{
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  "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",
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  "RoxygenNote": "7.3.1",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-23 06:59:15 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",
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  "MD5sum": "2c8243aa94d04f3f69a1d231d09a1129",
  "_user": "phylotastic",
  "_type": "src",
  "_file": "paleoTS_0.6.2.tar.gz",
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  "_created": "2026-06-23T06:59:15.000Z",
  "_published": "2026-06-23T07:01:53.318Z",
  "_distro": "noble",
  "_jobs": [
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  "_buildurl": "https://github.com/r-universe/phylotastic/actions/runs/28008200135",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_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"
  },
  "_registered": true,
  "_dependencies": [
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      "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": 396,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/paleoTS"
  },
  "_mentions": 5,
  "_searchresults": 242,
  "_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/paleoTS.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_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": [
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    "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",
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  "_nocasepkg": "paleots",
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