README.md

In FRBCesab/forcis: An R Client to Access the FORCIS Database

forcis

Table of contents

• Overview • Features • Installation • Get started • Long-form documentations • Citation • Contributing • Acknowledgments • References

Overview

The goal of the R package forcis is to provide an interface to the FORCIS database 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.

Features

The main purpose of the forcis package is to download, select, filter, homogenize, and visualize FORCIS data. The Functions page provides a full description of the features available in the package.

Installation

You can install the development version from GitHub with:

## 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("FRBCesab/forcis")

N.B. The forcis package depends on the sf package which requires some spatial system libraries (GDAL and PROJ). Please read this page if you have any trouble to install forcis.

Finally you can attach the package forcis with:

library("forcis")

Get started

For an overview of the main features of forcis, please read the Get started vignette.

Long-form documentations

forcis provides five vignettes to learn more about the package:

• the Get started vignette describes the core features of the package
• the Database versions vignette provides information on how to deal with the versioning of the database
• the Select and filter data vignette shows examples to handle the FORCIS data
• the Data conversion vignette describes the conversion functions available in forcis to compute abundances, concentrations, and frequencies
• the Data visualization 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 (2024) forcis: An R client to access the FORCIS database. R package version 0.1.0.9000. URL: https://frbcesab.github.io/forcis/.

You can also run:

citation("forcis")

Contributing

All types of contributions are encouraged and valued. For more information, check out our Contributor Guidelines.

Please note that the forcis project is released with a Contributor 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 working group 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) 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.

FRBCesab/forcis documentation built on Oct. 25, 2024, 9:26 a.m.