{
  "_id": "6a181a52acfb0bcc41db0b48",
  "Package": "RevGadgets",
  "Type": "Package",
  "Title": "Visualization and Post-Processing of 'RevBayes' Analyses",
  "Version": "1.2.1",
  "Authors@R": "c(\nperson(\"Carrie\", \"Tribble\",\nemail = \"ctribble09@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-7263-7885\")),\nperson(\"Michael R.\", \"May\", role = \"aut\"),\nperson(\"William A.\", \"Freyman\", role = \"aut\"),\nperson(\"Michael J.\", \"Landis\", role = \"aut\"),\nperson(\"Lim Jun\", \"Ying\", role = \"aut\"),\nperson(\"Joelle\", \"Barido-Sottani\", role = \"aut\"),\nperson(\"Andrew\", \"Magee\", role = \"aut\"),\nperson(\"Bjorn Tore\", \"Kopperud\", role = \"aut\"),\nperson(\"Sebastian\", \"Hohna\", role = \"aut\"),\nperson(\"Nagashima\", \"Kengo\", role = \"ctb\"),\nperson(\"Schliep\", \"Klaus\", role = \"ctb\"),\nperson(\"Ronja J.\", \"Billenstein\", role = \"aut\")\n)",
  "Maintainer": "Carrie Tribble <ctribble09@gmail.com>",
  "Description": "Processes and visualizes the output of complex\nphylogenetic analyses from the 'RevBayes' phylogenetic\ngraphical modeling software.",
  "URL": "https://github.com/revbayes/RevGadgets,\nhttps://revbayes.github.io/tutorials/intro/revgadgets",
  "BugReports": "https://github.com/revbayes/RevGadgets/issues",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.2.3",
  "biocViews": "",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libmagick++-dev gsfonts\nlibicu-dev libjpeg-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev",
  "Repository": "https://revbayes.r-universe.dev",
  "Date/Publication": "2023-11-29 23:29:03 UTC",
  "RemoteUrl": "https://github.com/revbayes/revgadgets",
  "RemoteRef": "HEAD",
  "RemoteSha": "2a7ce495aeeb10d9178b640267779ab82b58b122",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-28 10:27:57 UTC",
    "User": "root"
  },
  "Author": "Carrie Tribble [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-7263-7885>),\nMichael R. May [aut],\nWilliam A. Freyman [aut],\nMichael J. Landis [aut],\nLim Jun Ying [aut],\nJoelle Barido-Sottani [aut],\nAndrew Magee [aut],\nBjorn Tore Kopperud [aut],\nSebastian Hohna [aut],\nNagashima Kengo [ctb],\nSchliep Klaus [ctb],\nRonja J. Billenstein [aut]",
  "MD5sum": "4b0524d5c9603ae30493d0af48d2a9d6",
  "_user": "revbayes",
  "_type": "src",
  "_file": "RevGadgets_1.2.1.tar.gz",
  "_fileid": "3b38d101b8fb50da5388cb05ce3c07a4e8a669fa5e75d5de646874d5e80c1138",
  "_filesize": 1062229,
  "_sha256": "3b38d101b8fb50da5388cb05ce3c07a4e8a669fa5e75d5de646874d5e80c1138",
  "_created": "2026-05-28T10:27:57.000Z",
  "_published": "2026-05-28T10:34:58.419Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78271843411,
      "time": 189,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7263600419"
    },
    {
      "job": 78271843299,
      "time": 196,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7263602523"
    },
    {
      "job": 78271843473,
      "time": 357,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7263638946"
    },
    {
      "job": 78271843377,
      "time": 162,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7263582015"
    },
    {
      "job": 78271200913,
      "time": 251,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7263540304"
    },
    {
      "job": 78271843307,
      "time": 165,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7263592387"
    },
    {
      "job": 78271843467,
      "time": 167,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7263593343"
    },
    {
      "job": 78271843336,
      "time": 260,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7263622477"
    },
    {
      "job": 78271843417,
      "time": 168,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7263593624"
    }
  ],
  "_buildurl": "https://github.com/r-universe/revbayes/actions/runs/26569045640",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/revbayes/revgadgets",
  "_commit": {
    "id": "2a7ce495aeeb10d9178b640267779ab82b58b122",
    "author": "Carrie M Tribble <cmt2@hawaii.edu>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #26 from revbayes/development\n\nDevelopment",
    "time": 1701300543
  },
  "_maintainer": {
    "name": "Carrie Tribble",
    "email": "ctribble09@gmail.com",
    "login": "cmt2",
    "description": "Plant phylogeneticist and evolutionary biologist. Interested in underground morphology evolution, climatic niche evolution, and biogeography. ",
    "uuid": 25025386,
    "orcid": "0000-0001-7263-7885"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2.0",
      "role": "Depends"
    },
    {
      "package": "ape",
      "version": ">= 5.4",
      "role": "Imports"
    },
    {
      "package": "phytools",
      "version": ">= 0.7-70",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "version": ">= 1.0.0",
      "role": "Imports"
    },
    {
      "package": "ggtree",
      "version": ">= 3.6.1",
      "role": "Imports"
    },
    {
      "package": "tidytree",
      "version": ">= 0.3.4",
      "role": "Imports"
    },
    {
      "package": "treeio",
      "version": ">= 1.12.0",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.4.0",
      "role": "Imports"
    },
    {
      "package": "reshape",
      "version": ">= 0.8.8",
      "role": "Imports"
    },
    {
      "package": "methods",
      "version": ">= 4.1.0",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "version": ">= 1.1.0",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "version": ">= 3.0.1",
      "role": "Imports"
    },
    {
      "package": "gginnards",
      "version": ">= 0.0.3",
      "role": "Imports"
    },
    {
      "package": "ggplotify",
      "version": ">= 0.0.5",
      "role": "Imports"
    },
    {
      "package": "ggpp",
      "role": "Imports"
    },
    {
      "package": "ggimage",
      "role": "Imports"
    },
    {
      "package": "png",
      "version": ">= 0.1-7",
      "role": "Imports"
    },
    {
      "package": "stats",
      "version": ">= 4.0.1",
      "role": "Imports"
    },
    {
      "package": "utils",
      "version": ">= 4.0.1",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "version": ">= 4.0.1",
      "role": "Imports"
    },
    {
      "package": "deeptime",
      "version": ">= 0.1.0",
      "role": "Imports"
    },
    {
      "package": "scales",
      "version": ">= 1.1.1",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "phangorn",
      "role": "Suggests"
    }
  ],
  "_owner": "revbayes",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 14,
  "_contributors": [
    {
      "user": "mikeryanmay",
      "count": 69,
      "uuid": 4326609
    },
    {
      "user": "kopperud",
      "count": 27,
      "uuid": 18629226
    },
    {
      "user": "wf8",
      "count": 16,
      "uuid": 4967118
    },
    {
      "user": "hoehna",
      "count": 10,
      "uuid": 8191687
    },
    {
      "user": "afmagee",
      "count": 7,
      "uuid": 20982731
    },
    {
      "user": "junyinglim",
      "count": 7,
      "uuid": 3966018
    },
    {
      "user": "mlandis",
      "count": 7,
      "uuid": 438325
    },
    {
      "user": "rbillenstein",
      "count": 7,
      "uuid": 57236170
    },
    {
      "user": "jeremy-andreoletti",
      "count": 6,
      "uuid": 45073058
    },
    {
      "user": "jenna-tb-ekwealor",
      "count": 3,
      "uuid": 16724457
    }
  ],
  "_userbio": {
    "uuid": 8113632,
    "type": "organization",
    "name": "revbayes"
  },
  "_downloads": {
    "count": 275,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RevGadgets"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/revbayes/revgadgets",
  "_searchresults": 266,
  "_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/readme.html",
    "extra/readme.md",
    "extra/RevGadgets.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/revbayes/revgadgets",
  "_realowner": "revbayes",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2021-09-13"
    },
    {
      "version": "1.1.0",
      "date": "2022-12-03"
    },
    {
      "version": "1.1.1",
      "date": "2023-05-25"
    },
    {
      "version": "1.2.0",
      "date": "2023-11-16"
    },
    {
      "version": "1.2.1",
      "date": "2023-11-29"
    }
  ],
  "_exports": [
    "calculateShiftBayesFactor",
    "colFun",
    "combineTraces",
    "densiTreeWithBranchData",
    "dropTip",
    "geom_stepribbon",
    "GeomStepribbon",
    "getMAP",
    "matchNodes",
    "plotAncStatesMAP",
    "plotAncStatesPie",
    "plotDiversityOBDP",
    "plotDivRates",
    "plotFBDTree",
    "plotHiSSE",
    "plotMassExtinctions",
    "plotMuSSE",
    "plotPopSizes",
    "plotPostPredStats",
    "plotTrace",
    "plotTree",
    "posteriorSamplesToParametricPrior",
    "processAncStates",
    "processBranchData",
    "processDivRates",
    "processPopSizes",
    "processPostPredStats",
    "processSSE",
    "readOBDP",
    "readTrace",
    "readTrees",
    "removeBurnin",
    "rerootPhylo",
    "setMRFGlobalScaleHyperpriorNShifts",
    "simulateMRF",
    "summarizeTrace"
  ],
  "_help": [
    {
      "page": "calculateShiftBayesFactor",
      "title": "Bayes Factors in support of a shift in diversification rates over a given time interval.",
      "topics": [
        "calculateShiftBayesFactor"
      ]
    },
    {
      "page": "colFun",
      "title": "Color Function",
      "topics": [
        "colFun"
      ]
    },
    {
      "page": "combineTraces",
      "title": "Combine traces",
      "topics": [
        "combineTraces"
      ]
    },
    {
      "page": "densiTreeWithBranchData",
      "title": "DensiTree-style plot with branch-specific data",
      "topics": [
        "densiTreeWithBranchData"
      ]
    },
    {
      "page": "dropTip",
      "title": "dropTip",
      "topics": [
        "dropTip"
      ]
    },
    {
      "page": "geom_stepribbon",
      "title": "plot geom stepribbon for diversification rates",
      "topics": [
        "GeomStepribbon",
        "geom_stepribbon"
      ]
    },
    {
      "page": "getMAP",
      "title": "get MAP",
      "topics": [
        "getMAP"
      ]
    },
    {
      "page": "matchNodes",
      "title": "match Nodes",
      "topics": [
        "matchNodes"
      ]
    },
    {
      "page": "plotAncStatesMAP",
      "title": "plot Ancestral States MAP",
      "topics": [
        "plotAncStatesMAP"
      ]
    },
    {
      "page": "plotAncStatesPie",
      "title": "plot Ancestral States Pie",
      "topics": [
        "plotAncStatesPie"
      ]
    },
    {
      "page": "plotDiversityOBDP",
      "title": "Plot Diversity Distribution from OBDP Analysis",
      "topics": [
        "plotDiversityOBDP"
      ]
    },
    {
      "page": "plotDivRates",
      "title": "Plot Diversification Rates",
      "topics": [
        "plotDivRates"
      ]
    },
    {
      "page": "plotFBDTree",
      "title": "Plot FBD tree",
      "topics": [
        "plotFBDTree"
      ]
    },
    {
      "page": "plotHiSSE",
      "title": "plotHiSSE",
      "topics": [
        "plotHiSSE"
      ]
    },
    {
      "page": "plotMassExtinctions",
      "title": "Plot Mass Extinction Support",
      "topics": [
        "plotMassExtinctions"
      ]
    },
    {
      "page": "plotMuSSE",
      "title": "plotMuSSE",
      "topics": [
        "plotMuSSE"
      ]
    },
    {
      "page": "plotPopSizes",
      "title": "Plot Population Sizes",
      "topics": [
        "plotPopSizes"
      ]
    },
    {
      "page": "plotPostPredStats",
      "title": "plot Posterior Predictive Statistics",
      "topics": [
        "plotPostPredStats"
      ]
    },
    {
      "page": "plotTrace",
      "title": "Plot trace",
      "topics": [
        "plotTrace"
      ]
    },
    {
      "page": "plotTree",
      "title": "Plot tree",
      "topics": [
        "plotTree"
      ]
    },
    {
      "page": "plotTreeFull",
      "title": "Plot Full tree",
      "topics": [
        "plotTreeFull"
      ]
    },
    {
      "page": "posteriorSamplesToParametricPrior",
      "title": "Priors from MCMC samples",
      "topics": [
        "posteriorSamplesToParametricPrior"
      ]
    },
    {
      "page": "processAncStates",
      "title": "Process Ancestral States",
      "topics": [
        "processAncStates"
      ]
    },
    {
      "page": "processBranchData",
      "title": "processBranchData",
      "topics": [
        "processBranchData"
      ]
    },
    {
      "page": "processDivRates",
      "title": "Process Diversification Rates",
      "topics": [
        "processDivRates"
      ]
    },
    {
      "page": "processPopSizes",
      "title": "Process Population Sizes",
      "topics": [
        "processPopSizes"
      ]
    },
    {
      "page": "processPostPredStats",
      "title": "process Posterior Predictive Statistics",
      "topics": [
        "processPostPredStats"
      ]
    },
    {
      "page": "processSSE",
      "title": "Title",
      "topics": [
        "processSSE"
      ]
    },
    {
      "page": "readOBDP",
      "title": "Read OBDP Outputs",
      "topics": [
        "readOBDP"
      ]
    },
    {
      "page": "readTrace",
      "title": "Read trace",
      "topics": [
        "readTrace"
      ]
    },
    {
      "page": "readTrees",
      "title": "Read trees",
      "topics": [
        "readTrees"
      ]
    },
    {
      "page": "removeBurnin",
      "title": "Remove Burnin",
      "topics": [
        "removeBurnin"
      ]
    },
    {
      "page": "rerootPhylo",
      "title": "Reroot Phylo",
      "topics": [
        "rerootPhylo"
      ]
    },
    {
      "page": "RevGadgets",
      "title": "RevGadgets",
      "topics": [
        "RevGadgets"
      ]
    },
    {
      "page": "setMRFGlobalScaleHyperpriorNShifts",
      "title": "Sets a global scale parameter for a GMRF or HSMRF model given a prior mean number of effective shifts.",
      "topics": [
        "setMRFGlobalScaleHyperpriorNShifts"
      ]
    },
    {
      "page": "simulateMRF",
      "title": "Simulates a single Markov random field trajectory.",
      "topics": [
        "simulateMRF"
      ]
    },
    {
      "page": "summarizeTrace",
      "title": "Summarize trace",
      "topics": [
        "summarizeTrace"
      ]
    }
  ],
  "_readme": "https://github.com/revbayes/revgadgets/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "aplot",
    "base64enc",
    "bslib",
    "cachem",
    "cli",
    "clusterGeneration",
    "coda",
    "codetools",
    "combinat",
    "commonmark",
    "cpp11",
    "curl",
    "deeptime",
    "deeptimedata",
    "DEoptim",
    "digest",
    "doParallel",
    "dplyr",
    "evaluate",
    "expm",
    "farver",
    "fastmap",
    "fastmatch",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
    "fontquiver",
    "foreach",
    "fs",
    "gdtools",
    "generics",
    "ggfittext",
    "ggforce",
    "ggfun",
    "ggh4x",
    "ggimage",
    "gginnards",
    "ggiraph",
    "ggplot2",
    "ggplotify",
    "ggpp",
    "ggtree",
    "glue",
    "gridExtra",
    "gridGraphics",
    "gridtext",
    "grImport2",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "igraph",
    "isoband",
    "iterators",
    "jpeg",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lattice",
    "lazyeval",
    "lifecycle",
    "litedown",
    "lubridate",
    "magick",
    "magrittr",
    "maps",
    "markdown",
    "MASS",
    "Matrix",
    "memoise",
    "mime",
    "mnormt",
    "nlme",
    "numDeriv",
    "optimParallel",
    "patchwork",
    "phangorn",
    "phytools",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "polyclip",
    "polynom",
    "purrr",
    "quadprog",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "reshape",
    "rlang",
    "rmarkdown",
    "S7",
    "sass",
    "scales",
    "scatterplot3d",
    "shades",
    "stringi",
    "stringr",
    "systemfonts",
    "tibble",
    "tidyr",
    "tidyselect",
    "tidytree",
    "timechange",
    "tinytex",
    "treeio",
    "tweenr",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "xfun",
    "XML",
    "xml2",
    "xts",
    "yaml",
    "yulab.utils",
    "zoo"
  ],
  "_score": 6.224222186084649,
  "_indexed": true,
  "_nocasepkg": "revgadgets",
  "_universes": [
    "revbayes",
    "cmt2"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.1",
      "date": "2026-05-28T10:30:40.000Z",
      "distro": "noble",
      "commit": "2a7ce495aeeb10d9178b640267779ab82b58b122",
      "fileid": "3f1bca40f0d55bcc5ba6b5bb15a2d0dedf97820959f6b92cf9f969076c1e0629",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/revbayes/actions/runs/26569045640"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.2.1",
      "date": "2026-05-28T10:30:46.000Z",
      "distro": "noble",
      "commit": "2a7ce495aeeb10d9178b640267779ab82b58b122",
      "fileid": "61fe4db1ce177cf13504075a4b4bed799b04de56e750b1476428e55ff9cf835d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/revbayes/actions/runs/26569045640"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.1",
      "date": "2026-05-28T10:31:53.000Z",
      "commit": "2a7ce495aeeb10d9178b640267779ab82b58b122",
      "fileid": "a103cc878dfe197091241017a12b4827fb92bcfadeeb1c5b84e00c217c58a50a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/revbayes/actions/runs/26569045640"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.2.1",
      "date": "2026-05-28T10:30:02.000Z",
      "commit": "2a7ce495aeeb10d9178b640267779ab82b58b122",
      "fileid": "d328aa4d0d2a685418eacb9047f3760f272639d3b8bf566e104daaf1330331e1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/revbayes/actions/runs/26569045640"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.2.1",
      "date": "2026-05-28T10:31:12.000Z",
      "commit": "2a7ce495aeeb10d9178b640267779ab82b58b122",
      "fileid": "416b9dc71bc2192e8b8364f573fdc20b1f083432bd4294201c69b6d1021b93d1",
      "status": "success",
      "buildurl": "https://github.com/r-universe/revbayes/actions/runs/26569045640"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2.1",
      "date": "2026-05-28T10:29:56.000Z",
      "commit": "2a7ce495aeeb10d9178b640267779ab82b58b122",
      "fileid": "8ae57ccbf0379a9955f2d1ee03e22b7504abd65114a4089ba0cccbd0dd36eed4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/revbayes/actions/runs/26569045640"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.2.1",
      "date": "2026-05-28T10:31:35.000Z",
      "commit": "2a7ce495aeeb10d9178b640267779ab82b58b122",
      "fileid": "a4cc5cfb1ed0267b6a2f6b4abcfa65bda73f6c85a44bcfe73b35b8671c443710",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/revbayes/actions/runs/26569045640"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.2.1",
      "date": "2026-05-28T10:30:07.000Z",
      "commit": "2a7ce495aeeb10d9178b640267779ab82b58b122",
      "fileid": "da12ac81214f215c16846de3733ddd5f3ff16fbdf799a316effe6587ad8343c6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/revbayes/actions/runs/26569045640"
    }
  ]
}