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## `DiversityStats`: Diversity Indices with Statistical Inference

<img src="https://raw.githubusercontent.com/aravind-j/DiversityStats/master/inst/extdata/DiversityStats.png" align="right" alt="logo" width="173" height = "200" style = "border: none; float: right;">

###### Version : [0.1.0](https://aravind-j.github.io/DiversityStats/); License: [GPL-2\|GPL-3](https://www.r-project.org/Licenses/)

##### *Aravind, J., Roy, Suman and Singh, Anju M.*

Division of Germplasm Conservation, ICAR-National Bureau of Plant
Genetic Resources, New Delhi.

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## 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. -->

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 package can be installed from CRAN as follows: 
&#10;
-->

The development version can be installed from github as follows:

``` r
# Install development version from Github
devtools::install_github("aravind-j/DiversityStats")
```

<!-- ## Detailed tutorial
For a detailed tutorial (vignette) on how to used this package type:
&#10;
``` r
browseVignettes(package = 'DiversityStats')
```
The vignette for the latest version is also available [online](https://aravind-j.github.io/DiversityStats/articles.html).-->

## What’s new

To know whats new in this version type:

``` r
news(package='DiversityStats')
```

## Links

<!--[CRAN page](https://cran.r-project.org/package=DiversityStats) -->

[Github page](https://github.com/aravind-j/DiversityStats)

[Documentation website](https://aravind-j.github.io/DiversityStats/)

<!--[Zenodo DOI](https://doi.org/10.5281/zenodo.14889174) -->

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## CRAN checks
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| Flavour                           | CRAN check                                                                                                                                                                                                         |
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| r-devel-linux-x86_64-debian-clang | [![CRAN check -                                                                                                                                                                                                    |
|                                   | r-devel-linux-x86_64-debian-clang](https://badges.cranchecks.info/flavor/r-devel-linux-x86_64-debian-clang/DiversityStats.svg)](https://cran.r-project.org/web/checks/check_results_j.aravind_at_icar.org.in.html) |
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| r-devel-linux-x86_64-fedora-gcc   | [![CRAN check -                                                                                                                                                                                                    |
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| r-release-linux-x86_64            | [![CRAN check -                                                                                                                                                                                                    |
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| Flavour                  | CRAN check                                                                                                                                                                                       |
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| r-devel-windows-x86_64   | [![CRAN check -                                                                                                                                                                                  |
|                          | r-devel-windows-x86_64](https://badges.cranchecks.info/flavor/r-devel-windows-x86_64/DiversityStats.svg)](https://cran.r-project.org/web/checks/check_results_j.aravind_at_icar.org.in.html)     |
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| r-release-windows-x86_64 | [![CRAN check -                                                                                                                                                                                  |
|                          | r-release-windows-x86_64](https://badges.cranchecks.info/flavor/r-release-windows-x86_64/DiversityStats.svg)](https://cran.r-project.org/web/checks/check_results_j.aravind_at_icar.org.in.html) |
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| r-oldrel-windows-x86_64  | [![CRAN check -                                                                                                                                                                                  |
|                          | r-oldrel-windows-x86_64](https://badges.cranchecks.info/flavor/r-oldrel-windows-x86_64/DiversityStats.svg)](https://cran.r-project.org/web/checks/check_results_j.aravind_at_icar.org.in.html)   |
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| Flavour                | CRAN check                                                                                                                                                                                   |
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| r-release-macos-x86_64 | [![CRAN check -                                                                                                                                                                              |
|                        | r-release-macos-x86_64](https://badges.cranchecks.info/flavor/r-release-macos-x86_64/DiversityStats.svg)](https://cran.r-project.org/web/checks/check_results_j.aravind_at_icar.org.in.html) |
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## Citing `DiversityStats`

To cite the methods in the package use:

``` r
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.
