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https://github.com/CmlMagneville/mFD

:package: A Computation of Functional Spaces and Functional Diversity Indices
https://github.com/CmlMagneville/mFD

Last synced: about 2 months ago
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: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 (almost 4 years ago)
Default Branch: main
Last Pushed: 2024-07-26T07:53:58.000Z (5 months ago)
Last Synced: 2024-10-29T23:21:14.819Z (2 months ago)
Language: R
Homepage: https://cmlmagneville.github.io/mFD/
Size: 164 MB
Stars: 25
Watchers: 2
Forks: 5
Open Issues: 0
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- License: LICENSE

Awesome Lists containing this project

open-sustainable-technology - mFD - Provides a user friendly interface to compute a global assessment of functional diversity by gathering computation of alpha and beta functional indices. (Biosphere / Biodiversity Analysis and Metrics)

README

        ---

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.