Entropy Partitioning to Measure Diversity

Documentation for package ‘entropart’ version 1.6-13

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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