Diversity Indices with Statistical Inference • DiversityStats

`DiversityStats`: Diversity Indices with Statistical Inference

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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

Github page

Documentation website

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.

DiversityStats: Diversity Indices with Statistical Inference