{ "_id": "6ad29e886814ce853b657a93", "Package": "bioregion", "Type": "Package", "Title": "Comparison of Bioregionalization Methods", "Version": "1.5.0.9000", "Authors@R": "c(person(given = \"Maxime\",\nfamily = \"Lenormand\",\nemail = \"maxime.lenormand@inrae.fr\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-6362-3473\")),\nperson(given = \"Boris\",\nfamily = \"Leroy\",\nrole = c(\"aut\"),\nemail = \"boris.leroy@gmail.com\",\ncomment = c(ORCID = \"0000-0002-7686-4302\")),\nperson(given = \"Pierre\",\nfamily = \"Denelle\",\nrole = c(\"aut\"),\nemail = \"pierre.denelle@gmail.com\",\ncomment = c(ORCID = \"0000-0001-5037-2281\"))\n)", "Description": "The main purpose of this package is to propose a\ntransparent methodological framework to compare\nbioregionalization methods based on hierarchical and\nnon-hierarchical clustering algorithms (Kreft & Jetz (2010)\n) and network algorithms\n(Lenormand et al. (2019) and Leroy et\nal. (2019) ).", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "RdMacros": "mathjaxr, Rdpack", "VignetteBuilder": "knitr", "URL": "https://github.com/bioRgeo/bioregion,\nhttps://bioRgeo.github.io/bioregion/", "BugReports": "https://github.com/bioRgeo/bioregion/issues", "Config/testthat/edition": "3", "Roxygen": "list(markdown = TRUE)", "Config/roxygen2/version": "8.1.1", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibglpk-dev make libicu-dev libuv1-dev libxml2-dev libssl-dev\nlibproj-dev libsqlite3-dev libudunits2-dev", "Repository": "https://biorgeo.r-universe.dev", "Date/Publication": "2026-10-16 18:50:34 UTC", "RemoteUrl": "https://github.com/biorgeo/bioregion", "RemoteRef": "HEAD", "RemoteSha": "3de26b09f98a5e21a39cc106564b6682694e4e14", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-16 21:45:15 UTC", "User": "root" }, "Author": "Maxime Lenormand [aut, cre] (ORCID:\n),\nBoris Leroy [aut] (ORCID: ),\nPierre Denelle [aut] (ORCID: )", "Maintainer": "Maxime Lenormand ", "_user": "biorgeo", "_type": "src", "_file": "bioregion_1.5.0.9000.tar.gz", "_fileid": "https://r2.ropensci.org/30b9a15f20e8c7081553c4b4394dfcf04bde2a642427f4f9820f928166226e3e", "_filesize": 2026895, "_sha256": "30b9a15f20e8c7081553c4b4394dfcf04bde2a642427f4f9820f928166226e3e", "_expires": "2027-01-24T22:00:34.000Z", "_created": "2026-10-16T21:45:15.000Z", "_published": "2026-10-16T22:00:40.663Z", "_buildurl": "https://github.com/r-universe/biorgeo/actions/runs/38970961392", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 117210929449, "time": 191, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12077231825" }, { "job": 117210929238, "time": 228, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12076608472" }, { "job": 117210929349, "time": 178, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12076264955" }, { "job": 117210929341, "time": 216, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12077332381" }, { "job": 117210929327, "time": 139, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12077651426" }, { "job": 117210929514, "time": 368, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12076743593" }, { "job": 117210929293, "time": 193, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12077227656" }, { "job": 117210929491, "time": 450, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12076779500" }, { "job": 117209036742, "time": 312, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12076424023" }, { "job": 117210930019, "time": 165, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12076369466" }, { "job": 117210929324, "time": 270, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12077875032" }, { "job": 117210929397, "time": 225, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12077157594" }, { "job": 117210929424, "time": 183, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12076583269" }, { "job": 117210929463, "time": 305, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12076982979" }, { "job": 117210929296, "time": 235, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12077321755" } ], "_upstream": "https://github.com/biorgeo/bioregion", "_commit": { "id": "3de26b09f98a5e21a39cc106564b6682694e4e14", "author": "Boris Leroy ", "committer": "Boris Leroy ", "message": "Added 6 standard bioregionalization workflows in tests, which allowed to identify and correct a few bugs in compare_bioregionalization, find_optimal_n, generic print functions, and site_species_metrics. Also added missing unit tests for cut_tree, find_optimal_n, print, hclu_diana and hclu_hierarclust\n", "time": 1792176634 }, "_maintainer": { "name": "Maxime Lenormand", "email": "maxime.lenormand@inrae.fr", "login": "maximelenormand", "description": "", "uuid": 12052066, "orcid": "0000-0001-6362-3473" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "ape", "role": "Imports" }, { "package": "apcluster", "role": "Imports" }, { "package": "bipartite", "role": "Imports" }, { "package": "cluster", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "dbscan", "role": "Imports" }, { "package": "dynamicTreeCut", "role": "Imports" }, { "package": "fastcluster", "role": "Imports" }, { "package": "fastkmedoids", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "mathjaxr", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "phangorn", "role": "Imports" }, { "package": "rcartocolor", "role": "Imports" }, { "package": "Rdpack", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "rmarkdown", "role": "Imports" }, { "package": "segmented", "role": "Imports" }, { "package": "sf", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "vegan", "role": "Imports" }, { "package": "ade4", "role": "Suggests" }, { "package": "adespatial", "role": "Suggests" }, { "package": "betapart", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "ecodist", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "microbenchmark", "role": "Suggests" }, { "package": "parallel", "role": "Suggests" }, { "package": "rnaturalearth", "role": "Suggests" }, { "package": "rnaturalearthdata", "role": "Suggests" }, { "package": "terra", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "biorgeo", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-46", "n": 4 }, { "week": "2025-49", "n": 1 }, { "week": "2025-51", "n": 3 }, { "week": "2026-03", "n": 1 }, { "week": "2026-04", "n": 11 }, { "week": "2026-14", "n": 5 }, { "week": "2026-17", "n": 1 }, { "week": "2026-30", "n": 1 }, { "week": "2026-39", "n": 7 }, { "week": "2026-41", "n": 3 }, { "week": "2026-42", "n": 5 } ], "_tags": [ { "name": "v1.3.0", "date": "2026-01-23" }, { "name": "v1.4.0", "date": "2026-03-29" }, { "name": "v1.5.0", "date": "2026-10-10" } ], "_topics": [ "biogeography", "bioregion", "bioregionalization", "cpp" ], "_stars": 11, "_contributors": [ { "user": "maximelenormand", "count": 300, "uuid": 12052066 }, { "user": "farewe", "count": 181, "uuid": 7148016 }, { "user": "pierredenelle", "count": 147, "uuid": 15929897 }, { "user": "mcgoodman", "count": 2, "uuid": 54951664 }, { "user": "mhahsler", "count": 1, "uuid": 14900595 } ], "_userbio": { "uuid": 60508480, "type": "organization", "name": "bioRgeo", "followers": 3 }, "_downloads": { "count": 773, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bioregion" }, "_devurl": "https://github.com/biorgeo/bioregion", "_pkgdown": "https://bioRgeo.github.io/bioregion/", "_searchresults": 23, "_rbuild": "4.6.1", "_assets": [ "extra/bioregion.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/biorgeo/bioregion", "_realowner": "biorgeo", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2023-04-14" }, { "version": "1.1.0", "date": "2024-03-19" }, { "version": "1.1.1", "date": "2024-04-19" }, { "version": "1.1.1-1", "date": "2024-11-14" }, { "version": "1.2.0", "date": "2025-01-31" }, { "version": "1.3.0", "date": "2026-01-23" }, { "version": "1.4.0", "date": "2026-03-29" }, { "version": "1.5.0", "date": "2026-10-10" } ], "_exports": [ "as_bioregion_pairwise", "betapart_to_bioregion", "bind_pairwise", "bioregion_colors", "bioregion_metrics", "bioregionalization_metrics", "compare_bioregionalizations", "cut_tree", "dissimilarity", "dissimilarity_to_similarity", "exportGDF", "find_optimal_n", "hclu_diana", "hclu_hierarclust", "hclu_optics", "ihct", "install_binaries", "map_bioregions", "mat_to_net", "net_to_mat", "netclu_beckett", "netclu_greedy", "netclu_infomap", "netclu_labelprop", "netclu_leadingeigen", "netclu_leiden", "netclu_louvain", "netclu_oslom", "netclu_walktrap", "nhclu_affprop", "nhclu_clara", "nhclu_clarans", "nhclu_dbscan", "nhclu_kmeans", "nhclu_pam", "similarity", "similarity_to_dissimilarity", "site_species_metrics", "site_species_subset" ], "_datasets": [ { "name": "fishdf", "title": "Spatial distribution of fish in Europe (data.frame)", "object": "fishdf", "class": [ "data.frame" ], "fields": [ "Site", "Species", "Abundance" ], "rows": 2703, "table": true, "tojson": true }, { "name": "fishmat", "title": "Spatial distribution of fish in Europe (co-occurrence matrix)", "object": "fishmat", "class": [ "matrix", "array" ], "fields": [ "Abramis brama", "Alburnus alburnus", "Barbatula barbatula", "Blicca bjoerkna", "Cobitis taenia", "Esox lucius", "Gobio gobio", "Leuciscus leuciscus", "Phoxinus phoxinus", "Rhodeus amarus", "Rutilus rutilus", "Scardinius erythrophthalmus", "Tinca tinca", "Leucaspius delineatus", "Barbus albanicus", "Barbus peloponnesius", "Cobitis trichonica", "Pelasgus stymphalicus", "Rutilus panosi", "Scardinius acarnanicus", "Silurus aristotelis", "Telestes pleurobipunctatus", "Tropidophoxinellus hellenicus", "Valencia letourneuxi", "Alburnus arborella", "Barbus meridionalis", "Barbus plebejus", "Cobitis bilineata", "Rutilus aula", "Romanogobio benacensis", "Sabanejewia larvata", "Scardinius hesperidicus", "Squalius squalus", "Telestes muticellus", "Barbus barbus", "Gobio lozanoi", "Parachondrostoma toxostoma", "Squalius cephalus", "Barbus tyberinus", "Rutilus rubilio", "Pelasgus laconicus", "Squalius peloponensis", "Alburnoides bipunctatus", "Barbus balcanicus", "Barbus macedonicus", "Chondrostoma vardarense", "Cobitis meridionalis", "Cobitis vardarensis", "Pachychilon macedonicum", "Romanogobio elimeius", "Romanogobio kesslerii", "Romanogobio uranoscopus", "Sabanejewia balcanica", "Silurus glanis", "Vimba melanops", "Carassius carassius", "Gymnocephalus cernua", "Cobitis arachthosensis", "Pelasgus thesproticus", "Cobitis paludica", "Iberochondrostoma almacai", "Luciobarbus sclateri", "Pseudochondrostoma polylepis", "Squalius aradensis", "Telestes souffia", "Chondrostoma soetta", "Squalius lucumonis", "Leuciscus idus", "Aphanius iberus", "Valencia hispanica", "Achondrostoma oligolepis", "Cobitis calderoni", "Luciobarbus bocagei", "Pseudochondrostoma duriense", "Squalius carolitertii", "Barbus cyclolepis", "Rhodeus sericeus", "Zingel balcanicus", "Zingel streber", "Alburnus albidus", "Protochondrostoma genei", "Rutilus pigus", "Achondrostoma arcasii", "Chondrostoma knerii", "Squalius illyricus", "Squalius svallize", "Telestes ukliva", "Alburnoides ohridanus", "Alburnus scoranza", "Barbatula sturanyi", "Barbatula zetensis", "Barbus rebeli", "Chondrostoma nasus", "Chondrostoma scodrense", "Cobitis ohridana", "Gobio ohridanus", "Gobio skadarensis", "Rutilus ohridanus", "Rutilus prespensis", "Pachychilon pictum", "Pelasgus epiroticus", "Pelasgus minutus", "Phoxinus lumaireul", "Rutilus basak", "Scardinius knezevici", "Scardinius scardafa", "Telestes montenigrinus", "Leuciscus aspius", "Alburnus chalcoides", "Ballerus ballerus", "Ballerus sapa", "Barbus carpathicus", "Barbus petenyi", "Cobitis elongata", "Cobitis elongatoides", "Cyprinus carpio", "Gymnocephalus baloni", "Gymnocephalus schraetser", "Misgurnus fossilis", "Percarina demidoffii", "Petroleuciscus borysthenicus", "Romanichthys valsanicola", "Romanogobio albipinnatus", "Rutilus meidingeri", "Sabanejewia aurata", "Sabanejewia bulgarica", "Sander lucioperca", "Sander volgensis", "Umbra krameri", "Zingel zingel", "Leuciscus burdigalensis", "Cobitis tanaitica", "Gymnocephalus acerina", "Rhynchocypris percnurus", "Rutilus frisii", "Sander marinus", "Iberochondrostoma lemmingii", "Tropidophoxinellus alburnoides", "Barbus haasi", "Luciobarbus graellsii", "Parachondrostoma miegii", "Squalius pyrenaicus", "Capoeta capoeta", "Cobitis puncticulata", "Cobitis strumicae", "Gobio bulgaricus", "Oxynoemacheilus angorae", "Squalius orpheus", "Squalius keadicus", "Tropidophoxinellus spartiaticus", "Alburnus vistonicus", "Rhodeus meridionalis", "Squalius vardarensis", "Pseudochondrostoma willkommii", "Anaecypris hispanica", "Aphanius baeticus", "Cobitis maroccana", "Iberocypris palaciosi", "Luciobarbus comizo", "Luciobarbus microcephalus", "Luciobarbus steindachneri", "Luciobarbus guiraonis", "Cobitis hellenica", "Pelasgus marathonicus", "Luciobarbus graecus", "Rutilus ylikiensis", "Scardinius graecus", "Telestes beoticus", "Aulopyge huegelii", "Delminichthys ghetaldii", "Telestes polylepis", "Alburnus thessalicus", "Squalius torgalensis", "Oxynoemacheilus brandtii", "Oxynoemacheilus bureschi", "Barbus sperchiensis", "Cobitis stephanidisi", "Gobio feraeensis", "Barbus caninus", "Alburnoides prespensis", "Alburnus belvica", "Barbus prespensis", "Chondrostoma prespense", "Pelasgus prespensis", "Squalius prespensis", "Zingel asper", "Alburnus volviticus", "Barbus strumicae", "Iberochondrostoma lusitanicum", "Aphanius sureyanus", "Cobitis punctilineata", "Phoxinus strymonicus", "Cobitis vettonica", "Barbus tauricus", "Telestes croaticus" ], "rows": 338, "table": true, "tojson": true }, { "name": "fishsf", "title": "Spatial distribution of fish in Europe", "object": "fishsf", "class": [ "sf", "data.frame" ], "fields": [ "Site", "geometry" ], "rows": 338, "table": false, "tojson": true }, { "name": "vegedf", "title": "Spatial distribution of Mediterranean vegetation (data.frame)", "object": "vegedf", "class": [ "data.frame" ], "fields": [ "Site", "Species", "Abundance" ], "rows": 460878, "table": true, "tojson": true }, { "name": "vegemat", "title": "Spatial distribution of Mediterranean vegetation (co-occurrence matrix)", "object": "vegemat", "class": [ "matrix", "array" ], "fields": [], "rows": 715, "table": true, "tojson": true }, { "name": "vegesf", "title": "Spatial distribution of Mediterranean vegetation (sf data.frame)", "object": "vegesf", "class": [ "sf", "data.frame" ], "fields": [ "Site", "geometry" ], "rows": 728, "table": false, "tojson": true } ], "_help": [ { "page": "as_bioregion_pairwise", "title": "Convert a matrix or list of matrices to a bioregion (dis)similarity object", "topics": [ "as_bioregion_pairwise" ] }, { "page": "betapart_to_bioregion", "title": "Convert betapart dissimilarity to bioregion dissimilarity (DEPRECATED)", "topics": [ "betapart_to_bioregion" ] }, { "page": "bind_pairwise", "title": "Combine and enrich bioregion (dis)similarity object(s)", "topics": [ "bind_pairwise" ] }, { "page": "bioregion_colors", "title": "Add color palettes to bioregion cluster objects", "topics": [ "bioregion_colors" ] }, { "page": "bioregion_metrics", "title": "Calculate metrics for bioregions", "topics": [ "bioregion_metrics" ] }, { "page": "bioregionalization_metrics", "title": "Calculate metrics for a bioregionalization", "topics": [ "bioregionalization_metrics" ] }, { "page": "compare_bioregionalizations", "title": "Compare cluster memberships among multiple bioregionalizations", "topics": [ "compare_bioregionalizations" ] }, { "page": "cut_tree", "title": "Cut a hierarchical tree", "topics": [ "cut_tree" ] }, { "page": "dissimilarity", "title": "Compute dissimilarity metrics (beta-diversity) between sites based on species composition", "topics": [ "dissimilarity" ] }, { "page": "dissimilarity_to_similarity", "title": "Convert dissimilarity metrics to similarity metrics", "topics": [ "dissimilarity_to_similarity" ] }, { "page": "exportGDF", "title": "Export a network to GDF format for Gephi visualization", "topics": [ "exportGDF" ] }, { "page": "find_optimal_n", "title": "Search for an optimal number of bioregions in a bioregionalization", "topics": [ "find_optimal_n" ] }, { "page": "fishdf", "title": "Spatial distribution of fish in Europe (data.frame)", "topics": [ "fishdf" ] }, { "page": "fishmat", "title": "Spatial distribution of fish in Europe (co-occurrence matrix)", "topics": [ "fishmat" ] }, { "page": "fishsf", "title": "Spatial distribution of fish in Europe", "topics": [ "fishsf" ] }, { "page": "hclu_diana", "title": "Divisive hierarchical clustering based on dissimilarity or beta-diversity", "topics": [ "hclu_diana" ] }, { "page": "hclu_hierarclust", "title": "Hierarchical clustering based on dissimilarity or beta-diversity", "topics": [ "hclu_hierarclust" ] }, { "page": "hclu_optics", "title": "OPTICS hierarchical clustering algorithm", "topics": [ "hclu_optics" ] }, { "page": "ihct", "title": "Iterative hierarchical consensus tree from a dissimilarity matrix", "topics": [ "ihct" ] }, { "page": "install_binaries", "title": "Download, unzip, check permissions, and test the bioregion's binary files", "topics": [ "install_binaries" ] }, { "page": "map_bioregions", "title": "Create a map of bioregions", "topics": [ "map_bioregions" ] }, { "page": "mat_to_net", "title": "Create a data.frame from a contingency table", "topics": [ "mat_to_net" ] }, { "page": "net_to_mat", "title": "Create a contingency table from a data.frame", "topics": [ "net_to_mat" ] }, { "page": "netclu_beckett", "title": "Community structure detection in weighted bipartite networks via modularity optimization", "topics": [ "netclu_beckett" ] }, { "page": "netclu_greedy", "title": "Community structure detection via greedy optimization of modularity", "topics": [ "netclu_greedy" ] }, { "page": "netclu_infomap", "title": "Infomap community finding", "topics": [ "netclu_infomap" ] }, { "page": "netclu_labelprop", "title": "Finding communities based on propagating labels", "topics": [ "netclu_labelprop" ] }, { "page": "netclu_leadingeigen", "title": "Finding communities based on the leading eigenvector of the community matrix", "topics": [ "netclu_leadingeigen" ] }, { "page": "netclu_leiden", "title": "Finding communities using the Leiden algorithm", "topics": [ "netclu_leiden" ] }, { "page": "netclu_louvain", "title": "Louvain community finding", "topics": [ "netclu_louvain" ] }, { "page": "netclu_oslom", "title": "OSLOM community finding", "topics": [ "netclu_oslom" ] }, { "page": "netclu_walktrap", "title": "Community structure detection via short random walks", "topics": [ "netclu_walktrap" ] }, { "page": "nhclu_affprop", "title": "Non-hierarchical clustering: Affinity Propagation", "topics": [ "nhclu_affprop" ] }, { "page": "nhclu_clara", "title": "Non-hierarchical clustering: CLARA", "topics": [ "nhclu_clara" ] }, { "page": "nhclu_clarans", "title": "Non-hierarchical clustering: CLARANS", "topics": [ "nhclu_clarans" ] }, { "page": "nhclu_dbscan", "title": "Non-hierarchical clustering: DBSCAN", "topics": [ "nhclu_dbscan" ] }, { "page": "nhclu_kmeans", "title": "Non-hierarchical clustering: K-means analysis", "topics": [ "nhclu_kmeans" ] }, { "page": "nhclu_pam", "title": "Non-hierarchical clustering: Partitioning Around Medoids", "topics": [ "nhclu_pam" ] }, { "page": "similarity", "title": "Compute similarity metrics between sites based on species composition", "topics": [ "similarity" ] }, { "page": "similarity_to_dissimilarity", "title": "Convert similarity metrics to dissimilarity metrics", "topics": [ "similarity_to_dissimilarity" ] }, { "page": "site_species_metrics", "title": "Calculate metrics for sites and species relative to bioregions and chorotypes", "topics": [ "site_species_metrics" ] }, { "page": "site_species_subset", "title": "Extract a subset of sites or species from a 'bioregion.clusters' object", "topics": [ "site_species_subset" ] }, { "page": "vegedf", "title": "Spatial distribution of Mediterranean vegetation (data.frame)", "topics": [ "vegedf" ] }, { "page": "vegemat", "title": "Spatial distribution of Mediterranean vegetation (co-occurrence matrix)", "topics": [ "vegemat" ] }, { "page": "vegesf", "title": "Spatial distribution of Mediterranean vegetation (sf data.frame)", "topics": [ "vegesf" ] } ], "_pkglogo": "https://github.com/biorgeo/bioregion/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/biorgeo/bioregion/raw/HEAD/README.md", "_rundeps": [ "apcluster", "ape", "askpass", "base64enc", "bipartite", "bslib", "cachem", "class", "classInt", "cli", "cluster", "coda", "corpcor", "cpp11", "curl", "data.table", "DBI", "dbscan", "digest", "dotCall64", "dplyr", "dynamicTreeCut", "e1071", "evaluate", "farver", "fastcluster", "fastkmedoids", "fastmap", "fastmatch", "fields", "fontawesome", "fs", "generics", "ggplot2", "glue", "gtable", "highr", "htmltools", "httr", "igraph", "isoband", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "lattice", "lifecycle", "magrittr", "maps", "MASS", "mathjaxr", "Matrix", "memoise", "mgcv", "mime", "network", "nlme", "openssl", "permute", "phangorn", "pillar", "pkgconfig", "proxy", "purrr", "quadprog", "R6", "rappdirs", "rbibutils", "rcartocolor", "RColorBrewer", "Rcpp", "Rdpack", "rlang", "rmarkdown", "s2", "S7", "sass", "scales", "segmented", "sf", "sna", "spam", "statnet.common", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "units", "utf8", "vctrs", "vegan", "viridisLite", "withr", "wk", "xfun", "yaml" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "bioregion.Rmd", "filename": "bioregion.html", "title": "Tutorial for bioregion", "author": "Maxime Lenormand, Boris Leroy and Pierre Denelle", "engine": "knitr::rmarkdown", "headings": [ "0. Brief introduction", "1. Install binary files", "2. Matrix or network formats", "3. Pairwise similarity/dissimilarity metrics", "4. Bioregionalization algorithms", "4.1 Hierarchical clustering", "4.2 Non-hierarchical clustering", "4.3 Network clustering", "4.4 Microbenchmark", "5. Visualization and evaluation of the results", "5.1 Visualization", "5.2 Summary metrics", "5.3 Compare bioregionalizations" ], "created": "2023-03-10 14:42:46", "modified": "2026-10-13 18:42:09", "commits": 20 } ], "_score": 6.745543201998023, "_indexed": true, "_nocasepkg": "bioregion", "_universes": [ "biorgeo", "maximelenormand" ], "_previous": "1.5.0", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.5.0.9000", "date": "2026-10-16T21:48:08.000Z", "distro": "resolute", "arch": "aarch64", "commit": "3de26b09f98a5e21a39cc106564b6682694e4e14", "fileid": "https://r2.ropensci.org/a4f6d25c7187131f696b2f6602d1cf76292808d7ad9234323f6d5516dcaf8723", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biorgeo/actions/runs/38970961392" }, { "r": "4.7.0", "os": "linux", "version": "1.5.0.9000", "date": "2026-10-16T21:48:30.000Z", "distro": "resolute", "arch": "x86_64", "commit": "3de26b09f98a5e21a39cc106564b6682694e4e14", "fileid": "https://r2.ropensci.org/9bb7b57ae44f27762f8119c66f2ff45ff5542645742f95edac8c88879046e1c8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biorgeo/actions/runs/38970961392" }, { "r": "4.6.1", "os": "linux", "version": "1.5.0.9000", "date": "2026-10-16T21:48:04.000Z", "distro": "resolute", "arch": "aarch64", "commit": "3de26b09f98a5e21a39cc106564b6682694e4e14", "fileid": "https://r2.ropensci.org/c02fdaf7a1b024341e1be95a22b0f4d45ef54371931e6e3e39f5df46797a0feb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biorgeo/actions/runs/38970961392" }, { "r": "4.6.1", "os": "linux", "version": "1.5.0.9000", "date": "2026-10-16T21:48:24.000Z", "distro": "resolute", "arch": "x86_64", "commit": "3de26b09f98a5e21a39cc106564b6682694e4e14", "fileid": "https://r2.ropensci.org/8cb1e0325d2591c147325d8af6a171809bd71167ac8d6d81794cf1386061a5ce", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biorgeo/actions/runs/38970961392" }, { "r": "4.5.3", "os": "mac", "version": "1.5.0.9000", "date": "2026-10-16T21:50:28.000Z", "arch": "aarch64", "commit": "3de26b09f98a5e21a39cc106564b6682694e4e14", "fileid": "https://r2.ropensci.org/bfe00e7b3a5a233ed61a045e7767bac97f1d2fa2ce26f257b7f02ae425c0b7c5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biorgeo/actions/runs/38970961392" }, { "r": "4.5.3", "os": "mac", "version": "1.5.0.9000", "date": "2026-10-16T21:49:42.000Z", "arch": "x86_64", "commit": "3de26b09f98a5e21a39cc106564b6682694e4e14", "fileid": "https://r2.ropensci.org/ccee8a684e477de572f6deab1e9ae06b1feabf3e3eefd72f3cbe560122d1e862", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biorgeo/actions/runs/38970961392" }, { "r": "4.6.1", "os": "mac", "version": "1.5.0.9000", "date": "2026-10-16T21:55:23.000Z", "arch": "aarch64", "commit": "3de26b09f98a5e21a39cc106564b6682694e4e14", "fileid": "https://r2.ropensci.org/478b720fc67e139a58339e1954cb84ffbef63583589af871018f181e41a8e7cd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biorgeo/actions/runs/38970961392" }, { "r": "4.6.1", "os": "mac", "version": "1.5.0.9000", "date": "2026-10-16T21:57:15.000Z", "arch": "x86_64", "commit": "3de26b09f98a5e21a39cc106564b6682694e4e14", "fileid": "https://r2.ropensci.org/fa5c8f434e9b18c723a1d6c6fba800e889dedd3e33595ce53d92d218e4af1773", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biorgeo/actions/runs/38970961392" }, { "r": "4.6.0", "os": "wasm", "version": "1.5.0.9000", "date": "2026-10-16T21:48:38.000Z", "arch": "emscripten", "commit": "3de26b09f98a5e21a39cc106564b6682694e4e14", "fileid": "https://r2.ropensci.org/cc1e4180f7a6106249be038290e2ac4857810f43e992e11006e7ab0c0a862e43", "status": "success", "buildurl": "https://github.com/r-universe/biorgeo/actions/runs/38970961392" }, { "r": "4.7.0", "os": "win", "version": "1.5.0.9000", "date": "2026-10-16T21:49:03.000Z", "arch": "aarch64", "commit": "3de26b09f98a5e21a39cc106564b6682694e4e14", "fileid": "https://r2.ropensci.org/dca1ef4fe11ababf77657c23188590743a3bf1ccd66c990d04ddc40423dca106", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biorgeo/actions/runs/38970961392" }, { "r": "4.7.0", "os": "win", "version": "1.5.0.9000", "date": "2026-10-16T21:47:09.000Z", "arch": "x86_64", "commit": "3de26b09f98a5e21a39cc106564b6682694e4e14", "fileid": "https://r2.ropensci.org/6fb7ddacd7d230a56e966b9b1ce1e437fb4b0f3e3f8979c65d0d65f3fa79104e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biorgeo/actions/runs/38970961392" }, { "r": "4.5.3", "os": "win", "version": "1.5.0.9000", "date": "2026-10-16T21:47:19.000Z", "arch": "x86_64", "commit": "3de26b09f98a5e21a39cc106564b6682694e4e14", "fileid": "https://r2.ropensci.org/1bb62367859988e25b83069a313d74319ed77579d9e8b174a107541400f6d11b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biorgeo/actions/runs/38970961392" }, { "r": "4.6.1", "os": "win", "version": "1.5.0.9000", "date": "2026-10-16T21:49:42.000Z", "arch": "aarch64", "commit": "3de26b09f98a5e21a39cc106564b6682694e4e14", "fileid": "https://r2.ropensci.org/b7c9d99320caeb8f59ef74ea7558f11d303046a6673cabbff8d0fa195d4eedb8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biorgeo/actions/runs/38970961392" }, { "r": "4.6.1", "os": "win", "version": "1.5.0.9000", "date": "2026-10-16T21:48:26.000Z", "arch": "x86_64", "commit": "3de26b09f98a5e21a39cc106564b6682694e4e14", "fileid": "https://r2.ropensci.org/06415d01cd48ff498d7a25dd7b1cd4f3c5bcf8940d604ac979e8d8f5ee4f9ddf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biorgeo/actions/runs/38970961392" } ] }