Package: entropart 1.6-13.9001

entropart: Entropy Partitioning to Measure Diversity

Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>. 'entropart' provides functions to calculate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity. Estimation-bias corrections are available.

Authors:Eric Marcon [aut, cre], Bruno Herault [aut]

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NEWS

# Install 'entropart' in R:

install.packages('entropart', repos = c('https://ericmarcon.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ericmarcon/entropart/issues

Datasets:

EightSpAbundance - Abundances of 8 species to run examples.
EightSpTree - Functional tree with 8 species.
Paracou618.Functional - Functional tree of species of Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.
Paracou618.MC - Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.
Paracou618.Taxonomy - Taxonomy (Family - Genus - Species) of Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.
Paracou618.dist - Functional distances between pairs of species of Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.

On CRAN:

biodiversity diversity entropy-partitioning estimator measure species

7.61 score 8 stars 1 packages 114 scripts 831 downloads 17 mentions 102 exports 76 dependencies

Last updated 2 months agofrom:104c5ebd90. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 25 2024
R-4.5-win	OK	Oct 25 2024
R-4.5-linux	OK	Oct 25 2024
R-4.4-win	OK	Oct 25 2024
R-4.4-mac	OK	Oct 25 2024
R-4.3-win	OK	Oct 25 2024
R-4.3-mac	OK	Oct 25 2024

Exports:AbdFreqCount AllenH AlphaDiversity AlphaEntropy as.AbdVector as.AccumCurve as.CommunityProfile as.ProbaVector as.SimTest as.SpeciesDistribution autoplot bcDiversity bcDqz bcGenSimpson bcGenSimpsonD bcHqz bcHqzBeta bcHurlbert bcHurlbertD bcPhyloBetaEntropy bcPhyloDiversity bcPhyloEntropy bcRao bcRichness bcShannon bcShannonBeta bcSimpson bcSimpsonBeta bcTsallis bcTsallisBeta BetaDiversity BetaEntropy CEnvelope ChaoPD CommunityProfile Coverage Coverage2Size DivAC Diversity DivEst DivPart DivProfile Dqz Enq EntAC EntropyCI expq expq.CommunityProfile GammaDiversity GammaEntropy GenSimpson GenSimpsonD Hqz HqzBeta Hurlbert HurlbertD is.AbdVector is.AccumCurve is.CommunityProfile is.DivEst is.DivPart is.DivProfile is.MCdiversity is.MCentropy is.MetaCommunity is.PhyloDiversity is.PhyloEntropy is.PhyloValue is.PPtree is.ProbaVector is.SimTest is.SpeciesDistribution KLq lnq lnq.CommunityProfile mergeandlabel MergeC MergeMC MetaCommunity Optimal.Similarity PDFD PhyloApply PhyloBetaEntropy PhyloDiversity PhyloEntropy plot Preprocess.MC Preprocess.Tree RACbstick RACgeom RAClnorm RAClseries Rao rCommunity Richness Shannon ShannonBeta ShuffleMC Simpson SimpsonBeta Tsallis TsallisBeta

Dependencies:abind ape backports boot broom car carData cli cluster colorspace corrplot cowplot cpp11 Deriv digest doBy dplyr EntropyEstimation fansi farver Formula generics ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable isoband labeling lattice lifecycle lme4 magrittr MASS Matrix MatrixModels mgcv microbenchmark minqa modelr munsell nlme nloptr nnet numDeriv pbkrtest permute pillar pkgconfig plyr polynom purrr quantreg R6 RColorBrewer Rcpp RcppEigen reshape2 rlang rstatix scales SparseM stringi stringr survival tibble tidyr tidyselect utf8 vctrs vegan viridisLite withr

entropart

Rendered fromentropart.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2023-07-14
Started: 2018-11-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Entropy Partitioning to Measure Diversity	entropart-package entropart
Abundance Frequency Count of a Community	AbdFreqCount
Diversity accumulation.	as.AccumCurve autoplot.AccumCurve DivAC EntAC is.AccumCurve plot.AccumCurve
Phylogenetic Entropy of a Community	AllenH
Reduced-bias alpha diversity of a metacommunity	AlphaDiversity
Reduced-bias alpha entropy of a metacommunity	AlphaEntropy
Reduced-bias beta diversity of a metacommunity	BetaDiversity
Reduced-bias beta entropy of a metacommunity	BetaEntropy
Phylogenetic Diversity of a Community	ChaoPD
Diversity or Entropy Profile of a community	as.CommunityProfile autoplot.CommunityProfile CEnvelope CommunityProfile is.CommunityProfile plot.CommunityProfile
Sample coverage of a community	Coverage Coverage2Size
Hill number of a community	bcDiversity Diversity Diversity.AbdVector Diversity.integer Diversity.numeric Diversity.ProbaVector
Diversity Estimation of a metacommunity	autoplot.DivEst DivEst is.DivEst plot.DivEst summary.DivEst
Diversity Partition of a metacommunity	autoplot.DivPart DivPart is.DivPart plot.DivPart summary.DivPart
Diversity Profile of a metacommunity	autoplot.DivProfile DivProfile is.DivProfile plot.DivProfile summary.DivProfile
Similarity-based diversity of a community	bcDqz Dqz Dqz.AbdVector Dqz.integer Dqz.numeric Dqz.ProbaVector
Abundances of 8 species to run examples.	EightSpAbundance
Functional tree with 8 species.	EightSpTree
Grassberger's expectation of n^q	Enq
Entropy of Monte-Carlo simulated communities	EntropyCI
Exponential of order q	expq expq.CommunityProfile
Reduced-bias gamma diversity of a metacommunity	GammaDiversity
Reduced-bias gamma entropy of a metacommunity	GammaEntropy
Generalized Simpson's Entropy and Diversity	bcGenSimpson bcGenSimpsonD GenSimpson GenSimpson.AbdVector GenSimpson.integer GenSimpson.numeric GenSimpson.ProbaVector GenSimpsonD GenSimpsonD.AbdVector GenSimpsonD.integer GenSimpsonD.numeric GenSimpsonD.ProbaVector
Similarity-based entropy of a community	bcHqz Hqz Hqz.AbdVector Hqz.integer Hqz.numeric Hqz.ProbaVector
Similarity-based beta entropy of a community	bcHqzBeta HqzBeta HqzBeta.AbdVector HqzBeta.integer HqzBeta.numeric HqzBeta.ProbaVector
Hurlbert's Index and Explicit Diversity	bcHurlbert bcHurlbertD Hurlbert Hurlbert.AbdVector Hurlbert.integer Hurlbert.numeric Hurlbert.ProbaVector HurlbertD HurlbertD.AbdVector HurlbertD.integer HurlbertD.numeric HurlbertD.ProbaVector
Generalized Kullback-Leibler divergence	KLq
Logarithm of order q	lnq lnq.CommunityProfile
Manipulation of meta-communities	MergeC MergeMC ShuffleMC
Meta-Community diversity class.	autoplot.MCdiversity is.MCdiversity MCdiversity plot.MCdiversity summary.MCdiversity
Meta-Community entropy class.	autoplot.MCentropy is.MCentropy MCentropy plot.MCentropy summary.MCentropy
Metacommunity class	is.MetaCommunity MetaCommunity plot.MetaCommunity summary.MetaCommunity
Optimal scale parameter to transform a distance matrix into a similarity matrix	Optimal.Similarity
Functional distances between pairs of species of Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.	Paracou618.dist
Functional tree of species of Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.	Paracou618.Functional
Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.	Paracou618.MC
Taxonomy (Family - Genus - Species) of Paracou field station plots 6 and 18, two 1-ha plots inventoried by the Bridge project.	Paracou618.Taxonomy
Phylogenetic Diversity / Functional Diversity of a Community	PDFD
Apply a Function over a Phylogenetic Tree	PhyloApply
Phylogenetic Beta Entropy of a community	bcPhyloBetaEntropy PhyloBetaEntropy PhyloBetaEntropy.AbdVector PhyloBetaEntropy.integer PhyloBetaEntropy.numeric PhyloBetaEntropy.ProbaVector
Phylogenetic Diversity of a Community	bcPhyloDiversity is.PhyloDiversity PhyloDiversity PhyloDiversity.AbdVector PhyloDiversity.integer PhyloDiversity.numeric PhyloDiversity.ProbaVector summary.PhyloDiversity
Phylogenetic Entropy of a community	bcPhyloEntropy is.PhyloEntropy PhyloEntropy PhyloEntropy.AbdVector PhyloEntropy.integer PhyloEntropy.numeric PhyloEntropy.ProbaVector summary.PhyloEntropy
Phylogenetic entropy or diversity.	autoplot.PhyloValue is.PhyloValue PhyloValue plot.PhyloValue summary.PhyloValue
Preprocessed Trees.	is.PPtree plot.PPtree PPtree
Fit Distributions to Well-Known Rank Abundance Curves.	RACbstick RACgeom RAClnorm RAClseries
Rao Quadratic Entropy of a Community	bcRao Rao Rao.AbdVector Rao.integer Rao.numeric Rao.ProbaVector
Random Communities	rCommunity
Number of species of a community	bcRichness Richness Richness.AbdVector Richness.integer Richness.numeric Richness.ProbaVector
Shannon entropy of a community	bcShannon Shannon Shannon.AbdVector Shannon.integer Shannon.numeric Shannon.ProbaVector
Shannon beta entropy of a community	bcShannonBeta ShannonBeta ShannonBeta.AbdVector ShannonBeta.integer ShannonBeta.numeric ShannonBeta.ProbaVector
Simpson entropy of a community	bcSimpson Simpson Simpson.AbdVector Simpson.integer Simpson.numeric Simpson.ProbaVector
Simpson beta entropy of a community	bcSimpsonBeta SimpsonBeta SimpsonBeta.AbdVector SimpsonBeta.integer SimpsonBeta.numeric SimpsonBeta.ProbaVector
SimTest class	as.SimTest autoplot.SimTest is.SimTest plot.SimTest SimTest summary.SimTest
Species Distributions	AbdVector as.AbdVector as.AbdVector.data.frame as.AbdVector.integer as.AbdVector.numeric as.ProbaVector as.ProbaVector.data.frame as.ProbaVector.integer as.ProbaVector.numeric as.SpeciesDistribution as.SpeciesDistribution.data.frame as.SpeciesDistribution.integer as.SpeciesDistribution.numeric autoplot.SpeciesDistribution is.AbdVector is.ProbaVector is.SpeciesDistribution plot.SpeciesDistribution ProbaVector SpeciesDistribution
Tsallis (HCDT) Entropy of a community	bcTsallis Tsallis Tsallis.AbdVector Tsallis.integer Tsallis.numeric Tsallis.ProbaVector
Tsallis beta entropy of a community	bcTsallisBeta TsallisBeta TsallisBeta.AbdVector TsallisBeta.integer TsallisBeta.numeric TsallisBeta.ProbaVector