mFD

Provides a user friendly interface to compute a global assessment of functional diversity by gathering computation of alpha and beta functional indices.
https://github.com/cmlmagneville/mfd

Category: Biosphere
Sub Category: Biodiversity Analysis and Metrics

Keywords from Contributors

traits

Last synced: about 19 hours ago
JSON representation

Repository metadata

:package: A Computation of Functional Spaces and Functional Diversity Indices

• Host: GitHub
• URL: https://github.com/cmlmagneville/mfd
• Owner: CmlMagneville
• License: gpl-2.0
• Created: 2021-02-26T11:55:45.000Z (about 4 years ago)
• Default Branch: main
• Last Pushed: 2024-12-19T15:24:50.000Z (4 months ago)
• Last Synced: 2025-04-17T22:58:54.131Z (10 days ago)
• Language: R
• Homepage: https://cmlmagneville.github.io/mFD/
• Size: 167 MB
• Stars: 27
• Watchers: 2
• Forks: 5
• Open Issues: 0
• Releases: 7
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • License: LICENSE

README.Rmd

          ---
output: github_document
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse  = TRUE,
  comment   = "#>",
  fig.path  = "man/figures/README-",
  out.width = "100%"
)
```



mFD 
=========================================================




[![CRAN status](https://www.r-pkg.org/badges/version/mFD)](https://CRAN.R-project.org/package=mFD/)
[![R CMD check](https://github.com/CmlMagneville/mFD/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/CmlMagneville/mFD/actions/workflows/R-CMD-check.yaml)
[![Website deployment](https://github.com/CmlMagneville/mFD/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/CmlMagneville/mFD/actions/workflows/pkgdown.yaml)
[![License: GPL-2)](https://img.shields.io/badge/License-GPL%202-blue.svg)](https://choosealicense.com/licenses/gpl-2.0/)
[![LifeCycle](man/figures/lifecycle/lifecycle-stable.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![Project Status: Active](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![](http://cranlogs.r-pkg.org/badges/grand-total/mFD?color=blue)](https://cran.r-project.org/package=mFD)




The `mFD` package provides a **"user friendly" interface** to compute a 
**global assessment of functional diversity** by gathering computation of alpha 
and beta functional indices. As no package before, it guides users through 
functional analysis with one function per action to complete, several arguments 
that can be changed and allows personalized graphical outputs. Various tutorials 
are available on the mFD website to guide the user through the functional 
workflow.


## Installation

You can install the stable version from [CRAN](https://cran.r-project.org/) with:

```{r, eval = FALSE}
# Install stable version of < mFD > from CRAN ----
install.packages("mFD")
```

Or you can install the development version from [GitHub](https://github.com/) with:

```{r, eval = FALSE}
## Install < remotes > package (if not already installed) ----
if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}

## Install dev version of < mFD > from GitHub ----
remotes::install_github("CmlMagneville/mFD", build_vignettes = TRUE)
```


## Get started

```{r, eval = FALSE}
library("mFD")
```

To compute functional diversity indices, users need:

- a data frame summarizing species traits (species in rows, traits in columns). 
The `mFD` package works with all kind of traits: quantitative, ordinal, nominal, 
circular, and fuzzy-coded.

- a matrix summarizing species gathering into assemblages (assemblages in rows, 
species in columns). All assemblages must at least contain one species.

- a data frame summarizing traits category (first column with traits name, 
second column with traits type, third column with fuzzy name of fuzzy traits - 
if no fuzzy traits: NA).

For a complete understanding of the functional workflow and the package 
possibilities, please refer to the 
[mFD General Workflow](https://cmlmagneville.github.io/mFD/articles/mFD_general_workflow.html) and other tutorial on the [mFD website](https://cmlmagneville.github.io/mFD/).


## Citation

Please cite this package as:

_Magneville, C., Loiseau, N., Albouy, C., Casajus, N., Claverie, T., Escalas, A., Leprieur, F., Maire, E., Mouillot, D., Villéger, S._ (2022). 
mFD: an R package to compute and illustrate the multiple facets of functional diversity. 
_Ecography_ https://onlinelibrary.wiley.com/doi/10.1111/ecog.05904

You can also run:

```{r, eval = FALSE}
citation("mFD")
```


## Contributions

SV, NL, CA, FL and CM coded the functions and their help.
SV and CM led tutorial writings. All authors tested the functions
and contributed to writing of helps and tutorials.
NC optimized the package and made it ready for CRAN submission. 

        

---

Owner metadata

• Name: Camille Magneville
• Login: CmlMagneville
• Email:
• Kind: user
• Description:
• Website:
• Location:
• Twitter:
• Company:
• Icon url: https://avatars.githubusercontent.com/u/58591651?v=4
• Repositories: 3
• Last ynced at: 2023-03-05T17:19:06.009Z
• Profile URL: https://github.com/CmlMagneville

---

GitHub Events

Total

• Watch event: 1
• Push event: 2

Last Year

• Watch event: 1
• Push event: 2

---

Committers metadata

Last synced: 7 days ago

Name	Email	Commits
CmlMagneville	c****e@m****t	411
Cml_Magneville	c****e@g****m	116
Nicolas Casajus	n****s@g****m	42
Matthias Grenié	m****e@e****r	2

Committer domains:

• ens-lyon.fr: 1
• magneville.net: 1

---

Issue and Pull Request metadata

Last synced: about 19 hours ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/cmlmagneville/mfd

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Package metadata

• Total packages: 1
• Total downloads:
  • cran: 565 last-month
• Total dependent packages: 0
• Total dependent repositories: 0
• Total versions: 8
• Total maintainers: 1

---

Dependencies

Score: 11.020725305327403