{
  "_id": "6a5014e6c30f0868bbf1f97b",
  "Type": "Package",
  "Package": "TreEvo",
  "Title": "Using ABC to Understand Trait Evolution",
  "Version": "0.22.1",
  "Date": "2023-07-27",
  "Authors@R": "c(person(given = \"Brian\",\nfamily = \"O'Meara\",\nrole = \"aut\",\nemail = \"omeara.brian@gmail.com\"),\nperson(given = \"David\",\nfamily = \"Bapst\",\nrole = c(\"aut\", \"cre\"),\nemail = \"dwbapst@gmail.com\"),\nperson(given = \"Barb\",\nfamily = \"Banbury\",\nrole = \"aut\"))",
  "Maintainer": "Brian C. O'Meara <omeara.brian@gmail.com>",
  "Description": "Various functions for estimating parameters of trait\nevolution in comparative analyses using Approximate Bayesian\nComputation.",
  "License": "GPL",
  "URL": "https://github.com/bomeara/treevo",
  "BugReports": "https://github.com/bomeara/TreEvo/issues",
  "Remotes": [
    "rdpeng/gpclib"
  ],
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "LazyData": "yes",
  "Packaged": {
    "Date": "2026-07-09 21:25:35 UTC",
    "User": "root"
  },
  "RoxygenNote": "7.2.3",
  "Config/pak/sysreqs": "cmake libfreetype6-dev libglpk-dev libglu1-mesa-dev\nlibgmp3-dev make texlive libpng-dev libuv1-dev libxml2-dev\nlibgl1-mesa-dev libssl-dev zlib1g-dev",
  "Repository": "https://phylotastic.r-universe.dev",
  "Date/Publication": "2023-07-27 22:38:09 UTC",
  "RemoteUrl": "https://github.com/bomeara/treevo",
  "RemoteRef": "HEAD",
  "RemoteSha": "f0e13d5bb486b3da0e63e858cd9a00a502fe233d",
  "NeedsCompilation": "no",
  "Author": "Brian O'Meara [aut],\nDavid Bapst [aut, cre],\nBarb Banbury [aut]",
  "_user": "phylotastic",
  "_type": "src",
  "_file": "TreEvo_0.22.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/07fffe35ddaf16cba4ed922a5dcf7ec7b83827219f7d4a79fcf21878585e2e98",
  "_filesize": 1003833,
  "_sha256": "07fffe35ddaf16cba4ed922a5dcf7ec7b83827219f7d4a79fcf21878585e2e98",
  "_expires": "2026-10-17T21:38:45.000Z",
  "_created": "2026-07-09T21:25:35.000Z",
  "_published": "2026-07-09T21:38:46.774Z",
  "_jobs": [
    {
      "job": 86232583155,
      "time": 409,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8212055840"
    },
    {
      "job": 86232583202,
      "time": 410,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8212056455"
    },
    {
      "job": 86232583126,
      "time": 253,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8212173924"
    },
    {
      "job": 86232583137,
      "time": 215,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8212160802"
    },
    {
      "job": 86231564148,
      "time": 323,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8211913374"
    },
    {
      "job": 86232583125,
      "time": 163,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8211969834"
    },
    {
      "job": 86232583170,
      "time": 346,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "WARNING",
      "artifact": "8212033744"
    },
    {
      "job": 86232583154,
      "time": 352,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "WARNING",
      "artifact": "8212035468"
    },
    {
      "job": 86232583242,
      "time": 369,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "8212042509"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051037296",
  "_status": "success",
  "_upstream": "https://github.com/bomeara/treevo",
  "_commit": {
    "id": "f0e13d5bb486b3da0e63e858cd9a00a502fe233d",
    "author": "Brian O'Meara <omeara.brian@gmail.com>",
    "committer": "Brian O'Meara <omeara.brian@gmail.com>",
    "message": "putting doMC back in suggests because of windows issues\n",
    "time": 1690497489
  },
  "_maintainer": {
    "name": "Brian C. OMeara",
    "email": "omeara.brian@gmail.com",
    "login": "bomeara",
    "mastodon": "@omearabrian@mastodon.social",
    "bluesky": "@omearabrian.bsky.social",
    "description": "",
    "uuid": 1612612
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "ape",
      "role": "Depends"
    },
    {
      "package": "coda",
      "role": "Imports"
    },
    {
      "package": "fastmatch",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "partitions",
      "role": "Imports"
    },
    {
      "package": "phylolm",
      "role": "Imports"
    },
    {
      "package": "phytools",
      "role": "Imports"
    },
    {
      "package": "pls",
      "role": "Imports"
    },
    {
      "package": "RcppZiggurat",
      "role": "Imports"
    },
    {
      "package": "rgl",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "corpcor",
      "role": "Imports"
    },
    {
      "package": "mvtnorm",
      "role": "Imports"
    },
    {
      "package": "covr",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "paleotree",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "doMC",
      "role": "Suggests"
    },
    {
      "package": "doParallel",
      "role": "Suggests"
    }
  ],
  "_owner": "bomeara",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 1,
  "_contributors": [
    {
      "user": "dwbapst",
      "count": 494,
      "uuid": 1561903
    },
    {
      "user": "bbanbury",
      "count": 276,
      "uuid": 2235661
    },
    {
      "user": "bomeara",
      "count": 193,
      "uuid": 1612612
    },
    {
      "user": "danjgates",
      "count": 54,
      "uuid": 1730802
    },
    {
      "user": "zwickl",
      "count": 3,
      "uuid": 3407541
    }
  ],
  "_userbio": {
    "uuid": 1652822,
    "type": "organization",
    "name": "phylotastic",
    "followers": 5
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/TreEvo"
  },
  "_devurl": "https://github.com/bomeara/treevo",
  "_searchresults": 71,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/TreEvo.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "autoregressiveIntrinsic",
    "autoregressiveIntrinsicTimeSlices",
    "autoregressiveIntrinsicTimeSlicesConstantMean",
    "autoregressiveIntrinsicTimeSlicesConstantSigma",
    "boundaryIntrinsic",
    "boundaryMaxIntrinsic",
    "boundaryMinIntrinsic",
    "boxcoxTransformation",
    "boxcoxTransformationMatrix",
    "brownianIntrinsic",
    "compareListIPD",
    "doRun_prc",
    "doRun_rej",
    "doSimulation",
    "everyoneDisplacementExtrinsic",
    "ExponentiallyDecayingPushExtrinsic",
    "getBMRatePrior",
    "getTraitBoundsFPK",
    "getUnivariatePosteriorCurve",
    "getUnivariatePriorCurve",
    "highestDensityInterval",
    "landscapeFPK_Intrinsic",
    "maxBoundaryAutoregressiveIntrinsic",
    "minBoundaryAutoregressiveIntrinsic",
    "multiOptimaIntrinsic",
    "nearestNeighborDisplacementExtrinsic",
    "nullExtrinsic",
    "nullIntrinsic",
    "pairwiseESS",
    "pairwiseKS",
    "parallelSimulateWithPriors",
    "parentOffspringPlots",
    "plot_landscapeFPK_model",
    "plotABC_3D",
    "plotPosteriors",
    "plotPrior",
    "plotUnivariatePosteriorVsPrior",
    "PLSTransform",
    "returnPLSModel",
    "simulateWithPriors",
    "summarizePosterior",
    "testMultivarOutlierHDR"
  ],
  "_datasets": [
    {
      "name": "ancStateExample",
      "title": "Example Analysis Output of a Simulated Dataset",
      "object": "simRunExample",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "genRateExample",
      "title": "Example Analysis Output of a Simulated Dataset",
      "object": "simRunExample",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "resultsBMExample",
      "title": "Example Analysis Output of a Simulated Dataset",
      "object": "simRunExample",
      "class": [
        "multiRun_doRun_prc",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "resultsBoundExample",
      "title": "Example Analysis Output of a Simulated Dataset",
      "object": "simRunExample",
      "class": [
        "multiRun_doRun_prc",
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "simCharExample",
      "title": "Example Analysis Output of a Simulated Dataset",
      "object": "simRunExample",
      "class": [
        "data.frame"
      ],
      "fields": [
        "states"
      ],
      "rows": 20,
      "table": true,
      "tojson": true
    },
    {
      "name": "simPhyExample",
      "title": "Example Analysis Output of a Simulated Dataset",
      "object": "simRunExample",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "TreEvo-package",
      "title": "TreEvo-abc for comparative methods",
      "topics": [
        "TreEvo-package",
        "TreEvo",
        "Treevo",
        "treevo"
      ]
    },
    {
      "page": "boxcoxTransformation",
      "title": "Box-Cox Transformation for Simulation Summary Values",
      "topics": [
        "boxcoxTransformation",
        "boxcoxTransformationMatrix"
      ]
    },
    {
      "page": "compareListIPD",
      "title": "Plot Interparticle Distance between Runs",
      "topics": [
        "compareListIPD"
      ]
    },
    {
      "page": "doRun",
      "title": "Run Approximate Bayesian Computation for Phylogenetic Comparative Methods",
      "topics": [
        "doRun",
        "doRun_prc",
        "doRun_rej"
      ]
    },
    {
      "page": "doSimulation",
      "title": "Discrete-Time Character Simulation",
      "topics": [
        "doSimulation"
      ]
    },
    {
      "page": "extrinsicModels",
      "title": "Extrinsic Character Evolution Models",
      "topics": [
        "abcmodels.extrinsic",
        "everyoneDisplacementExtrinsic",
        "ExponentiallyDecayingPushExtrinsic",
        "extrinsicModels",
        "nearestNeighborDisplacementExtrinsic",
        "nullExtrinsic"
      ]
    },
    {
      "page": "getBMRatePrior",
      "title": "Get Brownian Motion Rate Prior",
      "topics": [
        "getBMRatePrior"
      ]
    },
    {
      "page": "highestDensityInterval",
      "title": "Highest Density Interval",
      "topics": [
        "highestDensityInterval"
      ]
    },
    {
      "page": "intrinsicModels",
      "title": "Intrinsic Character Evolution Models",
      "topics": [
        "abcmodels.intrinsic",
        "autoregressiveIntrinsic",
        "autoregressiveIntrinsicTimeSlices",
        "autoregressiveIntrinsicTimeSlicesConstantMean",
        "autoregressiveIntrinsicTimeSlicesConstantSigma",
        "boundaryIntrinsic",
        "boundaryMaxIntrinsic",
        "boundaryMinIntrinsic",
        "brownianIntrinsic",
        "intrinsicModels",
        "maxBoundaryAutoregressiveIntrinsic",
        "minBoundaryAutoregressiveIntrinsic",
        "nullIntrinsic"
      ]
    },
    {
      "page": "landscapeFPK_Intrinsic",
      "title": "Intrinsic Trait Evolution Model for a Macroevolutionary Landscape on a Fokker-Planck-Kolmogorov Potential Surface (Boucher et al., 2018)",
      "topics": [
        "getTraitBoundsFPK",
        "landscapeFPK_Intrinsic",
        "plot_landscapeFPK_model"
      ]
    },
    {
      "page": "methodsPLS",
      "title": "Fitting Univariate Partial Least Squares Models to Free Parameters in ABC",
      "topics": [
        "methodsPLS",
        "PLSTransform",
        "returnPLSModel"
      ]
    },
    {
      "page": "multiOptimaIntrinsic",
      "title": "Single Evolutionary Regime Model with Multiple Optima",
      "topics": [
        "multiOptimaIntrinsic"
      ]
    },
    {
      "page": "pairwiseESS",
      "title": "Pairwise Effective Sample Size",
      "topics": [
        "pairwiseESS"
      ]
    },
    {
      "page": "pairwiseKS",
      "title": "Pairwise Kolmogorov-Smirnov test",
      "topics": [
        "pairwiseKS"
      ]
    },
    {
      "page": "parentOffspringPlots",
      "title": "Plotting Parent-Offspring Particles",
      "topics": [
        "parentOffspringPlots"
      ]
    },
    {
      "page": "plotABC_3D",
      "title": "3D ABCplots",
      "topics": [
        "plotABC_3D"
      ]
    },
    {
      "page": "plotPosteriors",
      "title": "Plot posterior distributions",
      "topics": [
        "plotPosteriors"
      ]
    },
    {
      "page": "plotPriorPost",
      "title": "Plotting, Summarizing and Comparing the Prior and Posterior Distributions",
      "topics": [
        "getUnivariatePosteriorCurve",
        "getUnivariatePriorCurve",
        "plotPrior",
        "plotPriorPost",
        "plotUnivariatePosteriorVsPrior"
      ]
    },
    {
      "page": "simRunExample",
      "title": "Example Analysis Output of a Simulated Dataset",
      "topics": [
        "ancStateExample",
        "genRateExample",
        "resultsBMExample",
        "resultsBoundExample",
        "simCharExample",
        "simPhyExample",
        "simRunExample"
      ]
    },
    {
      "page": "simulateWithPriors",
      "title": "Simulate data for initial TreEvo analysis",
      "topics": [
        "parallelSimulateWithPriors",
        "simulateWithPriors"
      ]
    },
    {
      "page": "summarizePosterior",
      "title": "Summarize Posterior Distribution for a Free Parameter",
      "topics": [
        "summarizePosterior"
      ]
    },
    {
      "page": "testMultivarOutlierHDR",
      "title": "Test If an Outlier Is Within a Highest Density Region of a Multivariate Cloud of Data Points",
      "topics": [
        "testMultivarOutlierHDR"
      ]
    }
  ],
  "_readme": "https://github.com/bomeara/treevo/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "askpass",
    "backports",
    "base64enc",
    "bslib",
    "cachem",
    "checkmate",
    "cli",
    "clusterGeneration",
    "coda",
    "codetools",
    "combinat",
    "corpcor",
    "covr",
    "cpp11",
    "curl",
    "DEoptim",
    "digest",
    "doParallel",
    "evaluate",
    "expm",
    "fastmap",
    "fastmatch",
    "fontawesome",
    "foreach",
    "fs",
    "future",
    "future.apply",
    "generics",
    "globals",
    "glue",
    "gmp",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httr",
    "igraph",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "lattice",
    "lifecycle",
    "listenv",
    "magrittr",
    "maps",
    "MASS",
    "Matrix",
    "memoise",
    "mime",
    "mnormt",
    "mvtnorm",
    "nlme",
    "numDeriv",
    "openssl",
    "optimParallel",
    "osqp",
    "parallelly",
    "partitions",
    "phangorn",
    "phylolm",
    "phytools",
    "pkgconfig",
    "pls",
    "polynom",
    "progressr",
    "R6",
    "rappdirs",
    "rbibutils",
    "Rcpp",
    "RcppArmadillo",
    "RcppGSL",
    "RcppZiggurat",
    "Rdpack",
    "rex",
    "rgl",
    "rlang",
    "rmarkdown",
    "S7",
    "sass",
    "scatterplot3d",
    "sets",
    "sys",
    "tinytex",
    "vctrs",
    "withr",
    "xfun",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "treevo_ABC_vignette.Rmd",
      "filename": "treevo_ABC_vignette.html",
      "title": "Analyzing Trait Evolution with Approximate Bayesian Computation in TreEvo",
      "author": "David W. Bapst",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2017-12-01 01:58:39",
      "modified": "2020-08-20 18:20:34",
      "commits": 5
    }
  ],
  "_score": 4.152288344383057,
  "_indexed": false,
  "_nocasepkg": "treevo",
  "_universes": [
    "phylotastic"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.22.1",
      "date": "2026-07-09T21:28:43.000Z",
      "distro": "resolute",
      "commit": "f0e13d5bb486b3da0e63e858cd9a00a502fe233d",
      "fileid": "https://r2.ropensci.org/cd6a8a1fbc76292eb0cc8d6f94f712f4e4b0de8a2895ed4eb1d6f330090b98c6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051037296"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.22.1",
      "date": "2026-07-09T21:28:46.000Z",
      "distro": "resolute",
      "commit": "f0e13d5bb486b3da0e63e858cd9a00a502fe233d",
      "fileid": "https://r2.ropensci.org/f0f02c5d59946545535813eb7b2102a2b7fdcdaf7e018b890173a730c85ad0e2",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051037296"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.22.1",
      "date": "2026-07-09T21:35:49.000Z",
      "commit": "f0e13d5bb486b3da0e63e858cd9a00a502fe233d",
      "fileid": "https://r2.ropensci.org/1dc023d705d7353727bdf443db1196f01c959c979215b7f9dc5b1a6bde8f62a8",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051037296"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.22.1",
      "date": "2026-07-09T21:35:17.000Z",
      "commit": "f0e13d5bb486b3da0e63e858cd9a00a502fe233d",
      "fileid": "https://r2.ropensci.org/0d5d6ded87c0bb4e9c717adc840223b30a014c4a5e0c7593e8240c3660bef5d6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051037296"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.22.1",
      "date": "2026-07-09T21:28:40.000Z",
      "commit": "f0e13d5bb486b3da0e63e858cd9a00a502fe233d",
      "fileid": "https://r2.ropensci.org/b0fab560753517b2d62a543b95656105da883852eac9d12be4e614995b2ae1c2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051037296"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.22.1",
      "date": "2026-07-09T21:27:07.000Z",
      "commit": "f0e13d5bb486b3da0e63e858cd9a00a502fe233d",
      "fileid": "https://r2.ropensci.org/8ed05547e7c1f02a10503d3de3122916797181c4c737146992129db38cb4c8c6",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051037296"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.22.1",
      "date": "2026-07-09T21:27:09.000Z",
      "commit": "f0e13d5bb486b3da0e63e858cd9a00a502fe233d",
      "fileid": "https://r2.ropensci.org/6c9ed86178aff26907a0bc851f11fa724da3bf4098ae220b53507dbd1024b888",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051037296"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.22.1",
      "date": "2026-07-09T21:27:14.000Z",
      "commit": "f0e13d5bb486b3da0e63e858cd9a00a502fe233d",
      "fileid": "https://r2.ropensci.org/4eef9d2d777fde4aa2bcc318a07fbb43f4c6e032c0954247e2146f9ec5024c47",
      "status": "success",
      "check": "WARNING",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/29051037296"
    }
  ]
}