entropart: Entropy Partitioning to Measure Diversity

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Measurement and partitioning of diversity, based on Tsallis entropy.

Author
Eric Marcon, Bruno Herault
Date of publication
2016-02-17 22:03:19
Maintainer
Eric Marcon <Eric.Marcon@ecofog.gf>
License
GNU General Public License
Version
1.4-5

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
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/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/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/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