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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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Install

install.packages('entropart')

Monthly Downloads

675

Version

1.6-7

License

GNU General Public License

Issues

Pull Requests

Stars

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Repository

https://github.com/EricMarcon/entropart

Maintainer

Eric Marcon

Last Published

April 16th, 2021

Functions in entropart (1.6-7)

Phylogenetic Entropy of a Community

Reduced-bias alpha diversity of a metacommunity

CheckentropartArguments

Checks the arguments of a function of the package entropart

Phylogenetic Diversity of a Community

Diversity accumulation.

Abundance Frequency Count of a Community

Diversity Partition of a metacommunity

Diversity Estimation of a metacommunity

Similarity-based diversity of a community

EightSpAbundance

Abundances of 8 species to run examples.

Sample coverage of a community

Generalized Simpson's Entropy and Diversity

Reduced-bias alpha entropy of a metacommunity

ArgumentOriginalName

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

CommunityProfile

Diversity or Entropy Profile of a community

Reduced-bias gamma entropy of a metacommunity

Reduced-bias beta diversity of a metacommunity

Diversity Profile of a metacommunity

Reduced-bias beta entropy of a metacommunity

Entropy of Monte-Carlo simulated communities

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

Manipulation of meta-communities

PhyloBetaEntropy

Phylogenetic Beta Entropy of a community

Hill number of a community

Phylogenetic Diversity of a Community

Metacommunity class

Generalized Kullback-Leibler divergence

Grassberger's expectation of n^q

Hurlbert's Index and Explicit Diversity

Functional tree with 8 species.

Paracou618.Taxonomy

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

Similarity-based entropy of a community

Simpson entropy of a community

Simpson beta entropy of a community

Phylogenetic entropy or diversity.

Phylogenetic Entropy of a community

Reduced-bias gamma diversity of a metacommunity

Apply a Function over a Phylogenetic Tree

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.

Meta-Community diversity class.

Preprocessing of metacommunity data

Preprocess.Tree

Preprocessing of a phylogenetic tree

Random Communities

Merge community data

Meta-Community entropy class.

Shannon beta entropy of a community

Similarity-based beta entropy of a community

Preprocessed Trees.

Fit Distributions to Well-Known Rank Abundance Curves.

SpeciesDistribution

Species Distributions.

Paracou618.Functional

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

Tsallis (HCDT) Entropy of a community

Exponential of order q

Rao Quadratic Entropy of a Community

Logarithm of order q

Optimal.Similarity

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

Number of species of a community

Phylogenetic Diversity / Functional Diversity of a Community

Shannon entropy of a community

Tsallis beta entropy of a community

entropart-package

Entropy Partitioning to Measure Diversity