# Entropy Partitioning to Measure Diversity

## Documentation for package ‘entropart’ version 1.6-1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E G H I K L M O P R S T

entropart-package | Entropy Partitioning to Measure Diversity

## -- A --

AbdFreqCount | Abundance Frequency Count of a Community
AbdVector | Species Distributions.
AllenH | Phylogenetic Entropy of a Community
AlphaDiversity | Reduced-bias alpha diversity of a metacommunity
AlphaEntropy | Reduced-bias alpha entropy of a metacommunity
as.AbdVector | Species Distributions.
as.AbdVector.data.frame | Species Distributions.
as.AbdVector.integer | Species Distributions.
as.AbdVector.numeric | Species Distributions.
as.AccumCurve | Diversity accumulation.
as.CommunityProfile | Diversity or Entropy Profile of a community
as.ProbaVector | Species Distributions.
as.ProbaVector.data.frame | Species Distributions.
as.ProbaVector.integer | Species Distributions.
as.ProbaVector.numeric | Species Distributions.
as.SimTest | SimTest class
as.SpeciesDistribution | Species Distributions.
as.SpeciesDistribution.data.frame | Species Distributions.
as.SpeciesDistribution.integer | Species Distributions.
as.SpeciesDistribution.numeric | Species Distributions.
autoplot.AccumCurve | Diversity accumulation.
autoplot.CommunityProfile | Diversity or Entropy Profile of a community
autoplot.DivEst | Diversity Estimation of a metacommunity
autoplot.DivPart | Diversity Partition of a metacommunity
autoplot.DivProfile | Diversity Profile of a metacommunity
autoplot.MCdiversity | Meta-Community diversity class.
autoplot.MCentropy | Meta-Community entropy class.
autoplot.PhyloValue | Phylogenetic entropy or diversity.
autoplot.SimTest | SimTest class
autoplot.SpeciesDistribution | Species Distributions.

## -- B --

bcDiversity | Hill number of a community
bcDqz | Similarity-based diversity of a community
bcGenSimpson | Generalized Simpson's Entropy and Diversity
bcGenSimpsonD | Generalized Simpson's Entropy and Diversity
bcHqz | Similarity-based entropy of a community
bcHqzBeta | Similarity-based beta entropy of a community
bcHurlbert | Hurlbert's Index and Explicit Diversity
bcHurlbertD | Hurlbert's Index and Explicit Diversity
bcPhyloBetaEntropy | Phylogenetic Beta Entropy of a community
bcPhyloDiversity | Phylogenetic Diversity of a Community
bcPhyloEntropy | Phylogenetic Entropy of a community
bcRao | Rao Quadratic Entropy of a Community
bcRichness | Number of species 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 (HCDT) Entropy of a community
bcTsallisBeta | Tsallis beta entropy of a community
BetaDiversity | Reduced-bias beta diversity of a metacommunity
BetaEntropy | Reduced-bias beta entropy of a metacommunity

## -- C --

CEnvelope | Diversity or Entropy Profile of a community
ChaoPD | Phylogenetic Diversity of a Community
CommunityProfile | Diversity or Entropy Profile of a community
Coverage | Sample coverage of a community
Coverage2Size | Sample coverage of a community

## -- D --

DivAC | Diversity accumulation.
Diversity | Hill number of a community
Diversity.AbdVector | Hill number of a community
Diversity.integer | Hill number of a community
Diversity.numeric | Hill number of a community
Diversity.ProbaVector | Hill number 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
Dqz.AbdVector | Similarity-based diversity of a community
Dqz.integer | Similarity-based diversity of a community
Dqz.numeric | Similarity-based diversity of a community
Dqz.ProbaVector | Similarity-based diversity of a community

## -- E --

EightSpAbundance | Abundances of 8 species to run examples.
EightSpTree | Functional tree with 8 species.
Enq | Grassberger's expectation of n^q
EntAC | Diversity accumulation.
entropart | Entropy Partitioning to Measure Diversity
EntropyCI | Entropy of Monte-Carlo simulated communities
expq | Exponential of order q
expq.CommunityProfile | Exponential of order q

## -- G --

GammaDiversity | Reduced-bias gamma diversity of a metacommunity
GammaEntropy | Reduced-bias gamma entropy of a metacommunity
GenSimpson | Generalized Simpson's Entropy and Diversity
GenSimpson.AbdVector | Generalized Simpson's Entropy and Diversity
GenSimpson.integer | Generalized Simpson's Entropy and Diversity
GenSimpson.numeric | Generalized Simpson's Entropy and Diversity
GenSimpson.ProbaVector | Generalized Simpson's Entropy and Diversity
GenSimpsonD | Generalized Simpson's Entropy and Diversity
GenSimpsonD.AbdVector | Generalized Simpson's Entropy and Diversity
GenSimpsonD.integer | Generalized Simpson's Entropy and Diversity
GenSimpsonD.numeric | Generalized Simpson's Entropy and Diversity
GenSimpsonD.ProbaVector | Generalized Simpson's Entropy and Diversity

## -- H --

Hqz | Similarity-based entropy of a community
Hqz.AbdVector | Similarity-based entropy of a community
Hqz.integer | Similarity-based entropy of a community
Hqz.numeric | Similarity-based entropy of a community
Hqz.ProbaVector | Similarity-based entropy of a community
HqzBeta | Similarity-based beta entropy of a community
HqzBeta.AbdVector | Similarity-based beta entropy of a community
HqzBeta.integer | Similarity-based beta entropy of a community
HqzBeta.numeric | Similarity-based beta entropy of a community
HqzBeta.ProbaVector | Similarity-based beta entropy of a community
Hurlbert | Hurlbert's Index and Explicit Diversity
Hurlbert.AbdVector | Hurlbert's Index and Explicit Diversity
Hurlbert.integer | Hurlbert's Index and Explicit Diversity
Hurlbert.numeric | Hurlbert's Index and Explicit Diversity
Hurlbert.ProbaVector | Hurlbert's Index and Explicit Diversity
HurlbertD | Hurlbert's Index and Explicit Diversity
HurlbertD.AbdVector | Hurlbert's Index and Explicit Diversity
HurlbertD.integer | Hurlbert's Index and Explicit Diversity
HurlbertD.numeric | Hurlbert's Index and Explicit Diversity
HurlbertD.ProbaVector | Hurlbert's Index and Explicit Diversity

## -- I --

is.AbdVector | Species Distributions.
is.AccumCurve | Diversity accumulation.
is.CommunityProfile | Diversity or Entropy Profile of a community
is.DivEst | Diversity Estimation of a metacommunity
is.DivPart | Diversity Partition of a metacommunity
is.DivProfile | Diversity Profile of a metacommunity
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.PhyloValue | Phylogenetic entropy or diversity.
is.PPtree | Preprocessed Trees.
is.ProbaVector | Species Distributions.
is.SimTest | SimTest class
is.SpeciesDistribution | Species Distributions.

## -- K --

KLq | Generalized Kullback-Leibler divergence

## -- L --

lnq | Logarithm of order q
lnq.CommunityProfile | Logarithm of order q

## -- M --

MCdiversity | Meta-Community diversity class.
MCentropy | Meta-Community entropy class.
MergeC | Manipulation of meta-communities
MergeMC | Manipulation of meta-communities
MetaCommunity | Metacommunity class

## -- O --

Optimal.Similarity | Optimal scale parameter to transform a distance matrix into a similarity matrix

## -- P --

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
PhyloBetaEntropy.AbdVector | Phylogenetic Beta Entropy of a community
PhyloBetaEntropy.integer | Phylogenetic Beta Entropy of a community
PhyloBetaEntropy.numeric | Phylogenetic Beta Entropy of a community
PhyloBetaEntropy.ProbaVector | Phylogenetic Beta Entropy of a community
PhyloDiversity | Phylogenetic Diversity of a Community
PhyloDiversity.AbdVector | Phylogenetic Diversity of a Community
PhyloDiversity.integer | Phylogenetic Diversity of a Community
PhyloDiversity.numeric | Phylogenetic Diversity of a Community
PhyloDiversity.ProbaVector | Phylogenetic Diversity of a Community
PhyloEntropy | Phylogenetic Entropy of a community
PhyloEntropy.AbdVector | Phylogenetic Entropy of a community
PhyloEntropy.integer | Phylogenetic Entropy of a community
PhyloEntropy.numeric | Phylogenetic Entropy of a community
PhyloEntropy.ProbaVector | Phylogenetic Entropy of a community
PhyloValue | Phylogenetic entropy or diversity.
plot.AccumCurve | Diversity accumulation.
plot.CommunityProfile | Diversity or Entropy Profile 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 | Phylogenetic entropy or diversity.
plot.PPtree | Preprocessed Trees.
plot.SimTest | SimTest class
plot.SpeciesDistribution | Species Distributions.
PPtree | Preprocessed Trees.
ProbaVector | Species Distributions.

## -- R --

RACbstick | Fit Distributions to Well-Known Rank Abundance Curves.
RACgeom | Fit Distributions to Well-Known Rank Abundance Curves.
RAClnorm | Fit Distributions to Well-Known Rank Abundance Curves.
RAClseries | Fit Distributions to Well-Known Rank Abundance Curves.
Rao | Rao Quadratic Entropy of a Community
Rao.AbdVector | Rao Quadratic Entropy of a Community
Rao.integer | Rao Quadratic Entropy of a Community
Rao.numeric | Rao Quadratic Entropy of a Community
Rao.ProbaVector | Rao Quadratic Entropy of a Community
rCommunity | Random Communities
Richness | Number of species of a community
Richness.AbdVector | Number of species of a community
Richness.integer | Number of species of a community
Richness.numeric | Number of species of a community
Richness.ProbaVector | Number of species of a community

## -- S --

Shannon | Shannon entropy of a community
Shannon.AbdVector | Shannon entropy of a community
Shannon.integer | Shannon entropy of a community
Shannon.numeric | Shannon entropy of a community
Shannon.ProbaVector | Shannon entropy of a community
ShannonBeta | Shannon beta entropy of a community
ShannonBeta.AbdVector | Shannon beta entropy of a community
ShannonBeta.integer | Shannon beta entropy of a community
ShannonBeta.numeric | Shannon beta entropy of a community
ShannonBeta.ProbaVector | Shannon beta entropy of a community
ShuffleMC | Manipulation of meta-communities
Simpson | Simpson entropy of a community
Simpson.AbdVector | Simpson entropy of a community
Simpson.integer | Simpson entropy of a community
Simpson.numeric | Simpson entropy of a community
Simpson.ProbaVector | Simpson entropy of a community
SimpsonBeta | Simpson beta entropy of a community
SimpsonBeta.AbdVector | Simpson beta entropy of a community
SimpsonBeta.integer | Simpson beta entropy of a community
SimpsonBeta.numeric | Simpson beta entropy of a community
SimpsonBeta.ProbaVector | Simpson beta entropy of a community
SimTest | SimTest class
SpeciesDistribution | Species Distributions.
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.PhyloValue | Phylogenetic entropy or diversity.
summary.SimTest | SimTest class

## -- T --

Tsallis | Tsallis (HCDT) Entropy of a community
Tsallis.AbdVector | Tsallis (HCDT) Entropy of a community
Tsallis.integer | Tsallis (HCDT) Entropy of a community
Tsallis.numeric | Tsallis (HCDT) Entropy of a community
Tsallis.ProbaVector | Tsallis (HCDT) Entropy of a community
TsallisBeta | Tsallis beta entropy of a community
TsallisBeta.AbdVector | Tsallis beta entropy of a community
TsallisBeta.integer | Tsallis beta entropy of a community
TsallisBeta.numeric | Tsallis beta entropy of a community
TsallisBeta.ProbaVector | Tsallis beta entropy of a community