entropart: Entropy Partitioning to Measure Diversity

Measurement and partitioning of diversity, based on Tsallis entropy.

AuthorEric Marcon, Bruno Herault
Date of publication2016-12-09 08:58:50
MaintainerEric Marcon <Eric.Marcon@ecofog.gf>
LicenseGNU General Public License
Version1.4-6

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

Files in this package

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/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/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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