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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/",
out.width = "100%"
)
```
forcis <img src="man/figures/logo.png" height="120px" align="right" style="float:right; height:120px;"/>
=========================================================
<!-- badges: start -->
[](https://github.com/FRBCesab/forcis/actions/workflows/R-CMD-check.yaml)
[](https://github.com/FRBCesab/forcis/actions/workflows/pkgdown.yaml)
[](https://codecov.io/gh/frbcesab/forcis)
[](https://CRAN.R-project.org/package=forcis)
[](https://choosealicense.com/licenses/gpl-2.0/)
<!-- badges: end -->
## Table of contents
<p align="left">
• <a href="#overview">Overview</a><br>
• <a href="#features">Features</a><br>
• <a href="#installation">Installation</a><br>
• <a href="#get-started">Get started</a><br>
• <a href="#long-form-documentations">Long-form documentations</a><br>
• <a href="#citation">Citation</a><br>
• <a href="#contributing">Contributing</a><br>
• <a href="#acknowledgments">Acknowledgments</a><br>
• <a href="#references">References</a>
</p>
## 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.
## Features
The main purpose of the `forcis` package is to download, select, filter, homogenize, and visualize FORCIS data. The [Functions](https://frbcesab.github.io/forcis/reference/index.html) page provides a full description of the features available in the package.
## 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("FRBCesab/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")
```
## Get started
For an overview of the main features of `forcis`, please read the [Get started](https://frbcesab.github.io/forcis/articles/forcis.html) vignette.
## Long-form documentations
`forcis` provides five vignettes to learn more about the package:
- the [Get started](https://frbcesab.github.io/forcis/articles/forcis.html) vignette describes the core features of the package
- the [Database versions](https://frbcesab.github.io/forcis/articles/database-versions.html) vignette provides information on how to deal with the versioning of the database
- the [Select and filter data](https://frbcesab.github.io/forcis/articles/select-and-filter-data.html) vignette shows examples to handle the FORCIS data
- the [Data conversion](https://frbcesab.github.io/forcis/articles/data-conversion.html) vignette describes the conversion functions available in `forcis` to compute abundances, concentrations, and frequencies
- the [Data visualization](https://frbcesab.github.io/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 (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:
```{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/FRBCesab/forcis/blob/main/CONTRIBUTING.md).
Please note that the `forcis` project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). 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).