{"id":24790080,"url":"https://github.com/frbcesab/funbiogeo","last_synced_at":"2025-10-12T14:30:54.934Z","repository":{"id":37067229,"uuid":"335680958","full_name":"FRBCesab/funbiogeo","owner":"FRBCesab","description":":package: R package to streamline functional biogeography workflows and provide publication-ready plots","archived":false,"fork":false,"pushed_at":"2025-07-11T14:13:49.000Z","size":78485,"stargazers_count":12,"open_issues_count":8,"forks_count":1,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-09-04T18:58:30.273Z","etag":null,"topics":["functional-biogeography","functional-diversity","functional-trait","package","r"],"latest_commit_sha":null,"homepage":"https://frbcesab.github.io/funbiogeo/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/FRBCesab.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.md","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":"codemeta.json","zenodo":null}},"created_at":"2021-02-03T16:10:40.000Z","updated_at":"2025-07-11T14:09:25.000Z","dependencies_parsed_at":"2025-04-10T17:19:46.540Z","dependency_job_id":null,"html_url":"https://github.com/FRBCesab/funbiogeo","commit_stats":{"total_commits":353,"total_committers":4,"mean_commits":88.25,"dds":"0.40793201133144474","last_synced_commit":"417c058b55b4b9ef3e28aab15cf11b4e4ded3316"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/FRBCesab/funbiogeo","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FRBCesab%2Ffunbiogeo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FRBCesab%2Ffunbiogeo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FRBCesab%2Ffunbiogeo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FRBCesab%2Ffunbiogeo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/FRBCesab","download_url":"https://codeload.github.com/FRBCesab/funbiogeo/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FRBCesab%2Ffunbiogeo/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279011599,"owners_count":26084964,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-12T02:00:06.719Z","response_time":53,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["functional-biogeography","functional-diversity","functional-trait","package","r"],"created_at":"2025-01-29T18:14:37.468Z","updated_at":"2025-10-12T14:30:49.927Z","avatar_url":"https://github.com/FRBCesab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse  = TRUE,\n  comment   = \"#\u003e\",\n  fig.path  = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n\npkgload::load_all()\n```\n\n\n# funbiogeo - Streamlining functional biogeography analyses \u003cimg src=\"man/figures/logo.png\" align=\"right\" style=\"float:right; height:120px;\"/\u003e\n\n\n\u003c!-- badges: start --\u003e\n[![R-CMD-check](https://github.com/FRBCesab/funbiogeo/workflows/R-CMD-check/badge.svg)](https://github.com/FRBCesab/funbiogeo/actions)\n[![codecov](https://codecov.io/gh/FRBCesab/funbiogeo/branch/main/graph/badge.svg?token=JPXXVNMAJ0)](https://codecov.io/gh/FRBCesab/funbiogeo)\n[![CRAN status](https://www.r-pkg.org/badges/version/funbiogeo)](https://CRAN.R-project.org/package=funbiogeo)\n[![License: GPL v2](https://img.shields.io/badge/License-GPL%20v2-blue.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)\n\u003c!-- badges: end --\u003e\n\n\n\n\u003cp align=\"left\"\u003e\n  • \u003ca href=\"#overview\"\u003eOverview\u003c/a\u003e\u003cbr\u003e\n  • \u003ca href=\"#features\"\u003eFeatures\u003c/a\u003e\u003cbr\u003e\n  • \u003ca href=\"#installation\"\u003eInstallation\u003c/a\u003e\u003cbr\u003e\n  • \u003ca href=\"#first-steps\"\u003eFirst steps\u003c/a\u003e\u003cbr\u003e\n  • \u003ca href=\"#long-form-documentations\"\u003eLong-form documentations\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 package `funbiogeo` aims to help users with analyses in functional biogeography (Violle _et al._ 2014) by loading and combining data, computing trait coverage, as well as computing functional diversity indices, drawing maps, correlating them with the environment, and upscaling assemblages.\n\nIt is aimed at first-timers of functional biogeography as well as more experienced users who want to obtain quick and easy exploratory plots.\n\n\n\n## Features\n\n`funbiogeo` offers:\n\n* Standardized functions to filter and select your data for further analyses,\n* Pleasing default diagnostic plots to visualize the structure of your data,\n* Extensive documentation (multiple vignettes, well-documented functions,\n  real-life example dataset) to guide you through functional biogeography\n  analyses,\n* Nice default plotting functions using outputs from functional diversity\n  packages (`betapart`, `fundiversity`, `hillR`, `mFD`, etc.),\n* Automated standardized report that provide analyses and plots of your data,\n* Functions to easily \"upscale\" your data to coarser spatial resolutions.\n\n\n\n## Installation\n\nFor the moment `funbiogeo` is not on CRAN but you can install the development \nversion from GitHub as follow:\n\n```{r eval=FALSE}\n# install.packages(\"remotes\")  # Run this line if 'remotes' pkg is not installed\nremotes::install_github(\"FRBCesab/funbiogeo\")\n```\n\n\n\n## First steps\n\nThis section will show you some useful functions from `funbiogeo`. For a longer introduction please refer to the [\"Get started\" vignette](https://frbcesab.github.io/funbiogeo/).\n\nThe package contains default example data named `species_traits`, `site_species`, and `site_locations`. You can for example visualize to completeness of your trait dataset using the `fb_plot_species_traits_completeness()` function:\n\n```{r plot-sp-tr-complete}\nfb_plot_species_traits_completeness(species_traits)\n```\n\nOne other useful visualization is to see the trait coverage of each trait across all sites, using the function `fb_map_site_traits_completeness()`:\n\n```{r plot-site-tr-complete}\nfb_map_site_traits_completeness(site_locations, site_species, species_traits)\n```\n\nSee more features of `funbiogeo` in the [vignettes of the package](https://frbcesab.github.io/funbiogeo/articles/)\n\n\n\n## Long-form documentations\n\n`funbiogeo` provides four vignettes to explain its functioning:\n\n* A [\"Get started\" vignette](https://frbcesab.github.io/funbiogeo/articles/funbiogeo.html)\n  that describes its core features and guide you through a typical analysis.\n* A [vignette on all diagnostic plots](https://frbcesab.github.io/funbiogeo/articles/diagnostic-plots.html)\n  provided in the package, which details how to use each plotting function and\n  how to interpret their output.\n* A [vignette on formatting your data](https://frbcesab.github.io/funbiogeo/articles/long-format.html)\n  to the needs of `funbiogeo`, which shows you the use of specific functions.\n* And a [specific vignette on upscaling](https://frbcesab.github.io/funbiogeo/articles/upscaling.html)\n  which explains how to aggregate automatically your data to coarser grain and\n  use it in further analyses.\n\n\n\n## Citation\n\nFor the moment `funbiogeo` doesn't offer a companion paper. But if you happen to use it in your paper you can cite the package through:\n\n\u003e Casajus N \u0026 Grenié M (2024). _funbiogeo: Functional Biogeography Analyses_. R package version 0.0.0.9000, \u003chttps://github.com/frbcesab/funbiogeo\u003e.\n\nYou can also run:\n\n```{r eval=FALSE}\ncitation(\"funbiogeo\")\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/FRBCesab/funbiogeo/blob/main/CONTRIBUTING.md).\n\nPlease note that the `funbiogeo` 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.\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 [FREE](https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/free/) that aims to advance the concept of functional rarity and examine the causes and consequences of functional rarity from local to global scales.\n\n\n\n## References\n\nViolle C, Reich, PB Pacala SW, _et al._ (2014) The emergence and promise of functional biogeography. *Proceedings of the National Academy of Sciences*, **111**, 13690--13696. DOI: [10.1073/pnas.1415442111](https://doi.org/10.1073/pnas.1415442111)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffrbcesab%2Ffunbiogeo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffrbcesab%2Ffunbiogeo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffrbcesab%2Ffunbiogeo/lists"}