Package summary

entropart-package

Entropy Partitioning to Measure Diversity

Datasets

Paracou618

Functional tree of species of Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.

Paracou618

Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.

Paracou618

Taxonomy (Family - Genus - Species) of Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.

Paracou618

Functional distances between pairs of species of Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.

Paracou618

Abundances of 8 species to run examples.

Paracou618

Functional tree with 8 species.

Generate data

rCommunity()

Random Communities

Community diversity

AllenH()

Phylogenetic Entropy of a Community

ChaoPD()

Phylogenetic Diversity of a Community

CommunityProfile() as.CommunityProfile() is.CommunityProfile() plot(<CommunityProfile>) autoplot(<CommunityProfile>) CEnvelope()

Diversity or Entropy Profile of a community

Coverage() Coverage2Size()

Sample coverage of a community

as.AccumCurve() is.AccumCurve() EntAC() DivAC() plot(<AccumCurve>) autoplot(<AccumCurve>)

Diversity accumulation.

Diversity() bcDiversity()

Hill number of a community

Dqz() bcDqz()

Similarity-based diversity of a community

GenSimpson() bcGenSimpson() GenSimpsonD() bcGenSimpsonD()

Generalized Simpson's Entropy and Diversity

Hqz() bcHqz()

Similarity-based entropy of a community

HqzBeta() bcHqzBeta()

Similarity-based beta entropy of a community

Hurlbert() bcHurlbert() HurlbertD() bcHurlbertD()

Hurlbert's Index and Explicit Diversity

PDFD()

Phylogenetic Diversity / Functional Diversity of a Community

PhyloBetaEntropy() bcPhyloBetaEntropy()

Phylogenetic Beta Entropy of a community

PhyloDiversity() bcPhyloDiversity() is.PhyloDiversity() summary(<PhyloDiversity>)

Phylogenetic Diversity of a Community

PhyloEntropy() bcPhyloEntropy() is.PhyloEntropy() summary(<PhyloEntropy>)

Phylogenetic Entropy of a community

Rao() bcRao()

Rao Quadratic Entropy of a Community

Richness() bcRichness()

Number of species of a community

Shannon() bcShannon()

Shannon entropy of a community

ShannonBeta() bcShannonBeta()

Shannon beta entropy of a community

Simpson() bcSimpson()

Simpson entropy of a community

SimpsonBeta() bcSimpsonBeta()

Simpson beta entropy of a community

Tsallis() bcTsallis()

Tsallis (HCDT) Entropy of a community

TsallisBeta() bcTsallisBeta()

Tsallis beta entropy of a community

Rank Abundance Curves

RAClnorm() RACgeom() RAClseries() RACbstick()

Fit Distributions to Well-Known Rank Abundance Curves.

Metacommunity Diversity

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

DivEst() is.DivEst() plot(<DivEst>) autoplot(<DivEst>) summary(<DivEst>)

Diversity Estimation of a metacommunity

DivPart() is.DivPart() plot(<DivPart>) autoplot(<DivPart>) summary(<DivPart>)

Diversity Partition of a metacommunity

DivProfile() is.DivProfile() plot(<DivProfile>) autoplot(<DivProfile>) summary(<DivProfile>)

Diversity Profile of a metacommunity

GammaDiversity()

Reduced-bias gamma diversity of a metacommunity

GammaEntropy()

Reduced-bias gamma entropy of a metacommunity

Metacommunity utilities

MergeMC() MergeC() ShuffleMC()

Manipulation of meta-communities

MetaCommunity() is.MetaCommunity() summary(<MetaCommunity>) plot(<MetaCommunity>)

Metacommunity class

Classes

as.AccumCurve() is.AccumCurve() EntAC() DivAC() plot(<AccumCurve>) autoplot(<AccumCurve>)

Diversity accumulation.

CommunityProfile() as.CommunityProfile() is.CommunityProfile() plot(<CommunityProfile>) autoplot(<CommunityProfile>) CEnvelope()

Diversity or Entropy Profile of a community

DivEst() is.DivEst() plot(<DivEst>) autoplot(<DivEst>) summary(<DivEst>)

Diversity Estimation of a metacommunity

DivPart() is.DivPart() plot(<DivPart>) autoplot(<DivPart>) summary(<DivPart>)

Diversity Partition of a metacommunity

DivProfile() is.DivProfile() plot(<DivProfile>) autoplot(<DivProfile>) summary(<DivProfile>)

Diversity Profile of a metacommunity

is.MCdiversity() plot(<MCdiversity>) autoplot(<MCdiversity>) summary(<MCdiversity>)

Meta-Community diversity class.

is.MCentropy() plot(<MCentropy>) autoplot(<MCentropy>) summary(<MCentropy>)

Meta-Community entropy class.

is.PhyloValue() autoplot(<PhyloValue>) plot(<PhyloValue>) summary(<PhyloValue>)

Phylogenetic entropy or diversity.

is.PPtree() plot(<PPtree>)

Preprocessed Trees.

as.SimTest() is.SimTest() autoplot(<SimTest>) plot(<SimTest>) summary(<SimTest>)

SimTest class

as.SpeciesDistribution() autoplot(<SpeciesDistribution>) plot(<SpeciesDistribution>) is.SpeciesDistribution() as.ProbaVector() is.ProbaVector() as.AbdVector() is.AbdVector()

Species Distributions.

Arithmetics

Enq()

Grassberger's expectation of n^q

KLq()

Generalized Kullback-Leibler divergence

expq() expq.CommunityProfile()

Exponential of order q

lnq() lnq.CommunityProfile()

Logarithm of order q

Utilities

AbdFreqCount()

Abundance Frequency Count of a Community

ArgumentOriginalName()

Finds the original value (name of expression) of the argument of a function even in the case of embedded calls.

CheckentropartArguments()

Checks the arguments of a function of the package entropart

EntropyCI()

Entropy of Monte-Carlo simulated communities

mergeandlabel()

Merge community data

Optimal.Similarity()

Optimal scale parameter to transform a distance matrix into a similarity matrix

PhyloApply()

Apply a Function over a Phylogenetic Tree

Preprocess.MC()

Preprocessing of metacommunity data

Preprocess.Tree()

Preprocessing of a phylogenetic tree