{
  "_id": "6ab0dd0f3d719c1f84083de2",
  "Package": "paleoTS",
  "Title": "Analyze Paleontological Time-Series",
  "Version": "0.6.2",
  "Authors@R": "c(\nperson(\"Gene\", \"Hunt\", email = \"hunte@si.edu\", role = c(\"aut\", \"cre\", \"cph\"), comment = c(ORCID = \"0000-0001-6430-5020\")),\nperson(\"John\", \"Fricks\", email = \"jfricks@asu.edu\", role = \"ctb\") )",
  "Description": "Facilitates analysis of paleontological sequences of trait\nvalues. Functions are provided to fit, using maximum\nlikelihood, simple evolutionary models (including unbiased\nrandom walks, directional evolution,stasis, Ornstein-Uhlenbeck,\ncovariate-tracking) and complex models (punctuation, mode\nshifts).",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.1",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-09-21 07:27:19 UTC",
    "User": "root"
  },
  "Author": "Gene Hunt [aut, cre, cph]\n(<https://orcid.org/0000-0001-6430-5020>), John Fricks [ctb]",
  "Maintainer": "Gene Hunt <hunte@si.edu>",
  "Repository": "https://phylotastic.r-universe.dev",
  "Date/Publication": "2024-09-11 02:53:24 UTC",
  "RemoteUrl": "https://github.com/cran/paleoTS",
  "RemoteRef": "HEAD",
  "RemoteSha": "6fbc4f6fa35ef2c7de73e11b9f6dda8ba73e7bc6",
  "_user": "phylotastic",
  "_type": "src",
  "_file": "paleoTS_0.6.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/73608bf137b0f9afe103f0cdbcd68dd9a8ac8a9fbc809dda245e6560d23d8f40",
  "_filesize": 727347,
  "_sha256": "73608bf137b0f9afe103f0cdbcd68dd9a8ac8a9fbc809dda245e6560d23d8f40",
  "_expires": "2026-12-30T07:30:19.000Z",
  "_created": "2026-09-21T07:27:19.000Z",
  "_published": "2026-09-21T07:30:23.020Z",
  "_jobs": [
    {
      "job": 106248672339,
      "time": 133,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10626946780"
    },
    {
      "job": 106248672417,
      "time": 120,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10627445497"
    },
    {
      "job": 106248672315,
      "time": 100,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10626393057"
    },
    {
      "job": 106248672304,
      "time": 113,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10626783238"
    },
    {
      "job": 106247939145,
      "time": 178,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10627130931"
    },
    {
      "job": 106248672310,
      "time": 115,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "10627395725"
    },
    {
      "job": 106248672460,
      "time": 85,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "10626826711"
    },
    {
      "job": 106248672332,
      "time": 81,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "10627106269"
    },
    {
      "job": 106248672379,
      "time": 80,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "10627096297"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/35572798964",
  "_status": "success",
  "_upstream": "https://github.com/cran/paleoTS",
  "_commit": {
    "id": "6fbc4f6fa35ef2c7de73e11b9f6dda8ba73e7bc6",
    "author": "Gene Hunt <hunte@si.edu>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.6.2\n",
    "time": 1726023204
  },
  "_maintainer": {
    "name": "Gene Hunt",
    "email": "hunte@si.edu",
    "login": "genehunt99",
    "description": "",
    "uuid": 258256960,
    "orcid": "0000-0001-6430-5020"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4.0",
      "role": "Depends"
    },
    {
      "package": "mnormt",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 2,
  "_updates": [],
  "_tags": [],
  "_stars": 1,
  "_contributors": [
    {
      "user": "genehunt99",
      "count": 14,
      "uuid": 258256960
    }
  ],
  "_userbio": {
    "uuid": 1652822,
    "type": "organization",
    "name": "phylotastic",
    "followers": 5
  },
  "_downloads": {
    "count": 596,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/paleoTS"
  },
  "_mentions": 5,
  "_searchresults": 241,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/paleoTS.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_realowner": "genehunt99",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1-1",
      "date": "2006-07-25"
    },
    {
      "version": "0.1-2",
      "date": "2006-12-12"
    },
    {
      "version": "0.1-3",
      "date": "2007-06-18"
    },
    {
      "version": "0.2-1",
      "date": "2007-10-11"
    },
    {
      "version": "0.3-1",
      "date": "2008-05-25"
    },
    {
      "version": "0.3-2",
      "date": "2010-05-08"
    },
    {
      "version": "0.3-3",
      "date": "2010-08-31"
    },
    {
      "version": "0.4-1",
      "date": "2011-03-15"
    },
    {
      "version": "0.4-2",
      "date": "2011-12-22"
    },
    {
      "version": "0.4-3",
      "date": "2012-04-05"
    },
    {
      "version": "0.4-4",
      "date": "2012-06-12"
    },
    {
      "version": "0.5-1",
      "date": "2015-12-01"
    },
    {
      "version": "0.5.2",
      "date": "2019-03-12"
    },
    {
      "version": "0.5.3",
      "date": "2022-08-08"
    },
    {
      "version": "0.6.1",
      "date": "2024-06-06"
    },
    {
      "version": "0.6.2",
      "date": "2024-09-10"
    }
  ],
  "_exports": [
    "akaike.wts",
    "as.paleoTS",
    "as.paleoTSfit",
    "bootSimpleComplex",
    "checkSSMresiduals",
    "compareModels",
    "ESD",
    "fit.sgs",
    "fit3models",
    "fit4models",
    "fit9models",
    "fitGpunc",
    "fitModeShift",
    "fitMult",
    "fitSimple",
    "IC",
    "Kfiltertv",
    "ln.paleoTS",
    "LRI",
    "lynchD",
    "mle.GRW",
    "mle.Stasis",
    "mle.URW",
    "opt.covTrack",
    "opt.GRW",
    "opt.GRW.shift",
    "opt.joint.covTrack",
    "opt.joint.GRW",
    "opt.joint.OU",
    "opt.joint.punc",
    "opt.joint.Stasis",
    "opt.joint.StrictStasis",
    "opt.joint.URW",
    "opt.punc",
    "opt.ssm.ACDC",
    "opt.ssm.covOU",
    "opt.ssm.covOU_vshift",
    "opt.ssm.GRW",
    "opt.ssm.OU",
    "opt.ssm.Stasis",
    "opt.ssm.StrictStasis",
    "opt.ssm.URW",
    "opt.ssm.URWshift",
    "opt.Stasis",
    "opt.StrictStasis",
    "opt.URW",
    "pool.var",
    "read.paleoTS",
    "sim.covTrack",
    "sim.GRW",
    "sim.GRW.shift",
    "sim.OU",
    "sim.punc",
    "sim.sgs",
    "sim.Stasis",
    "sim.Stasis.RW",
    "std.paleoTS",
    "sub.paleoTS",
    "test.var.het"
  ],
  "_datasets": [
    {
      "name": "cantius_L",
      "title": "Time-series of the length of lower first molar for the Cantius lineage",
      "object": "cantius_L",
      "class": [
        "paleoTS"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "dorsal.spines",
      "title": "Time-series of dorsal spine data from a fossil stickleback lineage",
      "object": "dorsal.spines",
      "class": [
        "paleoTS"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "akaike.wts",
      "title": "Compute Akaike weights from AIC scores",
      "topics": [
        "akaike.wts"
      ]
    },
    {
      "page": "as.paleoTS",
      "title": "Make a Paleontological Time-series object",
      "topics": [
        "as.paleoTS"
      ]
    },
    {
      "page": "as.paleoTSfit",
      "title": "Create a 'paleoTSfit' object",
      "topics": [
        "as.paleoTSfit"
      ]
    },
    {
      "page": "bootSimpleComplex",
      "title": "Bootstrap test to see if a complex model is significantly better than a simple model.",
      "topics": [
        "bootSimpleComplex"
      ]
    },
    {
      "page": "cantius_L",
      "title": "Time-series of the length of lower first molar for the Cantius lineage",
      "topics": [
        "cantius_L"
      ]
    },
    {
      "page": "checkSSMresiduals",
      "title": "Compute and (optionally) plot residuals from SSM model fit",
      "topics": [
        "checkSSMresiduals"
      ]
    },
    {
      "page": "compareModels",
      "title": "Compare model fits for a paleontological time-series",
      "topics": [
        "compareModels"
      ]
    },
    {
      "page": "dorsal.spines",
      "title": "Time-series of dorsal spine data from a fossil stickleback lineage",
      "topics": [
        "dorsal.spines"
      ]
    },
    {
      "page": "ESD",
      "title": "Compute Expected Squared Divergence (ESD) for Evolutionary Models",
      "topics": [
        "ESD"
      ]
    },
    {
      "page": "fit.sgs",
      "title": "Fit a model of trait evolution with a protracted punctuation.",
      "topics": [
        "fit.sgs"
      ]
    },
    {
      "page": "fit3models",
      "title": "Fit a set of standard evolutionary models",
      "topics": [
        "fit3models",
        "fit4models"
      ]
    },
    {
      "page": "fit9models",
      "title": "Fit large set of models to a time-series",
      "topics": [
        "fit9models"
      ]
    },
    {
      "page": "fitGpunc",
      "title": "Fit trait evolution model with punctuations estimated from the data",
      "topics": [
        "fitGpunc"
      ]
    },
    {
      "page": "fitModeShift",
      "title": "Fit model in which the mode of trait evolution shifts once",
      "topics": [
        "fitModeShift"
      ]
    },
    {
      "page": "fitMult",
      "title": "Fit the same simple model across multiple time-series",
      "topics": [
        "fitMult"
      ]
    },
    {
      "page": "fitSimple",
      "title": "Fit simple models of trait evolution",
      "topics": [
        "fitSimple"
      ]
    },
    {
      "page": "IC",
      "title": "Compute Information Criteria",
      "topics": [
        "IC"
      ]
    },
    {
      "page": "Kfiltertv",
      "title": "Time-varying Kalman filter calculations",
      "topics": [
        "Kfiltertv"
      ]
    },
    {
      "page": "ln.paleoTS",
      "title": "Approximate log-transformation of time-series data",
      "topics": [
        "ln.paleoTS"
      ]
    },
    {
      "page": "LRI",
      "title": "Log-rate, Log-interval (LRI) method of Gingerich",
      "topics": [
        "LRI"
      ]
    },
    {
      "page": "lynchD",
      "title": "Compute Lynch's Delta rate metric",
      "topics": [
        "lynchD"
      ]
    },
    {
      "page": "mle.GRW",
      "title": "Analytical ML estimator for random walk and stasis models",
      "topics": [
        "mle.GRW",
        "mle.Stasis",
        "mle.URW"
      ]
    },
    {
      "page": "opt.covTrack",
      "title": "Fit a model in which a trait tracks a covariate",
      "topics": [
        "opt.covTrack",
        "opt.joint.covTrack"
      ]
    },
    {
      "page": "opt.GRW",
      "title": "Fit evolutionary model using \"AD\" parameterization",
      "topics": [
        "opt.GRW",
        "opt.Stasis",
        "opt.StrictStasis",
        "opt.URW"
      ]
    },
    {
      "page": "opt.GRW.shift",
      "title": "Fit random walk model with shift(s) in generating parameters",
      "topics": [
        "opt.GRW.shift"
      ]
    },
    {
      "page": "opt.joint.GRW",
      "title": "Fit evolutionary models using the \"Joint\" parameterization",
      "topics": [
        "opt.joint.GRW",
        "opt.joint.Stasis",
        "opt.joint.StrictStasis",
        "opt.joint.URW"
      ]
    },
    {
      "page": "opt.joint.OU",
      "title": "Fit Ornstein-Uhlenbeck model using the \"Joint\" parameterization",
      "topics": [
        "opt.joint.OU"
      ]
    },
    {
      "page": "opt.punc",
      "title": "Fit a model of trait evolution with specified punctuation(s)",
      "topics": [
        "opt.joint.punc",
        "opt.punc"
      ]
    },
    {
      "page": "opt.ssm.GRW",
      "title": "Fit evolutionary models using state-space models (SSM)",
      "topics": [
        "opt.ssm.ACDC",
        "opt.ssm.covOU",
        "opt.ssm.covOU_vshift",
        "opt.ssm.GRW",
        "opt.ssm.OU",
        "opt.ssm.Stasis",
        "opt.ssm.StrictStasis",
        "opt.ssm.URW",
        "opt.ssm.URWshift"
      ]
    },
    {
      "page": "plot.paleoTS",
      "title": "Plot a paleoTS object",
      "topics": [
        "plot.paleoTS"
      ]
    },
    {
      "page": "pool.var",
      "title": "Compute a pooled variance",
      "topics": [
        "pool.var"
      ]
    },
    {
      "page": "print.paleoTSfit",
      "title": "Print a paleoTSfit object",
      "topics": [
        "print.paleoTSfit"
      ]
    },
    {
      "page": "read.paleoTS",
      "title": "Read a text-file with data from a paleontological time-series",
      "topics": [
        "read.paleoTS"
      ]
    },
    {
      "page": "sim.covTrack",
      "title": "Simulate trait evolution that tracks a covariate",
      "topics": [
        "sim.covTrack"
      ]
    },
    {
      "page": "sim.GRW",
      "title": "Simulate random walk or directional time-series for trait evolution",
      "topics": [
        "sim.GRW"
      ]
    },
    {
      "page": "sim.GRW.shift",
      "title": "Simulate (general) random walk with shift(s) in generating parameters",
      "topics": [
        "sim.GRW.shift"
      ]
    },
    {
      "page": "sim.OU",
      "title": "Simulate an Ornstein-Uhlenbeck time-series",
      "topics": [
        "sim.OU"
      ]
    },
    {
      "page": "sim.punc",
      "title": "Simulate a punctuated time-series",
      "topics": [
        "sim.punc"
      ]
    },
    {
      "page": "sim.sgs",
      "title": "Simulate protracted punctuation",
      "topics": [
        "sim.sgs"
      ]
    },
    {
      "page": "sim.Stasis",
      "title": "Simulate Stasis time-series for trait evolution",
      "topics": [
        "sim.Stasis"
      ]
    },
    {
      "page": "sim.Stasis.RW",
      "title": "Simulate trait evolution with a mode shift",
      "topics": [
        "sim.Stasis.RW"
      ]
    },
    {
      "page": "std.paleoTS",
      "title": "Convert time-series to standard deviation units",
      "topics": [
        "std.paleoTS"
      ]
    },
    {
      "page": "sub.paleoTS",
      "title": "Subsample a paleontological time-series",
      "topics": [
        "sub.paleoTS"
      ]
    },
    {
      "page": "test.var.het",
      "title": "Test for heterogeneity of variances among samples in a time-series",
      "topics": [
        "test.var.het"
      ]
    }
  ],
  "_readme": "https://github.com/cran/paleoTS/raw/HEAD/README.md",
  "_rundeps": [
    "codetools",
    "doParallel",
    "foreach",
    "iterators",
    "mnormt"
  ],
  "_vignettes": [
    {
      "source": "paleoTS_basics.Rmd",
      "filename": "paleoTS_basics.html",
      "title": "Basics of paleoTS",
      "author": "Gene Hunt",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Getting data into paleoTS",
        "Fitting models",
        "An Empirical Example: Bell's stickleback data",
        "Joint versus AD parameterization",
        "References"
      ],
      "created": "2019-03-12 19:10:03",
      "modified": "2024-06-07 02:44:46",
      "commits": 3
    }
  ],
  "_score": 5.55810830163055,
  "_indexed": false,
  "_nocasepkg": "paleots",
  "_universes": [
    "phylotastic"
  ],
  "_indexurl": "https://genehunt99.r-universe.dev/paleoTS",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.6.2",
      "date": "2026-09-21T07:29:36.000Z",
      "distro": "resolute",
      "commit": "6fbc4f6fa35ef2c7de73e11b9f6dda8ba73e7bc6",
      "fileid": "https://r2.ropensci.org/a96e825b8ea31b457251fe7dfc12c2979a984e320577b3785aaf8880bf9f3ba3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/35572798964"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.6.2",
      "date": "2026-09-21T07:29:23.000Z",
      "distro": "resolute",
      "commit": "6fbc4f6fa35ef2c7de73e11b9f6dda8ba73e7bc6",
      "fileid": "https://r2.ropensci.org/3bf88b575d64a451d9a2f7265233a9b53c74b891b3e0406544934c17785b41d2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/35572798964"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.6.2",
      "date": "2026-09-21T07:29:07.000Z",
      "commit": "6fbc4f6fa35ef2c7de73e11b9f6dda8ba73e7bc6",
      "fileid": "https://r2.ropensci.org/4de52601a9538e1432aabc5eadad6940387befcbf8d16fb1bfb25ac9d80227b7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/35572798964"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.6.2",
      "date": "2026-09-21T07:29:15.000Z",
      "commit": "6fbc4f6fa35ef2c7de73e11b9f6dda8ba73e7bc6",
      "fileid": "https://r2.ropensci.org/99c0f5620d6cfa5abfbd9a5e2c3a6ddece51abd473ec6ff750b58199411d9074",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/35572798964"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.6.2",
      "date": "2026-09-21T07:29:34.000Z",
      "commit": "6fbc4f6fa35ef2c7de73e11b9f6dda8ba73e7bc6",
      "fileid": "https://r2.ropensci.org/217d0c4fcd535e51389756afdde38301256809ce922fe9815f60f0be0e6e4990",
      "status": "success",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/35572798964"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.6.2",
      "date": "2026-09-21T07:28:37.000Z",
      "commit": "6fbc4f6fa35ef2c7de73e11b9f6dda8ba73e7bc6",
      "fileid": "https://r2.ropensci.org/a45e2ccccb710898dedc0813b77223d1ccb10bc68cb3bce28a41832353d52298",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/35572798964"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.6.2",
      "date": "2026-09-21T07:28:36.000Z",
      "commit": "6fbc4f6fa35ef2c7de73e11b9f6dda8ba73e7bc6",
      "fileid": "https://r2.ropensci.org/867caae4c92aa065aa90d57373504419943f5b25d2cecf936048bd39bd5b374e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/35572798964"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.6.2",
      "date": "2026-09-21T07:28:34.000Z",
      "commit": "6fbc4f6fa35ef2c7de73e11b9f6dda8ba73e7bc6",
      "fileid": "https://r2.ropensci.org/5e6858b44826bd99dc4ce8f32955571cdcc826699b726725c5ffa1fc2a6dc148",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/phylotastic/actions/runs/35572798964"
    }
  ]
}