mfd

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

https://github.com/cmlmagneville/mfd

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 1 DOI reference(s) in README
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Academic publication links
Links to: wiley.com
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (17.2%) to scientific vocabulary

Keywords from Contributors

functional-trait

Last synced: 7 months ago · JSON representation

Repository

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

Basic Info

Host: GitHub
Owner: CmlMagneville
License: gpl-2.0
Language: R
Default Branch: main
Homepage: https://cmlmagneville.github.io/mFD/
Size: 167 MB

Statistics

Stars: 28
Watchers: 2
Forks: 5
Open Issues: 0
Releases: 7

Created about 5 years ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog 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

Name: Camille Magneville
Login: CmlMagneville
Kind: user

Repositories: 3
Profile: https://github.com/CmlMagneville

GitHub Events

Total

Watch event: 1
Issue comment event: 2
Push event: 2

Last Year

Watch event: 1
Issue comment event: 2
Push event: 2

Committers

Last synced: 7 months ago

All Time

Total Commits: 571
Total Committers: 5
Avg Commits per committer: 114.2
Development Distribution Score (DDS): 0.28

Past Year

Commits: 1
Committers: 1
Avg Commits per committer: 1.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
CmlMagneville	c**e@m**t	411
Cml_Magneville	c**e@g**m	113
Nicolas Casajus	n**s@g**m	42
CmlMagneville	5**e@u**m	3
Matthias Grenié	m**e@e**r	2

Committer Domains (Top 20 + Academic)

ens-lyon.fr: 1 magneville.net: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 34
Total pull requests: 10
Average time to close issues: 23 days
Average time to close pull requests: 7 days
Total issue authors: 17
Total pull request authors: 2
Average comments per issue: 1.74
Average comments per pull request: 0.2
Merged pull requests: 8
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

ahasverus (10)
CmlMagneville (6)
Klemet (3)
AlexArevalo1 (2)
Jaxsonp10 (1)
Rekyt (1)
beifenging (1)
zhangzhixin1102 (1)
Taiyou187 (1)
Alexia126 (1)
gxxin1994 (1)
sroblet (1)
mthompson89 (1)
acottin (1)
poudro1 (1)

Pull Request Authors

ahasverus (7)
Rekyt (3)

Top Labels

Issue Labels

enhancement (6) documentation (5) bug (3) final check (1) review code (1) help wanted (1)

Pull Request Labels

Packages

Total packages: 3
Total downloads:
- cran 715 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 22
Total maintainers: 1

proxy.golang.org: github.com/cmlmagneville/mfd

Documentation: https://pkg.go.dev/github.com/cmlmagneville/mfd#section-documentation
License: gpl-2.0
Latest release: v1.0.7
published about 2 years ago

Versions: 7
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 7 months ago

proxy.golang.org: github.com/CmlMagneville/mFD

Documentation: https://pkg.go.dev/github.com/CmlMagneville/mFD#section-documentation
License: gpl-2.0
Latest release: v1.0.7
published about 2 years ago

Versions: 7
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 7 months ago

cran.r-project.org: mFD

Compute and Illustrate the Multiple Facets of Functional Diversity

Homepage: https://cmlmagneville.github.io/mFD/
Documentation: http://cran.r-project.org/web/packages/mFD/mFD.pdf
License: GPL-2
Latest release: 1.0.7
published about 2 years ago

Versions: 8
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 715 Last month

Rankings

Forks count: 12.8%

Stargazers count: 15.1%

Average: 23.4%

Downloads: 23.9%

Dependent packages count: 29.8%

Dependent repos count: 35.5%

Maintainers (1)

camille.magneville@gmail.com

Last synced: 7 months ago

Dependencies

DESCRIPTION cran

R >= 3.5 depends
FactoMineR * imports
Hmisc * imports
ade4 * imports
ape * imports
betapart >= 1.5.4 imports
cluster * imports
dendextend * imports
gawdis * imports
geometry * imports
ggplot2 * imports
ggrepel * imports
grid * imports
patchwork * imports
reshape2 * imports
rstatix * imports
stats * imports
utils * imports
vegan * imports
dplyr >= 1.0.6 suggests
knitr * suggests
magrittr * suggests
rmarkdown >= 2.6 suggests
stringr * suggests
tibble * suggests
tidyr * suggests

.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

actions/cache v2 composite
actions/checkout v2 composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite