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README.Rmd
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---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
mFD <img src="man/figures/hexasticker_mFD.png" align="right" style="float:right; height:120px;"/>
=========================================================
<!-- badges: start -->
[](https://CRAN.R-project.org/package=mFD/)
[](https://github.com/CmlMagneville/mFD/actions/workflows/R-CMD-check.yaml)
[](https://github.com/CmlMagneville/mFD/actions/workflows/pkgdown.yaml)
[](https://choosealicense.com/licenses/gpl-2.0/)
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://www.repostatus.org/#active)
[](https://cran.r-project.org/package=mFD)
<!-- badges: end -->
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.