forcis

Handle the FORCIS foraminifera database

https://github.com/ropensci/forcis

Keywords from Contributors

interactive ecosystem-modeling mesh interpretability profiles distribution sequences generic projection standardization

Last synced: 6 months ago · JSON representation ·

Repository

Handle the FORCIS foraminifera database

Basic Info

Host: GitHub
Owner: ropensci
License: gpl-2.0
Language: R
Default Branch: main
Homepage: https://docs.ropensci.org/forcis
Size: 6.85 MB

Statistics

Stars: 5
Watchers: 1
Forks: 1
Open Issues: 0
Releases: 3

Created over 4 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Citation Codemeta

README.Rmd

---
output: github_document
---




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







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


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[![codecov](https://codecov.io/gh/ropensci/forcis/branch/main/graph/badge.svg)](https://app.codecov.io/gh/ropensci/forcis)
[![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, Greco M, Chaabane S, Giraud X & de Garidel-Thoron T (2025) forcis: Handle the FORCIS foraminifera database. R package version 1.0.1. URL: https://docs.ropensci.org/forcis/.

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).

Owner

Name: rOpenSci
Login: ropensci
Kind: organization
Email: info@ropensci.org
Location: Berkeley, CA

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

JOSS Publication

forcis: An R package for accessing, handling and analysing the FORCIS database

Published

October 13, 2025

DOI

10.21105/joss.09217

Volume 10, Issue 114, Page 9217

Authors

Nicolas Casajus

Fondation pour la Recherche sur la Biodiversité (FRB-CESAB), Montpellier, France

Sonia Chaabane

Fondation pour la Recherche sur la Biodiversité (FRB-CESAB), Montpellier, France, Aix-Marseille Université, CNRS, IRD, INRAE, CEREGE, Aix-en-Provence, France, Department of Climate Geochemistry, Max Planck Institute for Chemistry, Mainz, Germany

Xavier Giraud

Aix-Marseille Université, CNRS, IRD, INRAE, CEREGE, Aix-en-Provence, France

Thibault de Garidel-Thoron

Aix-Marseille Université, CNRS, IRD, INRAE, CEREGE, Aix-en-Provence, France

Mattia Greco

Institute of Marine Sciences (ICM), CSIC, Barcelona, Catalonia, Spain

Editor

Arfon Smith

Citation (CITATION.cff)

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  on global foraminifera distribution. This package allows to download and to handle
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Total

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Issues event: 2
Release event: 2
Delete event: 3
Issue comment event: 2
Push event: 16
Pull request event: 7

Last Year

Create event: 4
Issues event: 2
Release event: 2
Delete event: 3
Issue comment event: 2
Push event: 16
Pull request event: 7

Committers

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All Time

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Total Committers: 7
Avg Commits per committer: 54.143
Development Distribution Score (DDS): 0.121

Past Year

Commits: 109
Committers: 4
Avg Commits per committer: 27.25
Development Distribution Score (DDS): 0.119

Top Committers

Name	Email	Commits
Nicolas Casajus	a****s	333
Mattia Greco	m**o@o**m	27
Khalil Hammami	k**i@g**m	11
dependabot[bot]	4****]	3
Xavier Giraud	g**d@c**r	3
Sonia Chaabane	s**e@g**m	1
mgreco	m**o@P**e	1

Committer Domains (Top 20 + Academic)

pc-mgreco.intranet.marum.de: 1 cerege.fr: 1

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Last synced: 6 months ago

All Time

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Total pull requests: 40
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Average time to close pull requests: about 20 hours
Total issue authors: 2
Total pull request authors: 3
Average comments per issue: 0.6
Average comments per pull request: 0.58
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Past Year

Issues: 5
Pull requests: 40
Average time to close issues: about 10 hours
Average time to close pull requests: about 20 hours
Issue authors: 2
Pull request authors: 3
Average comments per issue: 0.6
Average comments per pull request: 0.58
Merged pull requests: 37
Bot issues: 0
Bot pull requests: 6

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Packages

Total packages: 1
Total downloads:
- cran 382 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 1
Total maintainers: 1

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
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Latest release: 1.0.1
published 10 months ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 382 Last month

Rankings

Dependent packages count: 26.5%

Dependent repos count: 32.6%

Average: 48.6%

Downloads: 86.7%

Maintainers (1)

nicolas.casajus@fondationbiodiversite.fr

Last synced: 6 months ago

forcis

Science Score: 67.0%

Keywords from Contributors

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README.Rmd

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JOSS Publication

forcis: An R package for accessing, handling and analysing the FORCIS database

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