entropart: Entropy Partitioning to Measure Diversity

Measurement and partitioning of diversity, based on Tsallis entropy.

AuthorEric Marcon, Bruno Herault
Date of publication2017-03-29 21:48:06 UTC
MaintainerEric Marcon <Eric.Marcon@ecofog.gf>
LicenseGNU General Public License
Version1.4-7

View on CRAN

Man pages

AbdFreqCount: Abundance Frequency Count of a Community

AllenH: Phylogenetic Entropy of a Community

AlphaDiversity: Reduced-bias alpha diversity of a metacommunity

AlphaEntropy: Reduced-bias alpha entropy of a metacommunity

ArgumentOriginalName: Finds the original value (name of expression) of the argument...

BetaDiversity: Reduced-bias beta diversity of a metacommunity

BetaEntropy: Reduced-bias beta entropy of a metacommunity

ChaoPD: Phylogenetic Diversity of a Community

CheckentropartArguments: Checks the arguments of a function of the package entropart

CommunityProfile: Diversity or Entropy Profile of a community

Coverage: Sample coverage of a community

Diversity: HCDT 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-package: Entropy Partitioning to Measure Diversity

EntropyCI: Entropy of Monte-Carlo simulated communities

expq: Exponential of order q

GammaDiversity: Reduced-bias gamma diversity of a metacommunity

GammaEntropy: Reduced-bias gamma entropy of a metacommunity

GenSimpson: Generalized Simpson's Entropy and Diversity

Hqz: Similarity-based entropy of a community

HqzBeta: Similarity-based beta entropy of a community

Hurlbert: Hurlbert's Index and Explicit Diversity

KLq: Generalized Kullback-Leibler divergence

lnq: Logarithm of order q

MCdiversity: Meta-Community diversity class.

MCentropy: Meta-Community entropy class.

mergeandlabel: Merge community data

MergeMC: Manipulation of meta-communities

MetaCommunity: Metacommunity class

Optimal.Similarity: Optimal scale parameter to transform a distance matrix into a...

Paracou618.dist: Functional distances between pairs of species of Paracou...

Paracou618.Functional: Functional tree of species of Paracou field station plots 6...

Paracou618.MC: Paracou field station plots 6 and 18, two 1-ha plots...

Paracou618.Taxonomy: Taxonomy (Family - Genus - Species) of Paracou field station...

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

PhyloValue: Phylogenetic entropy of diversity.

PPtree: Preprocessed Trees.

Preprocess.MC: Preprocessing of metacommunity data

Preprocess.Tree: Preprocessing of a phylogenetic tree

Rao: Rao Quadratic Entropy of a Community

rCommunity: Random Communities

Richness: Number of species of a community

Shannon: Shannon entropy of a community

ShannonBeta: Shannon beta entropy of a community

Simpson: Simpson entropy of a community

SimpsonBeta: Simpson beta entropy of a community

SimTest: SimTest class

SpeciesDistribution: Species Distributions.

Tsallis: Tsallis (HCDT) Entropy of a community

TsallisBeta: Tsallis beta entropy of a community

Functions

AbdFreqCount Man page
AbdVector Man page
AllenH Man page
AlphaDiversity Man page
AlphaEntropy Man page
ArgumentOriginalName Man page
as.AbdVector Man page
as.AbdVector.data.frame Man page
as.AbdVector.integer Man page
as.AbdVector.numeric Man page
as.CommunityProfile Man page
as.ProbaVector Man page
as.ProbaVector.data.frame Man page
as.ProbaVector.integer Man page
as.ProbaVector.numeric Man page
as.SimTest Man page
as.SpeciesDistribution Man page
as.SpeciesDistribution.data.frame Man page
as.SpeciesDistribution.integer Man page
as.SpeciesDistribution.numeric Man page
bcDiversity Man page
bcDqz Man page
bcGenSimpson Man page
bcGenSimpsonD Man page
bcHqz Man page
bcHqzBeta Man page
bcHurlbert Man page
bcHurlbertD Man page
bcPhyloBetaEntropy Man page
bcPhyloDiversity Man page
bcPhyloEntropy Man page
bcRao Man page
bcRichness Man page
bcShannon Man page
bcShannonBeta Man page
bcSimpson Man page
bcSimpsonBeta Man page
bcTsallis Man page
bcTsallisBeta Man page
BetaDiversity Man page
BetaEntropy Man page
CEnvelope Man page
ChaoPD Man page
CheckentropartArguments Man page
CommunityProfile Man page
Coverage Man page
Diversity Man page
Diversity.AbdVector Man page
Diversity.integer Man page
Diversity.numeric Man page
Diversity.ProbaVector Man page
DivEst Man page
DivPart Man page
DivProfile Man page
Dqz Man page
Dqz.AbdVector Man page
Dqz.integer Man page
Dqz.numeric Man page
Dqz.ProbaVector Man page
EightSpAbundance Man page
EightSpTree Man page
Enq Man page
entropart Man page
entropart-package Man page
EntropyCI Man page
expq Man page
expq.CommunityProfile Man page
GammaDiversity Man page
GammaEntropy Man page
GenSimpson Man page
GenSimpson.AbdVector Man page
GenSimpsonD Man page
GenSimpsonD.AbdVector Man page
GenSimpsonD.integer Man page
GenSimpsonD.numeric Man page
GenSimpsonD.ProbaVector Man page
GenSimpson.integer Man page
GenSimpson.numeric Man page
GenSimpson.ProbaVector Man page
Hqz Man page
Hqz.AbdVector Man page
HqzBeta Man page
HqzBeta.AbdVector Man page
HqzBeta.integer Man page
HqzBeta.numeric Man page
HqzBeta.ProbaVector Man page
Hqz.integer Man page
Hqz.numeric Man page
Hqz.ProbaVector Man page
Hurlbert Man page
Hurlbert.AbdVector Man page
HurlbertD Man page
HurlbertD.AbdVector Man page
HurlbertD.integer Man page
HurlbertD.numeric Man page
HurlbertD.ProbaVector Man page
Hurlbert.integer Man page
Hurlbert.numeric Man page
Hurlbert.ProbaVector Man page
is.AbdVector Man page
is.CommunityProfile Man page
is.DivEst Man page
is.DivPart Man page
is.DivProfile Man page
is.MCdiversity Man page
is.MCentropy Man page
is.MetaCommunity Man page
is.PhyloDiversity Man page
is.PhyloEntropy Man page
is.PhyloValue Man page
is.PPtree Man page
is.ProbaVector Man page
is.SimTest Man page
is.SpeciesDistribution Man page
KLq Man page
lnq Man page
lnq.CommunityProfile Man page
MCdiversity Man page
MCentropy Man page
mergeandlabel Man page
MergeC Man page
MergeMC Man page
MetaCommunity Man page
Optimal.Similarity Man page
Paracou618.dist Man page
Paracou618.Functional Man page
Paracou618.MC Man page
Paracou618.Taxonomy Man page
PDFD Man page
PhyloApply Man page
PhyloBetaEntropy Man page
PhyloBetaEntropy.AbdVector Man page
PhyloBetaEntropy.integer Man page
PhyloBetaEntropy.numeric Man page
PhyloBetaEntropy.ProbaVector Man page
PhyloDiversity Man page
PhyloDiversity.AbdVector Man page
PhyloDiversity.integer Man page
PhyloDiversity.numeric Man page
PhyloDiversity.ProbaVector Man page
PhyloEntropy Man page
PhyloEntropy.AbdVector Man page
PhyloEntropy.integer Man page
PhyloEntropy.numeric Man page
PhyloEntropy.ProbaVector Man page
PhyloValue Man page
plot.CommunityProfile Man page
plot.DivEst Man page
plot.DivPart Man page
plot.DivProfile Man page
plot.MCdiversity Man page
plot.MCentropy Man page
plot.MetaCommunity Man page
plot.PhyloValue Man page
plot.PPtree Man page
plot.SimTest Man page
plot.SpeciesDistribution Man page
PPtree Man page
Preprocess.MC Man page
Preprocess.Tree Man page
ProbaVector Man page
Rao Man page
Rao.AbdVector Man page
Rao.integer Man page
Rao.numeric Man page
Rao.ProbaVector Man page
rCommunity Man page
Richness Man page
Richness.AbdVector Man page
Richness.integer Man page
Richness.numeric Man page
Richness.ProbaVector Man page
Shannon Man page
Shannon.AbdVector Man page
ShannonBeta Man page
ShannonBeta.AbdVector Man page
ShannonBeta.integer Man page
ShannonBeta.numeric Man page
ShannonBeta.ProbaVector Man page
Shannon.integer Man page
Shannon.numeric Man page
Shannon.ProbaVector Man page
ShuffleMC Man page
Simpson Man page
Simpson.AbdVector Man page
SimpsonBeta Man page
SimpsonBeta.AbdVector Man page
SimpsonBeta.integer Man page
SimpsonBeta.numeric Man page
SimpsonBeta.ProbaVector Man page
Simpson.integer Man page
Simpson.numeric Man page
Simpson.ProbaVector Man page
SimTest Man page
SpeciesDistribution Man page
summary.DivEst Man page
summary.DivPart Man page
summary.DivProfile Man page
summary.MCdiversity Man page
summary.MCentropy Man page
summary.MetaCommunity Man page
summary.PhyloDiversity Man page
summary.PhyloEntropy Man page
summary.PhyloValue Man page
summary.SimTest Man page
Tsallis Man page
Tsallis.AbdVector Man page
TsallisBeta Man page
TsallisBeta.AbdVector Man page
TsallisBeta.integer Man page
TsallisBeta.numeric Man page
TsallisBeta.ProbaVector Man page
Tsallis.integer Man page
Tsallis.numeric Man page
Tsallis.ProbaVector Man page

Files

entropart
entropart/inst
entropart/inst/CITATION
entropart/inst/doc
entropart/inst/doc/entropart.pdf
entropart/inst/doc/entropart.Rnw
entropart/inst/doc/entropart.R
entropart/inst/doc/Introduction.Rnw
entropart/inst/doc/Introduction.R
entropart/inst/doc/Introduction.pdf
entropart/tests
entropart/tests/testthat.R
entropart/tests/testthat
entropart/tests/testthat/testPhyloEntropy.R
entropart/tests/testthat/testOrder2.R
entropart/tests/testthat/testTsallis.R
entropart/NAMESPACE
entropart/NEWS
entropart/data
entropart/data/Paracou618.RData
entropart/data/datalist
entropart/R
entropart/R/Rao.R entropart/R/PhyloDiversity.R entropart/R/ShannonBeta.R entropart/R/MCdiversity.R entropart/R/Optimal.Similarity.R entropart/R/expq.R entropart/R/Hqz.R entropart/R/Shannon.R entropart/R/AlphaEntropy.R entropart/R/CheckentropartArguments.R entropart/R/AlphaDiversity.R entropart/R/DivProfile.R entropart/R/PhyloValue.R entropart/R/PPtree.R entropart/R/Dqz.R entropart/R/BetaEntropy.R entropart/R/DivEst.R entropart/R/Simpson.R entropart/R/PhyloEntropy.R entropart/R/DivPart.R entropart/R/MergeC.R entropart/R/HurlbertD.R entropart/R/SimpsonBeta.R entropart/R/TsallisBeta.R entropart/R/ShuffleMC.R entropart/R/BetaDiversity.R entropart/R/Coverage.R entropart/R/ArgumentOriginalName.R entropart/R/SimTest.R entropart/R/CommunityProfile.R entropart/R/HqzBeta.R entropart/R/PhyloBetaEntropy.R entropart/R/Preprocess.Tree.R entropart/R/KLq.R entropart/R/lnq.R entropart/R/rCommunity.R entropart/R/Preprocess.MC.R entropart/R/Tsallis.R entropart/R/MetaCommunity.R entropart/R/MCentropy.R entropart/R/mergeandlabel.R entropart/R/Enq.R entropart/R/CEnvelope.R entropart/R/AbdFreqCount.R entropart/R/Hurlbert.R entropart/R/EntropyCI.R entropart/R/GenSimpsonD.R entropart/R/Richness.R entropart/R/GammaDiversity.R entropart/R/GammaEntropy.R entropart/R/ChaoPD.R entropart/R/SpeciesDistribution.R entropart/R/GenSimpson.R entropart/R/MergeMC.R entropart/R/AllenH.R entropart/R/PDFD.R entropart/R/Diversity.R entropart/R/PhyloApply.R
entropart/vignettes
entropart/vignettes/Tree.pdf
entropart/vignettes/entropart.Rnw
entropart/vignettes/Introduction.Rnw
entropart/vignettes/entropart.bib
entropart/MD5
entropart/build
entropart/build/vignette.rds
entropart/DESCRIPTION
entropart/man
entropart/man/Hurlbert.Rd entropart/man/DivPart.Rd entropart/man/Rao.Rd entropart/man/MergeMC.Rd entropart/man/Simpson.Rd entropart/man/SimpsonBeta.Rd entropart/man/SpeciesDistribution.Rd entropart/man/KLq.Rd entropart/man/BetaDiversity.Rd entropart/man/BetaEntropy.Rd entropart/man/CommunityProfile.Rd entropart/man/EightSpAbundance.Rd entropart/man/EntropyCI.Rd entropart/man/Hqz.Rd entropart/man/Tsallis.Rd entropart/man/PPtree.Rd entropart/man/Preprocess.Tree.Rd entropart/man/Dqz.Rd entropart/man/PDFD.Rd entropart/man/DivProfile.Rd entropart/man/expq.Rd entropart/man/AbdFreqCount.Rd entropart/man/CheckentropartArguments.Rd entropart/man/ArgumentOriginalName.Rd entropart/man/PhyloDiversity.Rd entropart/man/Richness.Rd entropart/man/GammaDiversity.Rd entropart/man/Preprocess.MC.Rd entropart/man/Diversity.Rd entropart/man/mergeandlabel.Rd entropart/man/Optimal.Similarity.Rd entropart/man/GenSimpson.Rd entropart/man/TsallisBeta.Rd entropart/man/DivEst.Rd entropart/man/ShannonBeta.Rd entropart/man/HqzBeta.Rd entropart/man/PhyloBetaEntropy.Rd entropart/man/Paracou618.Taxonomy.Rd entropart/man/Paracou618.dist.Rd entropart/man/MetaCommunity.Rd entropart/man/PhyloValue.Rd entropart/man/MCdiversity.Rd entropart/man/PhyloApply.Rd entropart/man/ChaoPD.Rd entropart/man/entropart-package.Rd entropart/man/AllenH.Rd entropart/man/EightSpTree.Rd entropart/man/Enq.Rd entropart/man/Coverage.Rd entropart/man/GammaEntropy.Rd entropart/man/AlphaEntropy.Rd entropart/man/Paracou618.Functional.Rd entropart/man/SimTest.Rd entropart/man/Shannon.Rd entropart/man/MCentropy.Rd entropart/man/PhyloEntropy.Rd entropart/man/lnq.Rd entropart/man/rCommunity.Rd entropart/man/Paracou618.MC.Rd entropart/man/AlphaDiversity.Rd

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