entropart: Entropy Partitioning to Measure Diversity
Version 1.4-7

Measurement and partitioning of diversity, based on Tsallis entropy.

Browse man pages Browse package API and functions Browse package files

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("entropart")

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

Files

inst
inst/CITATION
inst/doc
inst/doc/entropart.pdf
inst/doc/entropart.Rnw
inst/doc/entropart.R
inst/doc/Introduction.Rnw
inst/doc/Introduction.R
inst/doc/Introduction.pdf
tests
tests/testthat.R
tests/testthat
tests/testthat/testPhyloEntropy.R
tests/testthat/testOrder2.R
tests/testthat/testTsallis.R
NAMESPACE
NEWS
data
data/Paracou618.RData
data/datalist
R
R/Rao.R
R/PhyloDiversity.R
R/ShannonBeta.R
R/MCdiversity.R
R/Optimal.Similarity.R
R/expq.R
R/Hqz.R
R/Shannon.R
R/AlphaEntropy.R
R/CheckentropartArguments.R
R/AlphaDiversity.R
R/DivProfile.R
R/PhyloValue.R
R/PPtree.R
R/Dqz.R
R/BetaEntropy.R
R/DivEst.R
R/Simpson.R
R/PhyloEntropy.R
R/DivPart.R
R/MergeC.R
R/HurlbertD.R
R/SimpsonBeta.R
R/TsallisBeta.R
R/ShuffleMC.R
R/BetaDiversity.R
R/Coverage.R
R/ArgumentOriginalName.R
R/SimTest.R
R/CommunityProfile.R
R/HqzBeta.R
R/PhyloBetaEntropy.R
R/Preprocess.Tree.R
R/KLq.R
R/lnq.R
R/rCommunity.R
R/Preprocess.MC.R
R/Tsallis.R
R/MetaCommunity.R
R/MCentropy.R
R/mergeandlabel.R
R/Enq.R
R/CEnvelope.R
R/AbdFreqCount.R
R/Hurlbert.R
R/EntropyCI.R
R/GenSimpsonD.R
R/Richness.R
R/GammaDiversity.R
R/GammaEntropy.R
R/ChaoPD.R
R/SpeciesDistribution.R
R/GenSimpson.R
R/MergeMC.R
R/AllenH.R
R/PDFD.R
R/Diversity.R
R/PhyloApply.R
vignettes
vignettes/Tree.pdf
vignettes/entropart.Rnw
vignettes/Introduction.Rnw
vignettes/entropart.bib
MD5
build
build/vignette.rds
DESCRIPTION
man
man/Hurlbert.Rd
man/DivPart.Rd
man/Rao.Rd
man/MergeMC.Rd
man/Simpson.Rd
man/SimpsonBeta.Rd
man/SpeciesDistribution.Rd
man/KLq.Rd
man/BetaDiversity.Rd
man/BetaEntropy.Rd
man/CommunityProfile.Rd
man/EightSpAbundance.Rd
man/EntropyCI.Rd
man/Hqz.Rd
man/Tsallis.Rd
man/PPtree.Rd
man/Preprocess.Tree.Rd
man/Dqz.Rd
man/PDFD.Rd
man/DivProfile.Rd
man/expq.Rd
man/AbdFreqCount.Rd
man/CheckentropartArguments.Rd
man/ArgumentOriginalName.Rd
man/PhyloDiversity.Rd
man/Richness.Rd
man/GammaDiversity.Rd
man/Preprocess.MC.Rd
man/Diversity.Rd
man/mergeandlabel.Rd
man/Optimal.Similarity.Rd
man/GenSimpson.Rd
man/TsallisBeta.Rd
man/DivEst.Rd
man/ShannonBeta.Rd
man/HqzBeta.Rd
man/PhyloBetaEntropy.Rd
man/Paracou618.Taxonomy.Rd
man/Paracou618.dist.Rd
man/MetaCommunity.Rd
man/PhyloValue.Rd
man/MCdiversity.Rd
man/PhyloApply.Rd
man/ChaoPD.Rd
man/entropart-package.Rd
man/AllenH.Rd
man/EightSpTree.Rd
man/Enq.Rd
man/Coverage.Rd
man/GammaEntropy.Rd
man/AlphaEntropy.Rd
man/Paracou618.Functional.Rd
man/SimTest.Rd
man/Shannon.Rd
man/MCentropy.Rd
man/PhyloEntropy.Rd
man/lnq.Rd
man/rCommunity.Rd
man/Paracou618.MC.Rd
man/AlphaDiversity.Rd
entropart documentation built on May 19, 2017, 8:56 a.m.