor
    email: csardi.gabor@gmail.com
  year: '2025'
  doi: 10.32614/CRAN.package.fs
- type: software
  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Suggests
  url: https://dplyr.tidyverse.org
  repository: https://CRAN.R-project.org/package=dplyr
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: François
    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
  - family-names: Henry
    given-names: Lionel
  - family-names: Müller
    given-names: Kirill
    orcid: https://orcid.org/0000-0002-1416-3412
  - family-names: Vaughan
    given-names: Davis
    email: davis@posit.co
    orcid: https://orcid.org/0000-0003-4777-038X
  year: '2025'
  doi: 10.32614/CRAN.package.dplyr
- type: software
  title: httptest2
  abstract: 'httptest2: Test Helpers for ''httr2'''
  notes: Suggests
  url: https://enpiar.com/httptest2/
  repository: https://CRAN.R-project.org/package=httptest2
  authors:
  - family-names: Richardson
    given-names: Neal
    email: neal.p.richardson@gmail.com
    orcid: https://orcid.org/0009-0002-7992-3520
  year: '2025'
  doi: 10.32614/CRAN.package.httptest2
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2025'
  doi: 10.32614/CRAN.package.knitr
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@posit.co
  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Atkins
    given-names: Aron
    email: aron@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
    given-names: Richard
    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2025'
  doi: 10.32614/CRAN.package.rmarkdown
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2025'
  doi: 10.32614/CRAN.package.testthat
  version: '>= 3.0.0'
- type: software
  title: vdiffr
  abstract: 'vdiffr: Visual Regression Testing and Graphical Diffing'
  notes: Suggests
  url: https://vdiffr.r-lib.org/
  repository: https://CRAN.R-project.org/package=vdiffr
  authors:
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Luciani
    given-names: T Jake
    email: jake@apache.org
  - family-names: Decorde
    given-names: Matthieu
    email: matthieu.decorde@ens-lyon.fr
  - family-names: Lise
    given-names: Vaudor
    email: lise.vaudor@ens-lyon.fr
  year: '2025'
  doi: 10.32614/CRAN.package.vdiffr
- type: software
  title: withr
  abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
  notes: Suggests
  url: https://withr.r-lib.org
  repository: https://CRAN.R-project.org/package=withr
  authors:
  - family-names: Hester
    given-names: Jim
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Müller
    given-names: Kirill
    email: krlmlr+r@mailbox.org
  - family-names: Ushey
    given-names: Kevin
    email: kevinushey@gmail.com
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Chang
    given-names: Winston
  year: '2025'
  doi: 10.32614/CRAN.package.withr

Owner metadata

GitHub Events

Total
Last Year

Committers metadata

Last synced: 1 day ago

Total Commits: 392
Total Committers: 7
Avg Commits per committer: 56.0
Development Distribution Score (DDS): 0.13

Commits in past year: 74
Committers in past year: 3
Avg Commits per committer in past year: 24.667
Development Distribution Score (DDS) in past year: 0.203

Name Email Commits
Nicolas Casajus a****s 341
Mattia Greco m****o@o****m 27
Khalil Hammami k****i@g****m 11
dependabot[bot] 4****] 8
Xavier Giraud g****d@c****r 3
Sonia Chaabane s****e@g****m 1
mgreco m****o@P****e 1

Committer domains:

Issue and Pull Request metadata

Last synced: 27 days ago

Total issues: 5
Total pull requests: 43
Average time to close issues: about 10 hours
Average time to close pull requests: 1 day
Total issue authors: 2
Total pull request authors: 3
Average comments per issue: 0.6
Average comments per pull request: 0.53
Merged pull request: 40
Bot issues: 0
Bot pull requests: 9

Past year issues: 5
Past year pull requests: 43
Past year average time to close issues: about 10 hours
Past year average time to close pull requests: 1 day
Past year issue authors: 2
Past year pull request authors: 3
Past year average comments per issue: 0.6
Past year average comments per pull request: 0.53
Past year merged pull request: 40
Past year bot issues: 0
Past year bot pull requests: 9

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/ropensci/forcis

Top Issue Authors

  • khammami (3)
  • ahasverus (2)

Top Pull Request Authors

  • ahasverus (26)
  • dependabot[bot] (9)
  • khammami (8)

Top Issue Labels

  • documentation (2)
  • code review (2)

Top Pull Request Labels

  • dependencies (9)
  • github_actions (9)

Package metadata

cran.r-project.org: forcis

Handle the FORCIS Foraminifera Database

  • Homepage: https://docs.ropensci.org/forcis/
  • Documentation: http://cran.r-project.org/web/packages/forcis/forcis.pdf
  • Licenses: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
  • Latest release: 1.0.1 (published 8 months ago)
  • Last Synced: 2026-01-10T01:04:05.458Z (1 day ago)
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 533 Last month
  • Rankings:
    • Dependent packages count: 26.459%
    • Dependent repos count: 32.599%
    • Average: 48.589%
    • Downloads: 86.71%
  • Maintainers (1)

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • dplyr * imports
  • messages * imports
  • rlang * imports
  • tidyr * imports
  • utils * imports
  • knitr * suggests
  • rmarkdown * suggests

Score: 10.018065457243564