Package: divent 0.5-4.9002

divent: 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>. 'divent' provides functions to estimate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity.

Authors:Eric Marcon [aut, cre], Florence Puech [aut]

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manual.pdf |manual.html✨
card.svg |card.png
divent/json (API)
NEWS

# Install 'divent' in R:
install.packages('divent', repos = c('https://ericmarcon.r-universe.dev', 'https://cloud.r-project.org'))

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

Pkgdown/docs site:https://ericmarcon.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

biodiversitydiversityentropy-partitioningestimatormeasurespeciescpp

6.16 score 2 stars 3 packages 1 scripts 442 downloads 60 exports 80 dependencies

Last updated from:3c17e624c0. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK219
linux-devel-x86_64OK200
source / vignettesOK296
linux-release-arm64OK191
linux-release-x86_64OK191
macos-release-arm64OK165
macos-release-x86_64OK306
macos-oldrel-arm64OK162
macos-oldrel-x86_64OK320
windows-develOK169
windows-releaseOK162
windows-oldrelOK192
wasm-releaseOK143

Exports:abd_freq_countabd_speciesabd_sumabundancesaccum_div_phyloaccum_ent_phyloaccum_hillaccum_mixingaccum_sp_hillaccum_sp_tsallisaccum_tsallisalphahullas_abundancesas_phylo_diventas_probabilitiesas_species_distributionautoplotcheck_divent_argscoveragecoverage_to_sizediv_gen_simpsondiv_hilldiv_hurlbertdiv_partdiv_pddiv_phylodiv_richnessdiv_similaritye_n_qent_allenent_gen_simpsonent_hurlbertent_phyloent_raoent_shannonent_similarityent_simpsonent_sp_simpsonent_sp_simpsonEnvelopeent_tsallisexp_qfit_racfun_ordinarinessfun_similarityis_abundancesis_phylo_diventis_probabilitiesis_species_distributionln_qmetacommunityplot_mapprob_speciesprobabilitiesprofile_hillprofile_phyloprofile_similarityrcommunityrlseriesrspcommunityspecies_distribution

Dependencies:abindalphahullapecliclustercodetoolscpp11cubaturedbmssdeldirdigestdoFuturedplyrEntropyEstimationfarverforeachfuturefuture.applygenericsggplot2globalsgluegoftestgtableigraphinterpisobanditeratorslabelinglatticelifecyclelistenvmagrittrMASSMatrixmgcvnlmeparallellypermutepillarpkgconfigplyrpolyclipprogressrpurrrR.methodsS3R.ooR.utilsR6rbibutilsRColorBrewerRcppRcppEigenRcppParallelRdpackreshape2rlangS7scalessgeostatspspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilssplancsstringistringrtensortibbletidyrtidyselectutf8vctrsveganviridisLitewithr

divent

Rendered fromdivent.Rmdusingknitr::rmarkdownon Jun 08 2026.

Last update: 2026-03-04
Started: 2022-11-25

Readme and manuals

Help Manual

Help pageTopics
diventdivent-package divent
Abundance Frequency Count of a Communityabd_freq_count
Abundances of Communitiesabd_species abd_sum prob_species
Phylogenetic Diversity Accumulation of a Communityaccum_div_phylo accum_div_phylo.abundances accum_div_phylo.numeric accum_ent_phylo accum_ent_phylo.abundances accum_ent_phylo.numeric
Diversity Accumulation of a Communityaccum_hill accum_hill.abundances accum_hill.numeric accum_tsallis accum_tsallis.abundances accum_tsallis.numeric
Spatial Accumulation of Diversityaccum_sp accum_sp_diversity accum_sp_entropy accum_sp_mixing autoplot.accum_sp plot.accum_sp plot_map
Spatial Diversity Accumulation of a Communityaccum_mixing accum_sp_hill accum_sp_tsallis
alpha-shape calculationalphahull
Plot Accumulation Objectsautoplot.accumulation
Plot Profile Objectsautoplot.profile
ggplot method to plot wmppp objectsautoplot.wmppp
Sample Coverage of a Communitycoverage coverage.abundances coverage.numeric coverage_to_size coverage_to_size.abundances coverage_to_size.numeric
Generalized Simpson's Diversitydiv_gen_simpson div_gen_simpson.numeric div_gen_simpson.species_distribution
Hill number of a Communitydiv_hill div_hill.numeric div_hill.species_distribution
Hurlbert Diversity of a Communitydiv_hurlbert div_hurlbert.numeric div_hurlbert.species_distribution
Diversity partitiondiv_part
Faith's Phylogenetic Diversity of a Communitydiv_pd div_pd.numeric div_pd.species_distribution
Phylogenetic Diversity of a Communitydiv_phylo div_phylo.numeric div_phylo.species_distribution
Number of Species of a Communitydiv_richness div_richness.numeric div_richness.species_distribution
Similarity-Based Diversity of a Communitydiv_similarity div_similarity.numeric div_similarity.species_distribution
Grassberger's expectation of n^qe_n_q
Allen et al.'s Phylogenetic Entropy of a Communityent_allen ent_allen.numeric ent_allen.species_distribution
Generalized Simpson's Entropyent_gen_simpson ent_gen_simpson.numeric ent_gen_simpson.species_distribution
Hurlbert Entropy of a Communityent_hurlbert ent_hurlbert.numeric ent_hurlbert.species_distribution
Phylogenetic Entropy of a Communityent_phylo ent_phylo.numeric ent_phylo.species_distribution
Rao's Quadratic Entropy of a Communityent_rao ent_rao.numeric ent_rao.species_distribution
Shannon's Entropy of a Communityent_shannon ent_shannon.numeric ent_shannon.species_distribution
Similarity-Based Entropy of a Communityent_similarity ent_similarity.numeric ent_similarity.species_distribution
Simpson's Entropy of a Communityent_simpson ent_simpson.numeric ent_simpson.species_distribution
Spatially Explicit Simpson's Entropyent_sp_simpson ent_sp_simpsonEnvelope
Tsallis Entropy of a Communityent_tsallis ent_tsallis.numeric ent_tsallis.species_distribution
Deformed exponentialexp_q
Fit a distributionfit_rac fit_rac.numeric fit_rac.species_distribution
Functional ordinariness of a communityfun_ordinariness
Functional similarityfun_similarity
Deformed logarithmln_q
Aggregate communities into a metacommunitymetacommunity metacommunity.abundances metacommunity.matrix
Mock datamock_3sp mock_3sp_abd mock_3sp_dist mock_3sp_tree
Non-Species columnsnon_species_columns
Paracou plot 6paracou_6 paracou_6_abd paracou_6_wmppp
Functional distances between Paracou plot 6 speciesparacou_6_fundist
Taxonomy of Paracou plot 6 speciesparacou_6_taxo
Class phylo_diventas_phylo_divent is_phylo_divent phylo_divent
Plot phylo_divent Objectsplot.phylo_divent
Plot Profile Objectsautoplot.species_distribution plot.species_distribution
Probabilities of Speciesprobabilities probabilities.abundances probabilities.numeric
Diversity Profile of a Communityprofile_hill profile_hill.numeric profile_hill.species_distribution
Phylogenetic Diversity Profile of a Communityprofile_phylo profile_phylo.numeric profile_phylo.species_distribution
Similarity-Based Diversity Profile of a Communityprofile_similarity profile_similarity.numeric profile_similarity.species_distribution
Random communitiesrcommunity rspcommunity
Log-Series Distributionrlseries
Species Distributionsabundances as.double.species_distribution as.matrix.species_distribution as.numeric.species_distribution as_abundances as_abundances.character as_abundances.data.frame as_abundances.factor as_abundances.matrix as_abundances.numeric as_abundances.wmppp as_probabilities as_probabilities.character as_probabilities.data.frame as_probabilities.factor as_probabilities.matrix as_probabilities.numeric as_probabilities.wmppp as_species_distribution as_species_distribution.character as_species_distribution.data.frame as_species_distribution.factor as_species_distribution.matrix as_species_distribution.numeric as_species_distribution.wmppp is_abundances is_probabilities is_species_distribution species_distribution