Function reference • entropart

Package summary
`entropart-package` `entropart`	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

Reference

Package summary

Datasets

Generate data

Community diversity

Rank Abundance Curves

Metacommunity Diversity

Metacommunity utilities

Classes

Arithmetics

Utilities