{ "_id": "6a1046a2acfb0bcc41c9ebad", "Package": "FishPhyloMaker", "Type": "Package", "Title": "Phylogenies for a List of Finned-Ray Fishes", "Version": "0.2.0", "Authors@R": "c(person(given = \"Gabriel\",\nfamily = \"Nakamura\",\nrole = c(\"aut\", \"cre\"),\nemail = \"gabriel.nakamura.souza@gmail.com\",\ncomment = c(ORCID = \"0000-0002-5144-5312\")),\nperson(given = \"Aline\",\nfamily = \"Richter\",\nrole = \"aut\"),\nperson(given = \"Bruno\",\nfamily = \"Soares\",\nrole = \"aut\",\n))", "Description": "Provides an alternative to facilitate the construction of\na phylogeny for fish species from a list of species or a\ncommunity matrix using as a backbone the phylogenetic tree\nproposed by Rabosky et al. (2018)\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr, rmarkdown", "Remotes": [ "ropensci/rfishbase" ], "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev xz-utils", "Repository": "https://phylotastic.r-universe.dev", "Date/Publication": "2023-12-26 14:45:40 UTC", "RemoteUrl": "https://github.com/GabrielNakamura/FishPhyloMaker", "RemoteRef": "HEAD", "RemoteSha": "04373d07704296dcf64218dcb9f5afc4f9e06a9f", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-10 18:07:35 UTC", "User": "root" }, "Author": "Gabriel Nakamura [aut, cre] (ORCID:\n),\nAline Richter [aut],\nBruno Soares [aut]", "Maintainer": "Gabriel Nakamura ", "MD5sum": "a2e5003aa810da8dc17ea46eae07c8e9", "_user": "phylotastic", "_type": "src", "_file": "FishPhyloMaker_0.2.0.tar.gz", "_fileid": "281413bc0a2366a0ac147697a5402905f57e51a7d87b99a6d819fdf037d6f7db", "_filesize": 845783, "_sha256": "281413bc0a2366a0ac147697a5402905f57e51a7d87b99a6d819fdf037d6f7db", "_created": "2026-05-10T18:07:35.000Z", "_published": "2026-05-22T12:05:54.545Z", "_distro": "noble", "_jobs": [ { "job": 77375832212, "time": 160, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "6905833085" }, { "job": 77375832320, "time": 149, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "6905832013" }, { "job": 77375832041, "time": 73, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "6905824480" }, { "job": 77375831878, "time": 91, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "6905826166" }, { "job": 77375831787, "time": 188, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6905816680" }, { "job": 77375831541, "time": 153, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7160052955" }, { "job": 77375832129, "time": 92, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "6905826425" }, { "job": 77375832048, "time": 88, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "6905826102" }, { "job": 77375832006, "time": 72, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "6905824330" } ], "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25635888180", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/GabrielNakamura/FishPhyloMaker", "_commit": { "id": "04373d07704296dcf64218dcb9f5afc4f9e06a9f", "author": "GabrielNakamura ", "committer": "GabrielNakamura ", "message": "updating pkgdown docs\n", "time": 1703601940 }, "_maintainer": { "name": "Gabriel Nakamura", "email": "gabriel.nakamura.souza@gmail.com", "login": "gabrielnakamura", "orcid": "0000-0002-5144-5312", "uuid": 13869477 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "ape", "role": "Imports" }, { "package": "fishtree", "role": "Imports" }, { "package": "geiger", "role": "Imports" }, { "package": "knitr", "role": "Imports" }, { "package": "phytools", "role": "Imports" }, { "package": "progress", "role": "Imports" }, { "package": "rfishbase", "role": "Imports" }, { "package": "rmarkdown", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "markdown", "role": "Suggests" }, { "package": "gh", "role": "Suggests" } ], "_owner": "gabrielnakamura", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 10, "_contributors": [ { "user": "gabrielnakamura", "count": 219, "uuid": 13869477 }, { "user": "richterbine", "count": 8, "uuid": 63691368 }, { "user": "jobdiogenes", "count": 3, "uuid": 1182381 } ], "_userbio": { "uuid": 1652822, "type": "organization", "name": "phylotastic" }, "_downloads": { "count": 262, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/FishPhyloMaker" }, "_devurl": "https://github.com/gabrielnakamura/fishphylomaker", "_searchresults": 17, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/FishPhyloMaker.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/gabrielnakamura/fishphylomaker", "_realowner": "gabrielnakamura", "_cranurl": true, "_releases": [ { "version": "0.2.0", "date": "2021-09-15" } ], "_exports": [ "FishPhyloMaker", "FishTaxaMaker", "PD_deficit", "whichFishAdd" ], "_datasets": [ { "name": "neotropical_comm", "title": "Abundance of stream fish species in Parana and Paraguay streams", "object": "neotropical_comm", "class": [ "data.frame" ], "fields": [ "bacia", "pontos", "Astyanax_lacustris", "Astyanax_lineatus", "Astyanax_sp1", "Astyanax_sp2", "Astyanax_sp3", "Astyanax_eigenmanniorum", "Astyanax_fasciatus", "Apareiodon_ibitiensis", "Ancistrus_sp", "Astyanax_paranae", "Apareiodon_piracicabae", "Bryconamericus_exodon", "Piabarchus_stramineus", "Corydoras_aeneus", "Crenicichla_britskii", "Crenicichla_lepidota", "Crenicichla_sp", "Callichthys_callichthys", "Characidium_sp", "Characidium_gomesi", "Characidium_laterale", "Cichlasoma_paranaense", "Characidium_zebra", "Gymnotus_sp", "Gymnotus_inaequilabiatus", "Hypostomus_ancistroides", "Hypostomus_iheringii", "Hypostomus_khimaera", "Curculionichthys_insperatus", "Hisonotus_sp", "Hoplias_malabaricus", "Moenkhausia_bonita", "Hypostomus_sp", "Hypostomus_sp2", "Hypostomus_aff_latirostris", "Imparfinis_schubarti", "Imparfinis_sp", "Jupiaba_acantogaster", "Leporinus_friderici", "Loricaria_cf_coximensis", "Loricaria_luciae", "Loricariichthys_platymetopon", "Moenkhausia_forestii", "Moenkhausia_oligolepsis", "Oligosarcus_pintoi", "Piabina_argentea", "Piabarchus_torrenticola", "Creagrutus_meridionalis", "Pyrrhulina_australis", "Trachelyopterus_galeatus", "Psellogrammus_kennedyi", "Parodon_nasus", "Poecilia_reticulata", "Phenacorhamdia_tenebrosa", "Rineloricaria_lanceolata", "Roeboides_descalvadensis", "Rhamdia_quelen", "Synbranchus_marmoratus", "Serrapinnus_notomelas" ], "rows": 20, "table": true, "tojson": true }, { "name": "spp_afrotropic", "title": "List of fish species with occurrence in Afrotropical ecoregion", "object": "spp_afrotropic", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "taxon_data_PhyloMaker", "title": "Data frame with species names needed to assemble the phylogenetic tree", "object": "taxon_data_PhyloMaker", "class": [ "data.frame" ], "fields": [ "s", "f", "o" ], "rows": 45, "table": true, "tojson": true } ], "_help": [ { "page": "FishPhyloMaker", "title": "Obtaining fish phylogeny according to a local pool of species", "topics": [ "FishPhyloMaker" ] }, { "page": "FishTaxaMaker", "title": "Generate a list of species Auxiliary function to obtain taxonomic classification and check the names of species present in species pool", "topics": [ "FishTaxaMaker" ] }, { "page": "neotropical_comm", "title": "Abundance of stream fish species in Parana and Paraguay streams", "topics": [ "neotropical_comm" ] }, { "page": "PD_deficit", "title": "Title Calculate the amount of phylogenetic deficit in assemblages", "topics": [ "PD_deficit" ] }, { "page": "spp_afrotropic", "title": "List of fish species with occurrence in Afrotropical ecoregion", "topics": [ "spp_afrotropic" ] }, { "page": "taxon_data_PhyloMaker", "title": "Data frame with species names needed to assemble the phylogenetic tree", "topics": [ "taxon_data_PhyloMaker" ] }, { "page": "whichFishAdd", "title": "Function to inform which species must be added to the mega-tree phylogeny in the insertion process.", "topics": [ "whichFishAdd" ] } ], "_readme": "https://github.com/GabrielNakamura/FishPhyloMaker/raw/HEAD/README.md", "_rundeps": [ "ape", "backports", "base64enc", "blob", "bslib", "cachem", "checkmate", "cli", "clusterGeneration", "coda", "codetools", "colorspace", "combinat", "cpp11", "crayon", "DBI", "dbplyr", "DEoptim", "deSolve", "digest", "doParallel", "dplyr", "duckdb", "duckdbfs", "evaluate", "expm", "fastmap", "fishtree", "fontawesome", "foreach", "fs", "future", "future.apply", "geiger", "generics", "globals", "glue", "highr", "hms", "htmltools", "igraph", "iterators", "jquerylib", "jsonlite", "knitr", "lattice", "lifecycle", "listenv", "magrittr", "maps", "MASS", "Matrix", "memoise", "mime", "mnormt", "mvtnorm", "ncbit", "nlme", "numDeriv", "optimParallel", "osqp", "parallelly", "phangorn", "phytools", "pillar", "pkgconfig", "prettyunits", "progress", "progressr", "purrr", "R6", "rappdirs", "Rcpp", "RcppArmadillo", "rfishbase", "rlang", "rmarkdown", "S7", "sass", "scatterplot3d", "stringi", "stringr", "subplex", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "withr", "xfun", "xml2", "yaml" ], "_vignettes": [ { "source": "whichFishAdd_vignette.Rmd", "filename": "whichFishAdd_vignette.html", "title": "How to know which species must be added to phylogeny?", "engine": "knitr::rmarkdown", "headings": [], "created": "2021-03-31 23:40:00", "modified": "2021-08-27 21:48:03", "commits": 4 }, { "source": "mappingInsertions_vignette.Rmd", "filename": "mappingInsertions_vignette.html", "title": "How to map species insertions in phylogenetic tree?", "engine": "knitr::rmarkdown", "headings": [], "created": "2021-04-02 14:19:54", "modified": "2021-08-27 21:48:03", "commits": 6 }, { "source": "FishPhyloMaker_vignette.Rmd", "filename": "FishPhyloMaker_vignette.html", "title": "Using FishPhyloMaker to build phylogenies for finned-ray fishes", "engine": "knitr::rmarkdown", "headings": [], "created": "2021-03-30 22:09:02", "modified": "2021-09-08 12:15:00", "commits": 17 } ], "_score": 5.707570176097937, "_indexed": false, "_nocasepkg": "fishphylomaker", "_universes": [ "phylotastic" ], "_indexurl": "https://gabrielnakamura.r-universe.dev/FishPhyloMaker", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.0", "date": "2026-05-10T18:10:15.000Z", "distro": "noble", "commit": "04373d07704296dcf64218dcb9f5afc4f9e06a9f", "fileid": "197c1bfd547efea5bc806a5ed2f637a88d405c64ad781a66ceda96c80a221d04", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25635888180" }, { "r": "4.6.0", "os": "linux", "version": "0.2.0", "date": "2026-05-10T18:10:04.000Z", "distro": "noble", "commit": "04373d07704296dcf64218dcb9f5afc4f9e06a9f", "fileid": "4dfa0ba72fe5f23936e43be23c031b0d58adfed2edf3a5019262e1660fd7fd6e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25635888180" }, { "r": "4.5.3", "os": "mac", "version": "0.2.0", "date": "2026-05-10T18:08:55.000Z", "commit": "04373d07704296dcf64218dcb9f5afc4f9e06a9f", "fileid": "0f6bfc6e95ead0e629afbbd5d0e5a4d43a7c8ff5fc2799a0e78266ace16d886b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25635888180" }, { "r": "4.6.0", "os": "mac", "version": "0.2.0", "date": "2026-05-10T18:09:08.000Z", "commit": "04373d07704296dcf64218dcb9f5afc4f9e06a9f", "fileid": "e2c156269eaf1dc00dd30c2097e8b4eb89513ba572c691a127329e1f8ba79bdb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25635888180" }, { "r": "4.7.0", "os": "win", "version": "0.2.0", "date": "2026-05-10T18:09:03.000Z", "commit": "04373d07704296dcf64218dcb9f5afc4f9e06a9f", "fileid": "62506584057cbf6d61850071b2c5a1f9d9d200975555b1c0b71a1992cc67820e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25635888180" }, { "r": "4.5.3", "os": "win", "version": "0.2.0", "date": "2026-05-10T18:09:00.000Z", "commit": "04373d07704296dcf64218dcb9f5afc4f9e06a9f", "fileid": "b0ba821406e995a6cfed0d9961926df296f43dcf8f345fbc73b372dc9963e731", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25635888180" }, { "r": "4.6.0", "os": "win", "version": "0.2.0", "date": "2026-05-10T18:08:45.000Z", "commit": "04373d07704296dcf64218dcb9f5afc4f9e06a9f", "fileid": "15be9d15acb4c61fd807f244c41941c71710a4eb681b79f9006aa5929861928f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25635888180" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.0", "date": "2026-05-22T12:05:31.000Z", "commit": "04373d07704296dcf64218dcb9f5afc4f9e06a9f", "fileid": "b1f26d0e11244181b7fa97469097a36408679b2a553d7c9a8f09c73c20618b4a", "status": "success", "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/25635888180" } ] }