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), "How to partition diversity".
This package has now reached a stable release and is cross-validated against our Julia package Diversity.jl, which is developed independently. Please raise an issue if you find any problems.
To install rdiversity from CRAN, simply run the following from an R console:
install.packages("rdiversity")
The latest development version can be installed from GitHub:
# install.packages("devtools")
devtools::install_github("boydorr/rdiversity")
Examples of how to use the package are included in our docs, as well as in a vignette currently only available in the development version of this package:
install_github("boydorr/rdiversity", build_vignettes = TRUE)
vignette("examples", "rdiversity")