From 0a86a5839ffeef8d322731855e8c645f743ed63b Mon Sep 17 00:00:00 2001 From: Nicolas Casajus Date: Wed, 17 Jan 2024 10:55:10 +0100 Subject: [PATCH] doc: improve README - fix #25 --- README.Rmd | 78 ++++++++++++++++++++++++++++++++++++++--------- README.md | 83 ++++++++++++++++++++++++++++++++++++++++++++------- inst/CITATION | 2 +- 3 files changed, 138 insertions(+), 25 deletions(-) diff --git a/README.Rmd b/README.Rmd index 71cb8b6..29abbf8 100644 --- a/README.Rmd +++ b/README.Rmd @@ -31,42 +31,76 @@ forcis + • 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 package allows to download, handle, homogenize and visualize FORCIS data. + + + +## Features + +The main purpose of `forcis` is to... + + +**__LIST HERE THE MAIN FEATURES__** + + ## Installation You can install the development version from [GitHub](https://github.com/) with: -```{r eval = FALSE} -# install.packages("remotes") +```{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") ``` Then you can attach the package `forcis`: -```{r eval = FALSE} +```{r eval=FALSE} library("forcis") ``` -## Overview +## 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 + +Additional vignettes will be available soon. -Please read the [Get started](https://frbcesab.github.io/forcis/articles/forcis.html) vignette. ## Citation Please cite this package as: -> Casajus N, Greco M, Giraud X & Chaabane S (2023) forcis: An R client to access the FORCIS database. R package version 0.0.0.9000. URL: https://frbcesab.github.io/forcis/. +> Casajus N, Greco M, Giraud X & Chaabane S (2024) forcis: An R client to access the FORCIS database. R package version 0.0.0.9000. URL: https://frbcesab.github.io/forcis/. You can also run: @@ -75,8 +109,24 @@ citation("forcis") ``` -## Code of Conduct -Please note that the `forcis` project is released with a -[Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). -By contributing to this project, you agree to abide by its terms. +## 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). diff --git a/README.md b/README.md index 5bceca9..a140ae6 100644 --- a/README.md +++ b/README.md @@ -15,11 +15,32 @@ status](https://www.r-pkg.org/badges/version/forcis)](https://CRAN.R-project.org 2)](https://img.shields.io/badge/License-GPL%20%28%3E%3D%202%29-blue.svg)](https://choosealicense.com/licenses/gpl-2.0/) +## 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. This package allows -to download and to handle FORCIS data. This work is part of the -FRB-CESAB working group -[FORCIS](https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/forcis/). +FORCIS database on global foraminifera distribution (Chaabane *et al.* +2023). This package allows to download, handle, homogenize and visualize +FORCIS data. + +## Features + +The main purpose of `forcis` is to… + +****LIST HERE THE MAIN FEATURES**** ## Installation @@ -27,7 +48,12 @@ You can install the development version from [GitHub](https://github.com/) with: ``` r -# install.packages("remotes") +## 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") ``` @@ -37,17 +63,21 @@ Then you can attach the package `forcis`: library("forcis") ``` -## Overview +## Get started -Please read the [Get +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 + +Additional vignettes will be available soon. + ## Citation Please cite this package as: -> Casajus N, Greco M, Giraud X & Chaabane S (2023) forcis: An R client +> Casajus N, Greco M, Giraud X & Chaabane S (2024) forcis: An R client > to access the FORCIS database. R package version 0.0.0.9000. URL: > . @@ -57,9 +87,42 @@ You can also run: citation("forcis") ``` -## Code of Conduct +## 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/2/0/CODE_OF_CONDUCT.html). +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). diff --git a/inst/CITATION b/inst/CITATION index d0609ac..31d8109 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -4,7 +4,7 @@ bibentry( bibtype = "Manual", title = "forcis: {An} {R} client to access the {FORCIS} database", author = c(person("Casajus Nicolas"), person("Greco Mattia"), person("Giraud Xavier"), person("Chaabane Sonia")), - year = "2023", + year = "2024", note = "R package version 0.0.0.9000", url = "https://frbcesab.github.io/forcis" )