{ "_id": "6a2723af24555f66ed5295df", "Package": "divent", "Type": "Package", "Title": "Entropy Partitioning to Measure Diversity", "Version": "0.5-4.9002", "Authors@R": "c(\nperson(\"Eric\", \"Marcon\", email = \"eric.marcon@agroparistech.fr\", role = c(\"aut\", \"cre\"), comment = c(ORCID=\"0000-0002-5249-321X\")),\nperson(\"Florence\", \"Puech\", email = \"florence.puech@universite-paris-saclay.fr\", role = \"aut\", comment = c(ORCID = \"0000-0002-5279-6878\"))\n)", "Description": "Measurement and partitioning of diversity, based on\nTsallis entropy, following Marcon and Herault (2015)\n. 'divent' provides functions to\nestimate alpha, beta and gamma diversity of communities,\nincluding phylogenetic and functional diversity.", "URL": "https://ericmarcon.github.io/divent/,\nhttps://github.com/EricMarcon/divent", "BugReports": "https://github.com/EricMarcon/divent/issues", "License": "GPL (>= 3)", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", "RdMacros": "Rdpack", "Roxygen": "list(markdown = TRUE)", "SystemRequirements": "GNU make, pandoc", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "libglpk-dev make libicu-dev libxml2-dev", "Repository": "https://ericmarcon.r-universe.dev", "Date/Publication": "2026-06-08 17:15:16 UTC", "RemoteUrl": "https://github.com/ericmarcon/divent", "RemoteRef": "HEAD", "RemoteSha": "3c17e624c051163a1f6bb25e8892dccd1f1009a0", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-08 20:12:40 UTC", "User": "root" }, "Author": "Eric Marcon [aut, cre] (ORCID: ),\nFlorence Puech 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"Gustavia_hexapetala", "Hebepetalum_humiriifolium", "Henriettea_flavescens", "Hevea_guianensis", "Hirtella_bicornis", "Hirtella_glandistipula", "Hirtella_glandulosa", "Homalolepis_cedron", "Humiriastrum_subcrenatum", "Hymenopus_heteromorphus", "Indet.Lauraceae_Indet.", "Indet.Sapindaceae_Indet.", "Inga_gracilifolia", "Inga_Indet.", "Inga_loubryana", "Inga_sarmentosa", "Inga_stipularis", "Iryanthera_hostmannii", "Iryanthera_sagotiana", "Jacaranda_copaia", "Lacmellea_aculeata", "Lacunaria_jenmanii", "Lecythis_corrugata", "Lecythis_holcogyne", "Lecythis_persistens", "Lecythis_poiteaui", "Lecythis_zabucajo", "Leptobalanus_sprucei", "Licania_alba", "Licania_canescens", "Licania_laxiflora", "Licania_membranacea", "Licania_micrantha", "Licania_ovalifolia", "Licania_parvifructa", "Licaria_cannella", "Mabea_piriri", "Maytenus_oblongata", "Maytenus_sp.1-CAY", "Miconia_acuminata", "Micropholis_egensis", "Micropholis_guyanensis", "Micropholis_obscura", "Micropholis_venulosa", "Minquartia_guianensis", "Moronobea_coccinea", "Mouriri_crassifolia", "Myrcia_decorticans", "Ocotea_subterminalis", "Oenocarpus_bacaba", "Oenocarpus_bataua", "Oxandra_asbeckii", "Pachira_dolichocalyx", "Parinari_campestris", "Parinari_montana", "Parinari_parvifolia", "Parkia_nitida", "Peltogyne_paniculata", "Pogonophora_schomburgkiana", "Poraqueiba_guianensis", "Posoqueria_latifolia", "Pouteria_ambelaniifolia", "Pouteria_bilocularis", "Pouteria_eugeniifolia", "Pouteria_fimbriata", "Pouteria_grandis", "Pouteria_guianensis", "Pouteria_melanopoda", "Pouteria_sp.42-CAY", "Pradosia_cochlearia", "Protium_giganteum", "Protium_opacum", "Protium_stevensonii", "Protium_subserratum", "Protium_surinamense", "Protium_tenuifolium", "Quiina_obovata", "Recordoxylon_speciosum", "Rinorea_flavescens", "Rinorea_pectinosquamata", "Ruizterania_albiflora", "Sacoglottis_guianensis", "Sandwithia_guyanensis", "Sextonia_rubra", "Siparuna_decipiens", "Sloanea_brachytepala", "Sloanea_brevipes", "Sloanea_laxiflora", "Sloanea_sp.22-CAY", "Sloanea_sp.4-CAY", "Sterculia_pruriens", "Sterculia_speciosa", "Swartzia_guianensis", "Swartzia_panacoco", "Swartzia_polyphylla", "Symphonia_globulifera", "Symphonia_sp.1", "Tabernaemontana_attenuata", "Tachigali_melinonii", "Talisia_hexaphylla", "Talisia_praealta", "Tapirira_guianensis", "Tapirira_obtusa", "Tapura_capitulifera", "Theobroma_guianense", "Thyrsodium_guianense", "Tovomita_brevistaminea", "Tovomita_caloneura", "Tovomita_gazelii", "Tovomita_Indet.", "Tovomita_obovata", "Tovomita_sp.11-CAY", "Tovomita_sp.2-CAY", "Tovomita_sp.22-CAY", "Tovomita_sp.5-CAY", "Tovomita_umbellata", "Trattinnickia_demerarae", "Trichilia_schomburgkii", "Virola_michelii", "Vouacapoua_americana", "Xylopia_nitida", "Zygia_tetragona", "Albizia_pedicellaris", "Anacardium_spruceanum", "Anaxagorea_dolichocarpa", "Aniba_citrifolia", "Aniba_taubertiana", "Aniba_williamsii", "Byrsonima_aerugo", "Byrsonima_Indet.", "Byrsonima_laevigata", "Caraipa_punctulata", "Cecropia_obtusa", "Chrysophyllum_cuneifolium", "Couepia_obovata", "Coussarea_machadoana", "Dacryodes_nitens", "Drypetes_fanshawei", "Duroia_eriopila", "Endlicheria_melinonii", "Eschweilera_Indet.", "Eugenia_exaltata", "Fusaea_longifolia", "Garcinia_benthamiana", "Glycydendron_amazonicum", "Guarea_pubescens", "Guatteria_guianensis", "Guatteria_schomburgkiana", "Heisteria_densifrons", "Heisteria_Indet.", "Helicostylis_pedunculata", "Indet.Annonaceae_Indet.", "Indet.Burseraceae_Indet.", "Indet.Indet._Indet.", "Indet.Lecythidaceae_Indet.", "Indet.Myrtaceae_Indet.", "Indet.Sapotaceae_Indet.", "Inga_alba", "Inga_cylindrica", "Inga_melinonii", "Laetia_procera", "Limadendron_hostmannii", "Macoubea_guianensis", "Mahurea_palustris", "Melicoccus_pedicellaris", "Miconia_minutiflora", "Miconia_tschudyoides", "Micropholis_melinoniana", "Myrcia_fallax", "Neea_Indet.", "Ocotea_cinerea", "Ocotea_percurrens", "Ormosia_coutinhoi", "Parinariopsis_licaniiflora", "Perebea_guianensis", "Platonia_insignis", "Pourouma_bicolor", "Pouteria_bangii", "Pouteria_caimito", "Pouteria_flavilatex", "Pouteria_gonggrijpii", "Pouteria_jariensis", "Pouteria_singularis", "Protium_Indet.", "Rauvolfia_paraensis", "Rhodostemonodaphne_grandis", "Schefflera_decaphylla", "Simaba_polyphylla", "Siparuna_cuspidata", "Sloanea_Indet.", "Sloanea_synandra", "Talisia_simaboides", "Terminalia_grandis", "Tovomita_fanshawei", "Trichilia_micrantha", "Trymatococcus_oligandrus", "Vantanea_parviflora", "Vismia_sessilifolia", "Vochysia_tomentosa", "Votomita_guianensis", "Chrysophyllum_sanguinolentum", "Diplotropis_purpurea", "Duroia_aquatica", "Ecclinusa_guianensis", "Ecclinusa_ramiflora", "Eugenia_anastomosans", "Eugenia_tetramera", "Helicostylis_tomentosa", "Homalolepis_morettii", "Indet.Rubiaceae_Indet.", "Indet.Violaceae_Indet.", "Inga_cayennensis", "Inga_graciliflora", "Inga_lomatophylla", "Inga_marginata", "Inga_sp.12-CAY", "Lecythis_chartacea", "Leptobalanus_longistylus", "Lueheopsis_rugosa", "Manilkara_bidentata", "Matayba_opaca", "Mouriri_Indet.", "Ormosia_paraensis", "Parkia_pendula", "Perebea_rubra", "Pouteria_cicatricata", "Pouteria_torta", "Protium_plagiocarpium", "Quiina_integrifolia", "Rhodostemonodaphne_rufovirgata", "Sloanea_conferta", "Sloanea_granulosa", "Sloanea_guianensis", "Sloanea_parviflora", "Sloanea_sp.70-CAY", "Sterculia_Indet.", "Stryphnodendron_polystachyum", "Swartzia_arborescens", "Swartzia_grandifolia", "Tabebuia_insignis", "Talisia_furfuracea", "Unonopsis_rufescens", "Xylopia_frutescens", "Xylopia_pulcherrima", "Byrsonima_densa", "Copaifera_guyanensis", "Couma_guianensis", "Dendrobangia_boliviana", "Diospyros_carbonaria", "Duroia_micrantha", "Eriotheca_Indet.", "Eugenia_sp.FG21-Holst", "Inga_jenmanii", "Lacunaria_crenata", "Leonia_glycycarpa", "Maquira_guianensis", "Ocotea_amazonica", "Ocotea_glomerata", "Parahancornia_fasciculata", "Parkia_velutina", "Pouteria_cayennensis", "Protium_sagotianum", "Qualea_rosea", "Quiina_macrophylla", "Sagotia_racemosa", "Thyrsodium_puberulum", "Vitex_triflora", "Xylopia_crinita" ], "rows": 4, "table": true, "tojson": true }, { "name": "paracou_6_fundist", "title": "Functional distances between Paracou plot 6 species", "object": "paracou_6_fundist", "class": [ "dist" ], "fields": [], "table": false, "tojson": false }, { "name": "paracou_6_taxo", "title": "Taxonomy of Paracou plot 6 species", "object": "paracou_6_taxo", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "paracou_6_wmppp", "title": "Paracou plot 6", "object": "paracou_6_wmppp", "class": [ "wmppp", "ppp" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "divent-package", "title": "divent", "topics": [ "divent-package", "divent" ] }, { "page": "abd_freq_count", "title": "Abundance Frequency Count of a Community", "topics": [ "abd_freq_count" ] }, { "page": "abd_species", "title": "Abundances of Communities", "topics": [ "abd_species", "abd_sum", "prob_species" ] }, { "page": "accum_div_phylo", "title": "Phylogenetic Diversity Accumulation of a Community", "topics": [ "accum_div_phylo", "accum_div_phylo.abundances", "accum_div_phylo.numeric", "accum_ent_phylo", "accum_ent_phylo.abundances", "accum_ent_phylo.numeric" ] }, { "page": "accum_hill", "title": "Diversity Accumulation of a Community", "topics": [ "accum_hill", "accum_hill.abundances", "accum_hill.numeric", "accum_tsallis", "accum_tsallis.abundances", "accum_tsallis.numeric" ] }, { "page": "accum_sp", "title": "Spatial Accumulation of Diversity", "topics": [ "accum_sp", "accum_sp_diversity", "accum_sp_entropy", "accum_sp_mixing", "autoplot.accum_sp", "plot.accum_sp", "plot_map" ] }, { "page": "accum_sp_hill", "title": "Spatial Diversity Accumulation of a Community", "topics": [ "accum_mixing", "accum_sp_hill", "accum_sp_tsallis" ] }, { "page": "alphahull", "title": "alpha-shape calculation", "topics": [ "alphahull" ] }, { "page": "autoplot.accumulation", "title": "Plot Accumulation Objects", "topics": [ "autoplot.accumulation" ] }, { "page": "autoplot.profile", "title": "Plot Profile Objects", "topics": [ "autoplot.profile" ] }, { "page": "autoplot.wmppp", "title": "ggplot method to plot wmppp objects", "topics": [ "autoplot.wmppp" ] }, { "page": "coverage", "title": "Sample Coverage of a Community", "topics": [ "coverage", "coverage.abundances", "coverage.numeric", "coverage_to_size", "coverage_to_size.abundances", "coverage_to_size.numeric" ] }, { "page": "div_gen_simpson", "title": "Generalized Simpson's Diversity", "topics": [ "div_gen_simpson", "div_gen_simpson.numeric", "div_gen_simpson.species_distribution" ] }, { "page": "div_hill", "title": "Hill number of a Community", "topics": [ "div_hill", "div_hill.numeric", "div_hill.species_distribution" ] }, { "page": "div_hurlbert", "title": "Hurlbert Diversity of a Community", "topics": [ "div_hurlbert", "div_hurlbert.numeric", "div_hurlbert.species_distribution" ] }, { "page": "div_part", "title": "Diversity partition", "topics": [ "div_part" ] }, { "page": "div_pd", "title": "Faith's Phylogenetic Diversity of a Community", "topics": [ "div_pd", "div_pd.numeric", "div_pd.species_distribution" ] }, { "page": "div_phylo", "title": "Phylogenetic Diversity of a Community", "topics": [ "div_phylo", "div_phylo.numeric", "div_phylo.species_distribution" ] }, { "page": "div_richness", "title": "Number of Species of a Community", "topics": [ "div_richness", "div_richness.numeric", "div_richness.species_distribution" ] }, { "page": "div_similarity", "title": "Similarity-Based Diversity of a Community", "topics": [ "div_similarity", "div_similarity.numeric", "div_similarity.species_distribution" ] }, { "page": "e_n_q", "title": "Grassberger's expectation of n^q", "topics": [ "e_n_q" ] }, { "page": "ent_allen", "title": "Allen et al.'s Phylogenetic Entropy of a Community", "topics": [ "ent_allen", "ent_allen.numeric", "ent_allen.species_distribution" ] }, { "page": "ent_gen_simpson", "title": "Generalized Simpson's Entropy", "topics": [ "ent_gen_simpson", "ent_gen_simpson.numeric", "ent_gen_simpson.species_distribution" ] }, { "page": "ent_hurlbert", "title": "Hurlbert Entropy of a Community", "topics": [ "ent_hurlbert", "ent_hurlbert.numeric", "ent_hurlbert.species_distribution" ] }, { "page": "ent_phylo", "title": "Phylogenetic Entropy of a Community", "topics": [ "ent_phylo", "ent_phylo.numeric", "ent_phylo.species_distribution" ] }, { "page": "ent_rao", "title": "Rao's Quadratic Entropy of a Community", "topics": [ "ent_rao", "ent_rao.numeric", "ent_rao.species_distribution" ] }, { "page": "ent_shannon", "title": "Shannon's Entropy of a Community", "topics": [ "ent_shannon", "ent_shannon.numeric", "ent_shannon.species_distribution" ] }, { "page": "ent_similarity", "title": "Similarity-Based Entropy of a Community", "topics": [ "ent_similarity", "ent_similarity.numeric", "ent_similarity.species_distribution" ] }, { "page": "ent_simpson", "title": "Simpson's Entropy of a Community", "topics": [ "ent_simpson", "ent_simpson.numeric", "ent_simpson.species_distribution" ] }, { "page": "ent_sp_simpson", "title": "Spatially Explicit Simpson's Entropy", "topics": [ "ent_sp_simpson", "ent_sp_simpsonEnvelope" ] }, { "page": "ent_tsallis", "title": "Tsallis Entropy of a Community", "topics": [ "ent_tsallis", "ent_tsallis.numeric", "ent_tsallis.species_distribution" ] }, { "page": "exp_q", "title": "Deformed exponential", "topics": [ "exp_q" ] }, { "page": "fit_rac", "title": "Fit a distribution", "topics": [ "fit_rac", "fit_rac.numeric", "fit_rac.species_distribution" ] }, { "page": "fun_ordinariness", "title": "Functional ordinariness of a community", "topics": [ "fun_ordinariness" ] }, { "page": "fun_similarity", "title": "Functional similarity", "topics": [ "fun_similarity" ] }, { "page": "ln_q", "title": "Deformed logarithm", "topics": [ "ln_q" ] }, { "page": "metacommunity", "title": "Aggregate communities into a metacommunity", "topics": [ "metacommunity", 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