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Entropy Partitioning to Measure Diversity

entropart is an R package that provides functions to calculate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity.

Estimation-bias corrections are available.

Details

In the entropart package, individuals of different species are counted in several communities which may (or not) be agregated to define a metacommunity. In the metacommunity, the probability to find a species in the weighted average of probabilities in communities. This is a naming convention, which may correspond to plots in a forest inventory or any data organized the same way.

Basic functions allow computing diversity of a community. Data is simply a vector of probabilities (summing up to 1) or of abundances (integer values that are numbers of individuals). Calculate entropy with functions such as Tsallis, Shannon, Simpson, Hurlbert or GenSimpson and explicit diversity (i.e. effective number of species) with Diversity and others. By default, the best available estimator of diversity will be used, according to the data.

Communities can be simulated by rCommunity, explicitely declared as a species distribution (as.AbdVector or as.ProbaVector), and plotted.

Phylogenetic entropy and diversity can be calculated if a phylogenetic (or functional), ultrametric tree is provided. See PhyloEntropy, Rao for examples of entropy and PhyloDiversity to calculate phylodiversity, with the state-of-the-art estimation-bias correction. Similarity-based diversity is calculated with Dqz, based on a similarity matrix.

Vignettes

A quick introduction is in vignette("entropart").

A full documentation is available online, in the "Articles" section of the web site of the vignette. It is a continuous update of the paper published in the Journal of Statistical Software (Marcon & Hérault, 2015).

The development version documentation is also available.

Reference

Marcon, E. and Herault, B. (2015). entropart: An R Package to Measure and Partition Diversity. Journal of Statistical Software. 67(8): 1-26.

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Version

Install

install.packages('entropart')

Monthly Downloads

791

Version

1.6-16

License

GNU General Public License

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/EricMarcon/entropart/

Homepage

https://ericmarcon.github.io/entropart/

Maintainer

Eric Marcon

Last Published

February 7th, 2025

Functions in entropart (1.6-16)

Grassberger's expectation of n^q

Similarity-based diversity of a community

CommunityProfile

Diversity or Entropy Profile of a community

Sample coverage of a community

Functional tree with 8 species.

Diversity Profile of a metacommunity

Hill number of a community

Diversity Estimation of a metacommunity

EightSpAbundance

Abundances of 8 species to run examples.

Diversity Partition of a metacommunity

Generalized Simpson's Entropy and Diversity

Similarity-based entropy of a community

Hurlbert's Index and Explicit Diversity

Meta-Community entropy class.

Reduced-bias gamma diversity of a metacommunity

Meta-Community diversity class.

Reduced-bias gamma entropy of a metacommunity

Generalized Kullback-Leibler divergence

Similarity-based beta entropy of a community

Entropy of Monte-Carlo simulated communities

Phylogenetic Diversity / Functional Diversity of a Community

Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.

Optimal.Similarity

Optimal scale parameter to transform a distance matrix into a similarity matrix

Manipulation of meta-communities

Preprocessed Trees.

Paracou618.Functional

Functional tree of species of Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.

Paracou618.dist

Functional distances between pairs of species of Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.

Metacommunity class

Paracou618.Taxonomy

Taxonomy (Family - Genus - Species) of Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.

Apply a Function over a Phylogenetic Tree

Phylogenetic entropy or diversity.

Phylogenetic Entropy of a community

PhyloBetaEntropy

Phylogenetic Beta Entropy of a community

Phylogenetic Diversity of a Community

Preprocess.Tree

Preprocessing of a phylogenetic tree

Preprocessing of metacommunity data

Shannon entropy of a community

Number of species of a community

Rao Quadratic Entropy of a Community

Fit Distributions to Well-Known Rank Abundance Curves.

Simpson entropy of a community

Shannon beta entropy of a community

Simpson beta entropy of a community

Tsallis (HCDT) Entropy of a community

Logarithm of order q

Exponential of order q

SpeciesDistribution

Species Distributions

entropart-package

Entropy Partitioning to Measure Diversity

Tsallis beta entropy of a community

Objects exported from other packages

Merge community data

Random Communities

Diversity accumulation.

Phylogenetic Entropy of a Community

Reduced-bias beta diversity of a metacommunity

Phylogenetic Diversity of a Community

ArgumentOriginalName

Finds the original value (name of expression) of the argument of a function even in the case of embedded calls.

Abundance Frequency Count of a Community

Reduced-bias alpha entropy of a metacommunity

Reduced-bias beta entropy of a metacommunity

Reduced-bias alpha diversity of a metacommunity

CheckentropartArguments

Checks the arguments of a function of the package entropart