funbiogeo

:package: R package to streamline functional biogeography workflows and provide publication-ready plots

https://github.com/frbcesab/funbiogeo

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Keywords

functional-biogeography functional-diversity functional-trait package r

Keywords from Contributors

correlation

Last synced: 6 months ago · JSON representation ·

Repository

:package: R package to streamline functional biogeography workflows and provide publication-ready plots

Basic Info

Host: GitHub
Owner: FRBCesab
License: gpl-2.0
Language: R
Default Branch: main
Homepage: https://frbcesab.github.io/funbiogeo/
Size: 74.8 MB

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Stars: 12
Watchers: 3
Forks: 1
Open Issues: 8
Releases: 0

Topics

functional-biogeography functional-diversity functional-trait package r

Created about 5 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation Codemeta

README.Rmd

---
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 



[![R-CMD-check](https://github.com/FRBCesab/funbiogeo/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/FRBCesab/funbiogeo/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/FRBCesab/funbiogeo/graph/badge.svg?token=JPXXVNMAJ0)](https://app.codecov.io/gh/FRBCesab/funbiogeo)
[![CRAN status](https://www.r-pkg.org/badges/version/funbiogeo)](https://CRAN.R-project.org/package=funbiogeo)
[![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)


- [Overview](#overview)
- [Features](#features)
- [Installation](#installation)
- [First steps](#first-steps)
- [Long-form documentation (=vignettes)](#long-documentation)
- [Citation](#citation)
- [Contributing](#contributing)
- [Acknowledgments](#acknowledgments)
- [References](#references)


## Overview

The package `funbiogeo` aims to help users with analyses in functional biogeography ([Violle _et al._ 2014](#references)), the biogeography of species' traits, by loading and combining data, exploring the relationships between traits and their availability trait coverage, providing many diagnostic plots to understand how to filter them, producing maps, correlating them with the environment, and helping to aggregate data at different scales
It is aimed at first-timers of functional biogeography as well as more experienced users who want to obtain quick and easy exploratory plots.

Below is a quick introduction to the main features of `funbiogeo`, if you want some more details about them, check [our vignettes](#long-form-documentation).


## 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 fully compatible with the outputs of functional diversity packages (`betapart`, `fundiversity`, `hillR`, `mFD`, etc.),
* A publication-ready automated standardized report that provide analyses and plots of your data,
* Functions to easily "upscale" (=aggregate) your data to coarser spatial resolutions whatever the type of aggregation geometry you want (regular grid, irregular polygons, and rasters).

```{r functions-scheme, echo = FALSE, fig.cap = "Naming scheme of available functions in funbiogeo"}
knitr::include_graphics("inst/misc/functions_scheme.drawio.png")
```


## Installation

For the moment `funbiogeo` is not on CRAN but you can install the development 
version from [R-universe](https://r-universe.dev) as follow:

```{r eval=FALSE}
install.packages('funbiogeo', repos = c('https://frbcesab.r-universe.dev', 'https://cloud.r-project.org'))
```


## 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/articles/funbiogeo.html).

The package contains default example data named `woodiv_traits`, `woodiv_site_species`, and `woodiv_locations` all from the WOODIV database ([Monnet et al. 2021](#references)). You can, for example, visualize the completeness of your trait dataset (which traits are known for which proportion of species) using the `fb_plot_species_traits_completeness()` function:

```{r plot-sp-tr-complete}
fb_plot_species_traits_completeness(woodiv_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(woodiv_locations, woodiv_site_species, woodiv_traits)
```

See more features of `funbiogeo` in the [vignettes of the package](https://frbcesab.github.io/funbiogeo/articles/)


## Long-form documentation

`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 [the data format](https://frbcesab.github.io/funbiogeo/articles/long-format.html)
  that `funbiogeo` needs, which shows you the use of specific functions to format your data to work well within `funbiogeo`.
* A vignette on [data upscaling](https://frbcesab.github.io/funbiogeo/articles/upscaling.html)
  which explains how to leverage `funbiogeo` to aggregate automatically your data to coarser grain and
  use them in further analyses.



## Citation

For the moment `funbiogeo` doesn't offer a companion paper nor is it on CRAN.
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/) and its followup [FREE 2](https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/free-2/) that aims to advance the concept of functional rarity and examine the causes and consequences of functional rarity from local to global scales.



## References

Monnet, AC., Cilleros, K., Médail, F. et al. WOODIV, a database of occurrences, functional traits, and phylogenetic data for all Euro-Mediterranean trees. Sci Data 8, 89 (2021). https://doi.org/10.1038/s41597-021-00873-3

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)

Owner

Name: FRB CESAB
Login: FRBCesab
Kind: organization
Location: Montpellier, FRANCE

Website: https://www.fondationbiodiversite.fr/en/about-the-foundation/le-cesab/
Repositories: 17
Profile: https://github.com/FRBCesab

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "funbiogeo" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'funbiogeo: Functional Biogeography Analyses'
version: 0.0.0.9000
abstract: Helps users with analyses in functional biogeogeography 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.
authors:
- family-names: Casajus
  given-names: Nicolas
  email: nicolas.casajus@fondationbiodiversite.fr
  orcid: https://orcid.org/0000-0002-5537-5294
- family-names: Grenié
  given-names: Matthias
  email: matthias.grenie@idiv.de
  orcid: https://orcid.org/0000-0002-4659-7522
repository-code: https://github.com/frbcesab/funbiogeo
url: https://frbcesab.github.io/funbiogeo/
contact:
- family-names: Casajus
  given-names: Nicolas
  email: nicolas.casajus@fondationbiodiversite.fr
  orcid: https://orcid.org/0000-0002-5537-5294
keywords:
- functional-biogeography
- functional-diversity
- functional-trait
- package
- r
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    given-names: Winston
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Henry
    given-names: Lionel
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Takahashi
    given-names: Kohske
  - family-names: Wilke
    given-names: Claus
    orcid: https://orcid.org/0000-0002-7470-9261
  - family-names: Woo
    given-names: Kara
    orcid: https://orcid.org/0000-0002-5125-4188
  - family-names: Yutani
    given-names: Hiroaki
    orcid: https://orcid.org/0000-0002-3385-7233
  - family-names: Dunnington
    given-names: Dewey
    orcid: https://orcid.org/0000-0002-9415-4582
  - family-names: Brand
    given-names: Teun
    name-particle: van den
    orcid: https://orcid.org/0000-0002-9335-7468
  year: '2025'
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  abstract: 'rlang: Functions for Base Types and Core R and ''Tidyverse'' Features'
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    given-names: Lionel
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  abstract: 'scales: Scale Functions for Visualization'
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  authors:
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  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@posit.co
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Seidel
    given-names: Dana
  year: '2025'
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  authors:
  - family-names: Pebesma
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  year: '2025'
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  abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
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  authors:
  - family-names: Hester
    given-names: Jim
  - family-names: Henry
    given-names: Lionel
    email: lionel@posit.co
  - family-names: Müller
    given-names: Kirill
    email: krlmlr+r@mailbox.org
  - family-names: Ushey
    given-names: Kevin
    email: kevinushey@gmail.com
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Chang
    given-names: Winston
  year: '2025'
  doi: 10.32614/CRAN.package.withr

CodeMeta (codemeta.json)

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "@type": "SoftwareSourceCode",
  "identifier": "funbiogeo",
  "description": "Helps users with analyses in functional biogeogeography 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.",
  "name": "funbiogeo: Functional Biogeography Analyses",
  "relatedLink": "https://frbcesab.github.io/funbiogeo/",
  "codeRepository": "https://github.com/frbcesab/funbiogeo",
  "issueTracker": "https://github.com/frbcesab/funbiogeo/issues",
  "license": "https://spdx.org/licenses/GPL-2.0",
  "version": "0.0.0.9000",
  "programmingLanguage": {
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  "runtimePlatform": "R version 4.5.1 (2025-06-13)",
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      "email": "nicolas.casajus@fondationbiodiversite.fr",
      "@id": "https://orcid.org/0000-0002-5537-5294"
    },
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      "identifier": "rmarkdown",
      "name": "rmarkdown",
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        "name": "Comprehensive R Archive Network (CRAN)",
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      "sameAs": "https://CRAN.R-project.org/package=rmarkdown"
    },
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      "@type": "SoftwareApplication",
      "identifier": "rstudioapi",
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        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rstudioapi"
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      "version": ">= 3.0.0",
      "provider": {
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        "@type": "Organization",
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        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=testthat"
    },
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      "sameAs": "https://CRAN.R-project.org/package=vdiffr"
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  "softwareRequirements": {
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      "identifier": "R",
      "name": "R",
      "version": ">= 3.5.0"
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    "2": {
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  "fileSize": "47280.913KB",
  "releaseNotes": "https://github.com/frbcesab/funbiogeo/blob/master/NEWS.md",
  "readme": "https://github.com/FRBCesab/funbiogeo/blob/main/README.md",
  "contIntegration": [
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  ],
  "keywords": [
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}

GitHub Events

Total

Issues event: 27
Watch event: 2
Delete event: 15
Issue comment event: 29
Push event: 101
Pull request event: 25
Pull request review event: 13
Create event: 17

Last Year

Issues event: 27
Watch event: 2
Delete event: 15
Issue comment event: 29
Push event: 101
Pull request event: 25
Pull request review event: 13
Create event: 17

Committers

Last synced: about 2 years ago

All Time

Total Commits: 353
Total Committers: 4
Avg Commits per committer: 88.25
Development Distribution Score (DDS): 0.408

Past Year

Commits: 67
Committers: 3
Avg Commits per committer: 22.333
Development Distribution Score (DDS): 0.373

Top Committers

Name	Email	Commits
Matthias Grenié	m**e@e**r	209
Nicolas Casajus	n**s@g**m	139
GitHub Actions	a**s@g**m	4
olivroy	5****y	1

Committer Domains (Top 20 + Academic)

github.com: 1 ens-lyon.fr: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time

Total issues: 65
Total pull requests: 38
Average time to close issues: 3 months
Average time to close pull requests: 13 days
Total issue authors: 2
Total pull request authors: 4
Average comments per issue: 0.71
Average comments per pull request: 1.29
Merged pull requests: 37
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 14
Pull requests: 11
Average time to close issues: about 2 months
Average time to close pull requests: 1 day
Issue authors: 2
Pull request authors: 3
Average comments per issue: 0.43
Average comments per pull request: 1.45
Merged pull requests: 11
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

Rekyt (70)
ahasverus (13)

Pull Request Authors

Rekyt (32)
ahasverus (24)
olivroy (2)
KevCaz (1)

Top Labels

Issue Labels

enhancement (37) bug (21) documentation (12) plot (11) question (4) wontfix (2)

Pull Request Labels

documentation (1)

Dependencies

.github/workflows/R-CMD-check.yaml actions

actions/checkout v2 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/pkgdown.yaml actions

JamesIves/github-pages-deploy-action 4.1.4 composite
actions/checkout v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/test-coverage.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/update-citation-cff.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

DESCRIPTION cran

R >= 3.5.0 depends
ggplot2 * imports
rlang * imports
scales * imports
sf * imports
stats * imports
terra * imports
tidyr * imports
tidyselect * imports
utils * imports
xfun * imports
ggridges * suggests
knitr * suggests
mockery * suggests
patchwork * suggests
raster * suggests
rgdal * suggests
rmarkdown * suggests
rstudioapi * suggests
testthat >= 3.0.0 suggests

.github/workflows/update-codemeta.yaml actions

actions/checkout v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

funbiogeo

Science Score: 57.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

Citation (CITATION.cff)

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies