https://github.com/boydorr/rdiversity

rdiversity - An R package for measuring similarity-sensitive diversity
https://github.com/boydorr/rdiversity

biodiversity diversity-measurement partitioning-diversity r

Last synced: 4 months ago
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rdiversity - An R package for measuring similarity-sensitive diversity

• Host: GitHub
• URL: https://github.com/boydorr/rdiversity
• Owner: boydorr
• Created: 2016-02-18T15:10:43.000Z (over 9 years ago)
• Default Branch: main
• Last Pushed: 2022-05-06T08:58:51.000Z (about 3 years ago)
• Last Synced: 2024-03-27T03:55:13.380Z (about 1 year ago)
• Topics: biodiversity, diversity-measurement, partitioning-diversity, r
• Language: R
• Homepage: http://boydorr.github.io/rdiversity/
• Size: 1.81 MB
• Stars: 5
• Watchers: 4
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# rdiversity: diversity measurement in R 

[![](https://img.shields.io/badge/docs-rdiversity-blue)](https://boydorr.github.io/rdiversity/)

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`rdiversity` is a package for R based around a framework for measuring biodiversity using similarity-sensitive diversity measures. It provides functionality for measuring alpha, beta and gamma diversity of metacommunities (*e.g.* ecosystems) and their constituent subcommunities, where similarity may be defined as taxonomic, phenotypic, genetic, phylogenetic, functional, and so on. It uses the diversity framework described in the arXiv paper [arXiv:1404.6520 (q-bio.QM)](https://arxiv.org/abs/1404.6520), "How to partition diversity". 

This package has now reached a stable release and is cross-validated against our Julia package [Diversity.jl](https://github.com/EcoJulia/Diversity.jl), which is developed independently. Please [raise an issue](https://github.com/boydorr/rdiversity/issues) if you find any problems.

To install rdiversity from CRAN, simply run the following from an R console:

```{r}

install.packages("rdiversity")

```

The latest development version can be installed from GitHub:

```{r]

# install.packages("devtools")

devtools::install_github("boydorr/rdiversity")

```

Examples of how to use the package are included in our 

[docs](http://boydorr.github.io/rdiversity/articles/examples.html), as well 

as in a vignette currently only available in the development version of this package:

```{r}

install_github("boydorr/rdiversity", build_vignettes = TRUE)

vignette("examples", "rdiversity")

```