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Life and Fishery","monthly_downloads":567,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/\",\n  out.width = \"100%\"\n)\n```\n\n\n\n\n\n\n\nforcis \u003cimg src=\"man/figures/logo.png\" height=\"120px\" align=\"right\" style=\"float:right; height:120px;\"/\u003e\n=========================================================\n\n\u003c!-- badges: start --\u003e\n[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/660_status.svg)](https://github.com/ropensci/software-review/issues/660)\n[![CRAN status](https://www.r-pkg.org/badges/version/forcis)](https://CRAN.R-project.org/package=forcis)\n[![License: GPL (\u003e= 2)](https://img.shields.io/badge/License-GPL%20%28%3E%3D%202%29-blue.svg)](https://choosealicense.com/licenses/gpl-2.0/)\n[![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)\n[![codecov](https://codecov.io/gh/ropensci/forcis/branch/main/graph/badge.svg)](https://app.codecov.io/gh/ropensci/forcis)\n[![JOSS](https://joss.theoj.org/papers/10.21105/joss.09217/status.svg)](https://doi.org/10.21105/joss.09217)\n[![DOI](https://zenodo.org/badge/428715013.svg)](https://doi.org/10.5281/zenodo.15470664)\n\u003c!-- badges: end --\u003e\n\n\n## Table of contents\n\n\u003cp align=\"left\"\u003e\n  • \u003ca href=\"#overview\"\u003eOverview\u003c/a\u003e\u003cbr\u003e\n  • \u003ca href=\"#installation\"\u003eInstallation\u003c/a\u003e\u003cbr\u003e\n  • \u003ca href=\"#documentation\"\u003eDocumentation\u003c/a\u003e\u003cbr\u003e\n  • \u003ca href=\"#citation\"\u003eCitation\u003c/a\u003e\u003cbr\u003e\n  • \u003ca href=\"#contributing\"\u003eContributing\u003c/a\u003e\u003cbr\u003e\n  • \u003ca href=\"#acknowledgments\"\u003eAcknowledgments\u003c/a\u003e\u003cbr\u003e\n  • \u003ca href=\"#references\"\u003eReferences\u003c/a\u003e\n\u003c/p\u003e\n\n\n\n## Overview\n\nThe 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.\n\n![Figure 1: Recommended workflow and main features of `forcis`](man/figures/workflow.png)\n\n\u003cbr/\u003e\n\nThis 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.\n\n\n![Figure 2: Overview of visualizations available in `forcis`](man/figures/visualization.png)\n\n## Installation\n\nYou can install the development version from [GitHub](https://github.com/) with:\n\n```{r eval=FALSE}\n## Install \u003c remotes \u003e package (if not already installed) ----\nif (!requireNamespace(\"remotes\", quietly = TRUE)) {\n  install.packages(\"remotes\")\n}\n\n## Install dev version of \u003c forcis \u003e from GitHub ----\nremotes::install_github(\"ropensci/forcis\")\n```\n\n**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`.\n\n\nFinally you can attach the package `forcis` with:\n\n```{r eval=FALSE}\nlibrary(\"forcis\")\n```\n\n\n## Documentation\n\n`forcis` provides five vignettes to learn more about the package:\n\n- the [Get started](https://docs.ropensci.org/forcis/articles/forcis.html) vignette describes the core features of the package\n- 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\n- the [Select and filter data](https://docs.ropensci.org/forcis/articles/select-and-filter-data.html) vignette shows examples to handle the FORCIS data\n- 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\n- the [Data visualization](https://docs.ropensci.org/forcis/articles/data-visualization.html) vignette describes the plotting functions available in `forcis`\n\n\n\n\n## Citation\n\nPlease cite this package as: \n\n\u003e Casajus N, Chaabane S, de Garidel-Thoron T, Giraud X \u0026 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).\n\nYou can also run:\n\n```{r eval = FALSE}\ncitation(\"forcis\")\n```\n\n\n\n## Contributing\n\nAll types of contributions are encouraged and valued. For more information, check out our [Contributor Guidelines](https://github.com/ropensci/forcis/blob/main/CONTRIBUTING.md).\n\nPlease note that this package is released with a [Contributor\nCode of Conduct](https://ropensci.org/code-of-conduct/). \nBy contributing to this project, you agree to abide by its terms.\n\n\n\n## Acknowledgments\n\nThis 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. \n\nWe want to thanks Khalil Hammami ([@khammami](https://github.com/khammami)) for his valuable contribution to this package.\n\n\n\n## References\n\nChaabane 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 \u0026 Ziveri P (2023) The FORCIS database: A global census of planktonic Foraminifera from ocean waters. **Scientific Data**, 10, 354.\nDOI: [10.1038/s41597-023-02264-2](https://doi.org/10.1038/s41597-023-02264-2). \n","funding_links":[],"readme_doi_urls":["https://doi.org/10.21105/joss.09217","https://doi.org/10.5281/zenodo.15470664","https://doi.org/10.1038/s41597-023-02264-2"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["optimize","archiving","measur","transforms","animals","conversion","generic","observation","projection","compose"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/327633","html_url":"https://ost.ecosyste.ms/projects/327633"}