Diversity Indices with Statistical Inference.
DiversityStats: Diversity Indices with Statistical Inference
Version : 0.1.0; License: GPL-2|GPL-3
Aravind, J., Roy, Suman and Singh, Anju M.
Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi.
Description
Provides a comprehensive framework for analyzing diversity from frequency/abundance count data. Implements a wide range of classical and entropy-based diversity indices, including Berger-Parker, Simpson (and related variants), Shannon, Brillouin, McIntosh, Margalef, Menhinick and Smith-Wilson. Supports permutation-based hypothesis tests for comparing groups with respect to diversity (global and pairwise comparisons), as well as confidence interval estimation using multiple bootstrap methods. Includes functionality for generating diversity profiles based on parametric families such as Hill numbers, Rényi entropy, and Tsallis entropy. The methods are applicable to ecological community data (species abundance counts) and genetic or phenotypic class frequency data.
Installation
The development version can be installed from github as follows:
# Install development version from Github
devtools::install_github("aravind-j/DiversityStats")
What’s new
To know whats new in this version type:
news(package='DiversityStats')
Links
Citing DiversityStats
To cite the methods in the package use:
citation("DiversityStats")
To cite the R package 'DiversityStats' in publications use:
Aravind, J. (). DiversityStats: Diversity Indices with Statistical Inference. R package version 0.1.0,
https://aravind-j.github.io/DiversityStats/.
A BibTeX entry for LaTeX users is
@Manual{,
title = {DiversityStats: Diversity Indices with Statistical Inference},
author = {J. Aravind and Suman Roy and Anju Mahendru Singh},
note = {R package version 0.1.0 https://aravind-j.github.io/DiversityStats/},
}
This free and open-source software implements academic research by the authors and co-workers. If you use
it, please support the project by citing the package.