Package: entropart 1.6-13.9001
Eric Marcon
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:
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entropart.pdf |entropart.html✨
entropart/json (API)
NEWS
| # Install 'entropart' in R: |
| install.packages('entropart', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ericmarcon/entropart/issues
Pkgdown:https://ericmarcon.github.io
- 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.
biodiversitydiversityentropy-partitioningestimatormeasurespecies
Last updated 3 months agofrom:104c5ebd90. Checks:OK: 7. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 24 2024 |
| R-4.5-win | OK | Nov 24 2024 |
| R-4.5-linux | OK | Nov 24 2024 |
| R-4.4-win | OK | Nov 24 2024 |
| R-4.4-mac | OK | Nov 24 2024 |
| R-4.3-win | OK | Nov 24 2024 |
| R-4.3-mac | OK | Nov 24 2024 |
Exports:AbdFreqCountAllenHAlphaDiversityAlphaEntropyas.AbdVectoras.AccumCurveas.CommunityProfileas.ProbaVectoras.SimTestas.SpeciesDistributionautoplotbcDiversitybcDqzbcGenSimpsonbcGenSimpsonDbcHqzbcHqzBetabcHurlbertbcHurlbertDbcPhyloBetaEntropybcPhyloDiversitybcPhyloEntropybcRaobcRichnessbcShannonbcShannonBetabcSimpsonbcSimpsonBetabcTsallisbcTsallisBetaBetaDiversityBetaEntropyCEnvelopeChaoPDCommunityProfileCoverageCoverage2SizeDivACDiversityDivEstDivPartDivProfileDqzEnqEntACEntropyCIexpqexpq.CommunityProfileGammaDiversityGammaEntropyGenSimpsonGenSimpsonDHqzHqzBetaHurlbertHurlbertDis.AbdVectoris.AccumCurveis.CommunityProfileis.DivEstis.DivPartis.DivProfileis.MCdiversityis.MCentropyis.MetaCommunityis.PhyloDiversityis.PhyloEntropyis.PhyloValueis.PPtreeis.ProbaVectoris.SimTestis.SpeciesDistributionKLqlnqlnq.CommunityProfilemergeandlabelMergeCMergeMCMetaCommunityOptimal.SimilarityPDFDPhyloApplyPhyloBetaEntropyPhyloDiversityPhyloEntropyplotPreprocess.MCPreprocess.TreeRACbstickRACgeomRAClnormRAClseriesRaorCommunityRichnessShannonShannonBetaShuffleMCSimpsonSimpsonBetaTsallisTsallisBeta
Dependencies:abindapebackportsbootbroomcarcarDatacliclustercolorspacecorrplotcowplotcpp11DerivdigestdoBydplyrEntropyEstimationfansifarverFormulagenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtableisobandlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrnnetnumDerivpbkrtestpermutepillarpkgconfigplyrpolynompurrrquantregR6RColorBrewerRcppRcppEigenreshape2rlangrstatixscalesSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsveganviridisLitewithr
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 |
