https://github.com/frbcesab/funbiogeo
:package: R package to streamline functional biogeography workflows and provide publication-ready plots
https://github.com/frbcesab/funbiogeo
functional-biogeography functional-diversity functional-trait package r
Last synced: 9 months ago
JSON representation
:package: R package to streamline functional biogeography workflows and provide publication-ready plots
- Host: GitHub
- URL: https://github.com/frbcesab/funbiogeo
- Owner: FRBCesab
- License: gpl-2.0
- Created: 2021-02-03T16:10:40.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2025-07-11T14:13:49.000Z (12 months ago)
- Last Synced: 2025-09-04T18:58:30.273Z (10 months ago)
- Topics: functional-biogeography, functional-diversity, functional-trait, package, r
- Language: R
- Homepage: https://frbcesab.github.io/funbiogeo/
- Size: 74.8 MB
- Stars: 12
- Watchers: 3
- Forks: 1
- Open Issues: 8
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATION.cff
- Codemeta: codemeta.json
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
pkgload::load_all()
```
# funbiogeo - Streamlining functional biogeography analyses 
[](https://github.com/FRBCesab/funbiogeo/actions)
[](https://codecov.io/gh/FRBCesab/funbiogeo)
[](https://CRAN.R-project.org/package=funbiogeo)
[](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)
• Overview
• Features
• Installation
• First steps
• Long-form documentations
• Citation
• Contributing
• Acknowledgments
• References
## Overview
The 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.
It is aimed at first-timers of functional biogeography as well as more experienced users who want to obtain quick and easy exploratory plots.
## Features
`funbiogeo` offers:
* Standardized functions to filter and select your data for further analyses,
* Pleasing default diagnostic plots to visualize the structure of your data,
* Extensive documentation (multiple vignettes, well-documented functions,
real-life example dataset) to guide you through functional biogeography
analyses,
* Nice default plotting functions using outputs from functional diversity
packages (`betapart`, `fundiversity`, `hillR`, `mFD`, etc.),
* Automated standardized report that provide analyses and plots of your data,
* Functions to easily "upscale" your data to coarser spatial resolutions.
## Installation
For the moment `funbiogeo` is not on CRAN but you can install the development
version from GitHub as follow:
```{r eval=FALSE}
# install.packages("remotes") # Run this line if 'remotes' pkg is not installed
remotes::install_github("FRBCesab/funbiogeo")
```
## First steps
This 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/).
The 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:
```{r plot-sp-tr-complete}
fb_plot_species_traits_completeness(species_traits)
```
One other useful visualization is to see the trait coverage of each trait across all sites, using the function `fb_map_site_traits_completeness()`:
```{r plot-site-tr-complete}
fb_map_site_traits_completeness(site_locations, site_species, species_traits)
```
See more features of `funbiogeo` in the [vignettes of the package](https://frbcesab.github.io/funbiogeo/articles/)
## Long-form documentations
`funbiogeo` provides four vignettes to explain its functioning:
* A ["Get started" vignette](https://frbcesab.github.io/funbiogeo/articles/funbiogeo.html)
that describes its core features and guide you through a typical analysis.
* A [vignette on all diagnostic plots](https://frbcesab.github.io/funbiogeo/articles/diagnostic-plots.html)
provided in the package, which details how to use each plotting function and
how to interpret their output.
* A [vignette on formatting your data](https://frbcesab.github.io/funbiogeo/articles/long-format.html)
to the needs of `funbiogeo`, which shows you the use of specific functions.
* And a [specific vignette on upscaling](https://frbcesab.github.io/funbiogeo/articles/upscaling.html)
which explains how to aggregate automatically your data to coarser grain and
use it in further analyses.
## Citation
For 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:
> Casajus N & Grenié M (2024). _funbiogeo: Functional Biogeography Analyses_. R package version 0.0.0.9000, .
You can also run:
```{r eval=FALSE}
citation("funbiogeo")
```
## Contributing
All types of contributions are encouraged and valued. For more information, check out our [Contributor Guidelines](https://github.com/FRBCesab/funbiogeo/blob/main/CONTRIBUTING.md).
Please 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.
## Acknowledgments
This 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.
## References
Violle 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)