{ "_id": "6a1f2710b401979e73422471", "Package": "nichevol", "Type": "Package", "Title": "Tools for Ecological Niche Evolution Assessment Considering\nUncertainty", "Version": "0.1.20", "Authors@R": "c(\nperson(\"Marlon E.\", \"Cobos\", email = \"manubio13@gmail.com\", role = c(\"aut\",\"cre\")),\nperson(\"Hannah L.\", \"Owens\", email = \"hannah.owens@gmail.com\", role = \"aut\"),\nperson(\"A. Townsend\", \"Peterson\", email = \"town@ku.edu\", role = \"aut\"))", "Author": "Marlon E. Cobos [aut, cre], Hannah L. Owens [aut], A. Townsend\nPeterson [aut]", "Maintainer": "Marlon E. Cobos ", "Date": "2023-03-09", "Description": "A collection of tools that allow users to perform critical\nsteps in the process of assessing ecological niche evolution\nover phylogenies, with uncertainty incorporated explicitly in\nreconstructions. The method proposed here for ancestral\nreconstruction of ecological niches characterizes species'\nniches using a bin-based approach that incorporates uncertainty\nin estimations. Compared to other existing methods, the\napproaches presented here reduce risk of overestimation of\namounts and rates of ecological niche evolution. The main\nanalyses include: initial exploration of environmental data in\noccurrence records and accessible areas, preparation of data\nfor phylogenetic analyses, executing comparative phylogenetic\nanalyses of ecological niches, and plotting for\ninterpretations. Details on the theoretical background and\nmethods used can be found in: Owens et al. (2020)\n, Peterson et al. (1999)\n, Soberón and Peterson\n(2005) , Peterson (2011)\n, Barve et al. (2011)\n, Machado-Stredel et al. (2021)\n, Owens et al. (2013)\n, Saupe et al. (2018)\n, and Cobos et al. (2021)\n.", "URL": "https://github.com/marlonecobos/nichevol", "BugReports": "https://github.com/marlonecobos/nichevol/issues", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.1.2", "Config/pak/sysreqs": "libgdal-dev gdal-bin libgeos-dev libglpk-dev\nlibicu-dev libxml2-dev libproj-dev libsqlite3-dev", "Repository": "https://marlonecobos.r-universe.dev", "Date/Publication": "2023-03-10 19:02:37 UTC", "RemoteUrl": "https://github.com/marlonecobos/nichevol", "RemoteRef": "HEAD", "RemoteSha": "e3a1112b803b5ac38c5bc5b1422423f80e509b5a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-16 05:45:49 UTC", "User": "root" }, "MD5sum": "e26fc863a2ee1f98f76289bb18e4e685", "_user": "marlonecobos", "_type": "src", "_file": "nichevol_0.1.20.tar.gz", "_fileid": "b66a6ae9fdcc82859846e2ceb9f4a63fe64a2c4484af59fcce56b51dac47a011", "_filesize": 497183, "_sha256": "b66a6ae9fdcc82859846e2ceb9f4a63fe64a2c4484af59fcce56b51dac47a011", "_created": "2026-05-16T05:45:49.000Z", "_published": "2026-06-02T18:55:12.832Z", "_distro": "noble", "_jobs": [ { "job": 79148279228, "time": 234, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7030952260" }, { "job": 79148279125, "time": 210, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7030950091" }, { "job": 79148279587, "time": 162, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7030945416" }, { "job": 79148279080, "time": 152, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7030944482" }, { "job": 79148278453, "time": 201, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7030929168" }, { "job": 79148278477, "time": 143, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7367040210" }, { "job": 79148279073, "time": 177, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7030946771" }, { "job": 79148279638, "time": 199, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7030948992" }, { "job": 79148279092, "time": 164, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7030945571" } ], "_buildurl": "https://github.com/r-universe/marlonecobos/actions/runs/25954145649", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/marlonecobos/nichevol", "_commit": { "id": "e3a1112b803b5ac38c5bc5b1422423f80e509b5a", "author": "marlonecobos ", "committer": "marlonecobos ", "message": "V 0.1.20 fix description\n", "time": 1678474957 }, "_maintainer": { "name": "Marlon E. Cobos", "email": "manubio13@gmail.com", "login": "marlonecobos", "linkedin": "in/marlon-e-cobos-009203b4", "twitter": "@Marlon_E_Cobos", "uuid": 19596631 }, "_registered": true, "_dependencies": [ { "package": "ape", "version": ">= 5.3", "role": "Depends" }, { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "castor", "version": ">= 1.4", "role": "Imports" }, { "package": "geiger", "version": ">= 2.0", "role": "Imports" }, { "package": "graphics", "version": ">= 3.6", "role": "Imports" }, { "package": "grDevices", "version": ">= 3.6", "role": "Imports" }, { "package": "stringr", "version": ">= 1.4", "role": "Imports" }, { "package": "stats", "version": ">= 3.6", "role": "Imports" }, { "package": "terra", "version": ">= 1.6", "role": "Imports" }, { "package": "utils", "version": ">= 3.6", "role": "Imports" }, { "package": "knitr", "version": ">= 1.25", "role": "Suggests" }, { "package": "phytools", "version": ">= 0.6", "role": "Suggests" } ], "_owner": "marlonecobos", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 15, "_contributors": [ { "user": "marlonecobos", "count": 236, "uuid": 19596631 }, { "user": "hannahlowens", "count": 27, "uuid": 11444247 } ], "_userbio": { "uuid": 19596631, "type": "user", "name": "Marlon E. Cobos", "description": "Postdoctoral Fellow at the University of Kansas" }, "_downloads": { "count": 192, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/nichevol" }, "_mentions": 1, "_devurl": "https://github.com/marlonecobos/nichevol", "_searchresults": 5, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/nichevol.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/marlonecobos/nichevol", "_realowner": "marlonecobos", "_cranurl": true, "_releases": [ { "version": "0.1.19", "date": "2020-03-02" }, { "version": "0.1.20", "date": "2023-03-11" } ], "_exports": [ "bin_env", "bin_ml_rec", "bin_par_rec", "bin_table", "bin_tables", "bin_tables0", "hist_evalues", "histograms_env", "map_nichevol", "niche_bars", "niche_labels", "niche_legend", "nichevol_bars", "nichevol_labels", "nichevol_legend", "pdf_histograms", "read_bin_table", "read_bin_tables", "rename_tips", "score_tip", "score_tree", "set_uncertainty", "sig_sq", "smooth_rec", "stats_eval", "stats_evalues" ], "_datasets": [ { "name": "character_table", "title": "Example of character table for six species", "object": "character_table", "class": [ "matrix", "array" ], "fields": [ "21 to 30", "31 to 40", "41 to 50", "51 to 60", "61 to 70", "71 to 80", "81 to 90", "91 to 100", "101 to 110", "111 to 120", "121 to 130", "131 to 140", "141 to 150", "151 to 160", "161 to 170", "171 to 180", "181 to 190", "191 to 200", "201 to 210", "211 to 220", "221 to 230", "231 to 240", "241 to 250", "251 to 260", "261 to 270", "271 to 280", "281 to 290", "291 to 300" ], "rows": 6, "table": true, "tojson": true }, { "name": "occ_list", "title": "Example of occurrence records for six species", "object": "occ_list", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "par_rec_table", "title": "Example of table with results from parsimony reconstructions", "object": "par_rec_table", "class": [ "matrix", "array" ], "fields": [ "3.93 to 5.179", "5.179 to 6.428", "6.428 to 7.677", "7.677 to 8.926", "8.926 to 10.175", "10.175 to 11.424", "11.424 to 12.673", "12.673 to 13.922", "13.922 to 15.171", "15.171 to 16.42", "16.42 to 17.669", "17.669 to 18.918", "18.918 to 20.167", "20.167 to 21.416", "21.416 to 22.665", "22.665 to 23.914", "23.914 to 25.163", "25.163 to 26.412", "26.412 to 27.661", "27.661 to 28.91" ], "rows": 11, "table": true, "tojson": true }, { "name": "tree", "title": "Example of a phylogenetic tree for six species", "object": "tree", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false }, { "name": "tree_data", "title": "Example of a list containing a tree and a table of characters for six species", "object": "tree_data", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "tree5", "title": "Example of a phylogenetic tree for five species", "object": "tree5", "class": [ "phylo" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "bin_env", "title": "Helper function to prepare bin tables", "topics": [ "bin_env" ] }, { "page": "bin_ml_rec", "title": "Maximum likelihood reconstruction of ancestral character states", "topics": [ "bin_ml_rec" ] }, { "page": "bin_par_rec", "title": "Maximum parsimony reconstruction of ancestral character states", "topics": [ "bin_par_rec" ] }, { "page": "bin_table", "title": "Bin table of environmental conditions in M and for occurrences", "topics": [ "bin_table" ] }, { "page": "bin_tables", "title": "Bin tables of environmental conditions in M and for occurrences from objects", "topics": [ "bin_tables" ] }, { "page": "bin_tables0", "title": "Bin tables of environmental conditions in M and for occurrences from data", "topics": [ "bin_tables0" ] }, { "page": "character_table", "title": "Example of character table for six species", "topics": [ "character_table" ] }, { "page": "hist_evalues", "title": "Histograms of environmental conditions in M and for occurrences (one species)", "topics": [ "hist_evalues" ] }, { "page": "histograms_env", "title": "Histograms of environmental conditions in M and for occurrences", "topics": [ "histograms_env" ] }, { "page": "m", "title": "Example of accessible areas for a species", "topics": [ "m", "m1", "m2", "m3", "m4", "m5", "m6" ] }, { "page": "map_nichevol", "title": "Maps of niche reconstructions and changes detected", "topics": [ "map_nichevol" ] }, { "page": "niche_bars", "title": "PNG bar figures to represent ecological niches of distinct taxa", "topics": [ "niche_bars" ] }, { "page": "niche_labels", "title": "Labels to represent niches of tips and ancestors", "topics": [ "niche_labels" ] }, { "page": "niche_legend", "title": "Legends for niche labels in phylogenetic trees", "topics": [ "niche_legend" ] }, { "page": "nichevol", "title": "nichevol: Assessment of Species’ Ecological Niche Evolution Considering Uncertainty in Reconstructions", "topics": [ "nichevol" ] }, { "page": "nichevol_bars", "title": "PNG bar figures for representing niche evolution", "topics": [ "nichevol_bars" ] }, { "page": "nichevol_labels", "title": "Labels to represent changes of niche characteristics between ancestors and descendants", "topics": [ "nichevol_labels" ] }, { "page": "nichevol_legend", "title": "Legends for niche evolution labels in phylogenetic trees", "topics": [ "nichevol_legend" ] }, { "page": "occ_list", "title": "Example of occurrence records for six species", "topics": [ "occ_list" ] }, { "page": "par_rec_table", "title": "Example of table with results from parsimony reconstructions", "topics": [ "par_rec_table" ] }, { "page": "pdf_histograms", "title": "Helper function to create PDF files with histograms", "topics": [ "pdf_histograms" ] }, { "page": "read_bin_table", "title": "Read tables of binary niche characters from directory", "topics": [ "read_bin_table", "read_bin_tables" ] }, { 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