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