Entropy partitioning to measure diversity


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Documentation for package ‘entropart’ version 1.1.3

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entropart-package Entropy partitioning to measure diversity
AllenH Phylogenetic Entropy of a Community
AlphaDiversity Unbiased alpha diversity of a metacommunity
AlphaEntropy Unbiased alpha entropy of a metacommunity
as.SimTest SimTest class
bcDiversity Generalized diversity of a community
bcPhyloBetaEntropy Phylogenetic Beta Entropy of a community
bcPhyloDiversity Phylogenetic Diversity of a Community
bcPhyloEntropy Phylogenetic Entropy of a community
bcShannon Shannon entropy of a community
bcShannonBeta Shannon beta entropy of a community
bcSimpson Simpson entropy of a community
bcSimpsonBeta Simpson beta entropy of a community
bcTsallis Tsallis Entropy of a community
bcTsallisBeta Tsallis beta entropy of a community
BetaDiversity Unbiased beta diversity of a metacommunity
BetaEntropy Unbiased beta entropy of a metacommunity
ChaoPD Phylogenetic Diversity of a Community
CommunityProfile Diversity or Entropy Profile of a community
Coverage Sample coverage of a community
Diversity Generalized diversity of a community
DivEst Diversity Estimation of a metacommunity
DivPart Diversity Partition of a metacommunity
DivProfile Diversity Profile of a metacommunity
Dqz Similarity-based diversity of a community
EightSpAbundance Abundances of 8 species to run examples.
EightSpTree Functional tree with 8 species.
Enq Grassberger's expectation of n^q
entropart Entropy partitioning to measure diversity
EntropyCI Entropy of Monte-Carlo simulated communities
expq Exponential of order q
GammaDiversity Unbiased gamma diversity of a metacommunity
GammaEntropy Unbiased gamma entropy of a metacommunity
Hqz Similarity-based entropy of a community
is.MCdiversity Meta-Community diversity class.
is.MCentropy Meta-Community entropy class.
is.MetaCommunity Metacommunity class
is.PhyloDiversity Phylogenetic Diversity of a Community
is.PhyloEntropy Phylogenetic Entropy of a community
is.PPtree Preprocessed Trees.
is.SimTest SimTest class
KLq Generalized Kullback-Leibler divergence
lnq Logarithm of order q
MCdiversity Meta-Community diversity class.
MCentropy Meta-Community entropy class.
MergeC Manipulation of meta-communities
MergeMC Manipulation of meta-communities
MetaCommunity Metacommunity class
Originality.Species Originality of species
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.
Paracou618.Functional Functional tree of species of Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.
Paracou618.MC Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.
Paracou618.Taxonomy Taxonomy (Family - Genus - Species) of Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.
PDFD Phylogenetic Diversity / Functional Diversity of a Community
PhyloApply Apply a Function over a Phylogenetic Tree
PhyloBetaEntropy Phylogenetic Beta Entropy of a community
PhyloDiversity Phylogenetic Diversity of a Community
PhyloEntropy Phylogenetic Entropy of a community
plot.DivEst Diversity Estimation of a metacommunity
plot.DivPart Diversity Partition of a metacommunity
plot.DivProfile Diversity Profile of a metacommunity
plot.MCdiversity Meta-Community diversity class.
plot.MCentropy Meta-Community entropy class.
plot.MetaCommunity Metacommunity class
plot.PhyloValue Plot phylogenetic entropy of diversity.
plot.PPtree Preprocessed Trees.
plot.SimTest SimTest class
PPtree Preprocessed Trees.
Rao Rao Quadratic Entropy of a Community
Richness Simpson entropy of a community
Shannon Shannon entropy of a community
ShannonBeta Shannon beta entropy of a community
ShuffleMC Manipulation of meta-communities
Simpson Simpson entropy of a community
SimpsonBeta Simpson beta entropy of a community
SimTest SimTest class
summary.DivEst Diversity Estimation of a metacommunity
summary.DivPart Diversity Partition of a metacommunity
summary.DivProfile Diversity Profile of a metacommunity
summary.MCdiversity Meta-Community diversity class.
summary.MCentropy Meta-Community entropy class.
summary.MetaCommunity Metacommunity class
summary.PhyloDiversity Phylogenetic Diversity of a Community
summary.PhyloEntropy Phylogenetic Entropy of a community
summary.SimTest SimTest class
Tsallis Tsallis Entropy of a community
TsallisBeta Tsallis beta entropy of a community