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entropart (version 1.4-6)

Entropy Partitioning to Measure Diversity

Description

Measurement and partitioning of diversity, based on Tsallis entropy.

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Version

Install

install.packages('entropart')

Monthly Downloads

634

Version

1.4-6

License

GNU General Public License

Maintainer

Eric Marcon

Last Published

December 9th, 2016

Functions in entropart (1.4-6)

BetaDiversity

Reduced-bias beta diversity of a metacommunity
AlphaDiversity

Reduced-bias alpha diversity of a metacommunity
CommunityProfile

Diversity or Entropy Profile of a community
AbdFreqCount

Abundance Frequency Count of a Community
ArgumentOriginalName

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

Checks the arguments of a function of the package entropart
ChaoPD

Phylogenetic Diversity of a Community
AllenH

Phylogenetic Entropy of a Community
BetaEntropy

Reduced-bias beta entropy of a metacommunity
AlphaEntropy

Reduced-bias alpha entropy of a metacommunity
DivProfile

Diversity Profile of a metacommunity
Coverage

Sample coverage of a community
Dqz

Similarity-based diversity of a community
Enq

Grassberger's expectation of n^q
EightSpAbundance

Abundances of 8 species to run examples.
entropart-package

Entropy Partitioning to Measure Diversity
EightSpTree

Functional tree with 8 species.
DivEst

Diversity Estimation of a metacommunity
Diversity

HCDT diversity of a community
DivPart

Diversity Partition of a metacommunity
EntropyCI

Entropy of Monte-Carlo simulated communities
expq

Exponential of order q
lnq

Logarithm of order q
GammaEntropy

Reduced-bias gamma entropy of a metacommunity
GammaDiversity

Reduced-bias gamma diversity of a metacommunity
HqzBeta

Similarity-based beta entropy of a community
KLq

Generalized Kullback-Leibler divergence
Hurlbert

Hurlbert's Index and Explicit Diversity
Hqz

Similarity-based entropy of a community
GenSimpson

Generalized Simpson's Entropy and Diversity
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

Metacommunity class
mergeandlabel

Merge community data
Paracou618.Taxonomy

Taxonomy (Family - Genus - Species) of Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.
Paracou618.Functional

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

Meta-Community diversity class.
MC Utilities

Manipulation of meta-communities
MCentropy

Meta-Community entropy class.
Optimal.Similarity

Optimal scale parameter to transform a distance matrix into a similarity matrix
Paracou618.MC

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

Preprocessing of a phylogenetic tree
Rao

Rao Quadratic Entropy of a Community
PhyloBetaEntropy

Phylogenetic Beta Entropy of a community
PhyloDiversity

Phylogenetic Diversity of a Community
PhyloApply

Apply a Function over a Phylogenetic Tree
PDFD

Phylogenetic Diversity / Functional Diversity of a Community
PhyloEntropy

Phylogenetic Entropy of a community
PhyloValue

Phylogenetic entropy of diversity.
PPtree

Preprocessed Trees.
SimTest

SimTest class
Preprocess.MC

Preprocessing of metacommunity data
Richness

Number of species of a community
SimpsonBeta

Simpson beta entropy of a community
Shannon

Shannon entropy of a community
SpeciesDistribution

Species Distributions.
ShannonBeta

Shannon beta entropy of a community
Simpson

Simpson entropy of a community
rCommunity

Random Communities
Tsallis

Tsallis (HCDT) Entropy of a community
TsallisBeta

Tsallis beta entropy of a community