Entropy Partitioning to Measure Diversity


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Documentation for package ‘entropart’ version 1.6-8

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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