Package: divent 0.4-99.9013
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:
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divent.pdf |divent.html✨
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
- mock_3sp_abd - Mock data
- mock_3sp_dist - Mock data
- mock_3sp_tree - Mock data
- paracou_6_abd - Paracou plot 6
- paracou_6_fundist - Functional distances between Paracou plot 6 species
- paracou_6_taxo - Taxonomy of Paracou plot 6 species
- paracou_6_wmppp - Paracou plot 6
Last updated 1 days agofrom:1db262ffe7. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 20 2024 |
| R-4.5-win-x86_64 | OK | Nov 20 2024 |
| R-4.5-linux-x86_64 | OK | Nov 20 2024 |
| R-4.4-win-x86_64 | OK | Nov 20 2024 |
| R-4.4-mac-x86_64 | OK | Nov 20 2024 |
| R-4.4-mac-aarch64 | OK | Nov 20 2024 |
| R-4.3-win-x86_64 | OK | Nov 20 2024 |
| R-4.3-mac-x86_64 | OK | Nov 20 2024 |
| R-4.3-mac-aarch64 | OK | Nov 20 2024 |
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_hilldiv_hurlbertdiv_partdiv_phylodiv_richnessdiv_similaritye_n_qent_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:abindalphahullapecliclustercolorspacecpp11cubaturedbmssdeldirdigestdplyrEntropyEstimationfansifarvergenericsggplot2gluegoftestgtableigraphinterpisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepermutepillarpkgconfigplyrpolyclippurrrR.methodsS3R.ooR.utilsR6rbibutilsRColorBrewerRcppRcppEigenRcppParallelRdpackreshape2rlangscalessgeostatspspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilssplancsstringistringrtensortibbletidyrtidyselectutf8vctrsveganviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| divent | divent-package divent |
| Abundance Frequency Count of a Community | abd_freq_count |
| Abundances of Communities | abd_species abd_sum prob_species |
| Phylogenetic Diversity Accumulation of a Community | accum_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 Community | accum_hill accum_hill.abundances accum_hill.numeric accum_tsallis accum_tsallis.abundances accum_tsallis.numeric |
| Spatial Accumulation of Diversity | accum_sp accum_sp_diversity accum_sp_entropy accum_sp_mixing autoplot.accum_sp plot.accum_sp plot_map |
| Spatial Diversity Accumulation of a Community | accum_mixing accum_sp_hill accum_sp_tsallis |
| alpha-shape calculation | alphahull |
| Plot Accumulation Objects | autoplot.accumulation |
| Plot Profile Objects | autoplot.profile |
| ggplot method to plot wmppp objects | autoplot.wmppp |
| Sample Coverage of a Community | coverage coverage.abundances coverage.numeric coverage_to_size coverage_to_size.abundances coverage_to_size.numeric |
| Hill number of a Community | div_hill div_hill.numeric div_hill.species_distribution |
| Hurlbert Diversity of a Community | div_hurlbert div_hurlbert.numeric div_hurlbert.species_distribution |
| Diversity partition | div_part |
| Phylogenetic Diversity of a Community | div_phylo div_phylo.numeric div_phylo.species_distribution |
| Number of Species of a Community | div_richness div_richness.numeric div_richness.species_distribution |
| Similarity-Based Diversity of a Community | div_similarity div_similarity.numeric div_similarity.species_distribution |
| Grassberger's expectation of n^q | e_n_q |
| Hurlbert Entropy of a Community | ent_hurlbert ent_hurlbert.numeric ent_hurlbert.species_distribution |
| Phylogenetic Entropy of a Community | ent_phylo ent_phylo.numeric ent_phylo.species_distribution |
| Rao's Quadratic Entropy of a Community | ent_rao ent_rao.numeric ent_rao.species_distribution |
| Shannon's Entropy of a Community | ent_shannon ent_shannon.numeric ent_shannon.species_distribution |
| Similarity-Based Entropy of a Community | ent_similarity ent_similarity.numeric ent_similarity.species_distribution |
| Simpson's Entropy of a Community | ent_simpson ent_simpson.numeric ent_simpson.species_distribution |
| Spatially Explicit Simpson's Entropy | ent_sp_simpson ent_sp_simpsonEnvelope |
| Tsallis Entropy of a Community | ent_tsallis ent_tsallis.numeric ent_tsallis.species_distribution |
| Deformed exponential | exp_q |
| Fit a distribution | fit_rac fit_rac.numeric fit_rac.species_distribution |
| Functional ordinariness of a community | fun_ordinariness |
| Functional similarity | fun_similarity |
| Deformed logarithm | ln_q |
| Aggregate communities into a metacommunity | metacommunity metacommunity.abundances metacommunity.matrix |
| Mock data | mock_3sp mock_3sp_abd mock_3sp_dist mock_3sp_tree |
| Paracou plot 6 | paracou_6 paracou_6_abd paracou_6_wmppp |
| Functional distances between Paracou plot 6 species | paracou_6_fundist |
| Taxonomy of Paracou plot 6 species | paracou_6_taxo |
| Class phylo_divent | as_phylo_divent is_phylo_divent phylo_divent |
| Plot phylo_divent Objects | plot.phylo_divent |
| Plot Profile Objects | autoplot.species_distribution plot.species_distribution |
| Probabilities of Species | probabilities probabilities.abundances probabilities.numeric |
| Diversity Profile of a Community | profile_hill profile_hill.numeric profile_hill.species_distribution |
| Phylogenetic Diversity Profile of a Community | profile_phylo profile_phylo.numeric profile_phylo.species_distribution |
| Similarity-Based Diversity Profile of a Community | profile_similarity profile_similarity.numeric profile_similarity.species_distribution |
| Random communities | rcommunity rspcommunity |
| Log-Series Distribution | rlseries |
| Species Distributions | abundances 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 |
