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      "title": "ctExample1",
      "object": "ctExample1",
      "class": [
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        "LeisureTime_T3",
        "Happiness_T3",
        "LeisureTime_T4",
        "Happiness_T4",
        "LeisureTime_T5",
        "Happiness_T5",
        "dT1",
        "dT2",
        "dT3",
        "dT4",
        "dT5"
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      "rows": 100,
      "table": true,
      "tojson": true
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    {
      "name": "ctExample1TIpred",
      "title": "ctExample1TIpred",
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        "LeisureTime_T3",
        "Happiness_T3",
        "LeisureTime_T4",
        "Happiness_T4",
        "LeisureTime_T5",
        "Happiness_T5",
        "dT1",
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        "dT4",
        "dT5",
        "NumFriends"
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      "rows": 100,
      "table": true,
      "tojson": true
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      "name": "ctExample2",
      "title": "ctExample2",
      "object": "ctExample2",
      "class": [
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        "array"
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        "LeisureTime_T3",
        "Happiness_T3",
        "LeisureTime_T4",
        "Happiness_T4",
        "LeisureTime_T5",
        "Happiness_T5",
        "LeisureTime_T6",
        "Happiness_T6",
        "LeisureTime_T7",
        "Happiness_T7",
        "MoneyInt_T0",
        "MoneyInt_T1",
        "MoneyInt_T2",
        "MoneyInt_T3",
        "MoneyInt_T4",
        "MoneyInt_T5",
        "MoneyInt_T6",
        "MoneyInt_T7",
        "dT1",
        "dT2",
        "dT3",
        "dT4",
        "dT5",
        "dT6",
        "dT7"
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      "rows": 10,
      "table": true,
      "tojson": true
    },
    {
      "name": "ctExample3",
      "title": "ctExample3",
      "object": "ctExample3",
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        "array"
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      "rows": 1,
      "table": true,
      "tojson": true
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      "title": "ctExample4",
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        "dT1",
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        "dT18",
        "dT19"
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        "TD1",
        "TI1",
        "TI2",
        "TI3"
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      "rows": 300,
      "table": true,
      "tojson": true
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      "name": "ctstantestfit",
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      "class": [
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        "TD1_T0",
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        "dT2",
        "TI1",
        "TI2"
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      "table": true,
      "tojson": true
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        "time",
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        "TD1",
        "TI1",
        "TI2"
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      "rows": 7,
      "table": true,
      "tojson": true
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    {
      "name": "Oscillating",
      "title": "Oscillating",
      "object": "Oscillating",
      "class": [
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      ],
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        "dT8",
        "dT9",
        "dT10"
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      "rows": 200,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ctsem-package",
      "title": "ctsem",
      "topics": [
        "ctsem-package",
        "ctsem"
      ]
    },
    {
      "page": "AnomAuth",
      "title": "AnomAuth",
      "topics": [
        "AnomAuth"
      ]
    },
    {
      "page": "ctACF",
      "title": "Continuous Time Autocorrelation Function (ctACF)",
      "topics": [
        "ctACF"
      ]
    },
    {
      "page": "ctACFresiduals",
      "title": "Calculate Continuous Time Autocorrelation Function (ACF) for Standardized Residuals of ctsem fit.",
      "topics": [
        "ctACFresiduals"
      ]
    },
    {
      "page": "ctCheckFit",
      "title": "Visual model fit diagnostics for ctsem fit objects.",
      "topics": [
        "ctCheckFit"
      ]
    },
    {
      "page": "ctChisqTest",
      "title": "Chi Square test wrapper for ctStanFit objects.",
      "topics": [
        "ctChisqTest"
      ]
    },
    {
      "page": "ctCollapse",
      "title": "ctCollapse Easily collapse an array margin using a specified function.",
      "topics": [
        "ctCollapse"
      ]
    },
    {
      "page": "ctDeintervalise",
      "title": "ctDeintervalise",
      "topics": [
        "ctDeintervalise"
      ]
    },
    {
      "page": "ctDiscretePars",
      "title": "ctDiscretePars",
      "topics": [
        "ctDiscretePars",
        "ctStanDiscretePars"
      ]
    },
    {
      "page": "ctDiscreteParsPlot",
      "title": "ctDiscreteParsPlot",
      "topics": [
        "ctDiscreteParsPlot",
        "ctStanDiscreteParsPlot"
      ]
    },
    {
      "page": "ctDiscretiseData",
      "title": "Discretise long format continuous time (ctsem) data to specific timestep.",
      "topics": [
        "ctDiscretiseData"
      ]
    },
    {
      "page": "ctDocs",
      "title": "Get documentation pdf for ctsem",
      "topics": [
        "ctDocs"
      ]
    },
    {
      "page": "ctEmpiricalBayesFit",
      "title": "Empirical Bayes subject-wise ctsem fits",
      "topics": [
        "ctEmpiricalBayesFit"
      ]
    },
    {
      "page": "ctExample1",
      "title": "ctExample1",
      "topics": [
        "ctExample1"
      ]
    },
    {
      "page": "ctExample1TIpred",
      "title": "ctExample1TIpred",
      "topics": [
        "ctExample1TIpred"
      ]
    },
    {
      "page": "ctExample2",
      "title": "ctExample2",
      "topics": [
        "ctExample2"
      ]
    },
    {
      "page": "ctExample2level",
      "title": "ctExample2level",
      "topics": [
        "ctExample2level"
      ]
    },
    {
      "page": "ctExample3",
      "title": "ctExample3",
      "topics": [
        "ctExample3"
      ]
    },
    {
      "page": "ctExample4",
      "title": "ctExample4",
      "topics": [
        "ctExample4"
      ]
    },
    {
      "page": "ctExtract",
      "title": "Extract samples from a ctStanFit object",
      "topics": [
        "ctExtract",
        "extract"
      ]
    },
    {
      "page": "ctFit",
      "title": "Fit a ctsem model",
      "topics": [
        "ctFit",
        "ctStanFit"
      ]
    },
    {
      "page": "ctFitAddSamples",
      "title": "Sample more values from an optimized ctstanfit object",
      "topics": [
        "ctAddSamples",
        "ctFitAddSamples"
      ]
    },
    {
      "page": "ctFitCovCheck",
      "title": "Visual lagged covariance or correlation diagnostics for ctsem fits.",
      "topics": [
        "ctFitCovCheck"
      ]
    },
    {
      "page": "ctFitCovCheckPlot",
      "title": "ctFitCovCheckPlot",
      "topics": [
        "ctFitCovCheckPlot"
      ]
    },
    {
      "page": "ctFitUpdate",
      "title": "Update a ctStanFit object",
      "topics": [
        "ctFitUpdate",
        "ctStanFitUpdate"
      ]
    },
    {
      "page": "ctFitUpdateModel",
      "title": "Update model/data for an already compiled and fit ctsem object",
      "topics": [
        "ctFitUpdateModel",
        "ctStanUpdModel"
      ]
    },
    {
      "page": "ctGenerate",
      "title": "ctGenerate",
      "topics": [
        "ctGenerate"
      ]
    },
    {
      "page": "ctGenerateFromFit",
      "title": "Add a '$generated' object to ctstanfit object, with random data generated from posterior of ctstanfit object",
      "topics": [
        "ctGenerateFromFit",
        "ctStanGenerateFromFit"
      ]
    },
    {
      "page": "ctGenerateFromPriors",
      "title": "Generate data from a ctstanmodel object",
      "topics": [
        "ctGenerateFromPriors",
        "ctStanGenerate"
      ]
    },
    {
      "page": "ctIntervalise",
      "title": "Converts absolute times to intervals for wide format ctsem panel data",
      "topics": [
        "ctIntervalise"
      ]
    },
    {
      "page": "ctKalmanArray",
      "title": "Get Kalman filter estimates from a ctStanFit object",
      "topics": [
        "ctKalmanArray",
        "ctStanKalman"
      ]
    },
    {
      "page": "ctLongToWide",
      "title": "ctLongToWide Restructures time series / panel data from long format to wide format for ctsem analysis",
      "topics": [
        "ctLongToWide"
      ]
    },
    {
      "page": "ctLOO",
      "title": "K fold cross validation for ctStanFit objects",
      "topics": [
        "ctLOO"
      ]
    },
    {
      "page": "ctModel",
      "title": "Define a ctsem model",
      "topics": [
        "ctModel"
      ]
    },
    {
      "page": "ctModelConvertOMX",
      "title": "Convert an old OpenMx-style ctsem model to the modern ctsem model format.",
      "topics": [
        "ctModelConvertOMX",
        "ctStanModel"
      ]
    },
    {
      "page": "ctModelCoverage_check",
      "title": "Coverage Check Function",
      "topics": [
        "ctModelCoverage_check"
      ]
    },
    {
      "page": "ctModelHigherOrder",
      "title": "Raise the order of a ctsem type ='omx' model object.",
      "topics": [
        "ctModelHigherOrder"
      ]
    },
    {
      "page": "ctModelLatex",
      "title": "Generate and optionally compile latex equation of subject level ctsem model.",
      "topics": [
        "ctModelLatex"
      ]
    },
    {
      "page": "ctModelMatrices",
      "title": "Matrix view for ctStanModel objects",
      "topics": [
        "ctModelMatrices",
        "ctModelMatrices<-"
      ]
    },
    {
      "page": "ctOptimUncertainty",
      "title": "Update optimized ctsem uncertainty estimates",
      "topics": [
        "ctOptimUncertainty"
      ]
    },
    {
      "page": "ctPlotArray",
      "title": "Plots three dimensional y values for quantile plots",
      "topics": [
        "ctPlotArray"
      ]
    },
    {
      "page": "ctPlotPosterior",
      "title": "ctPlotPosterior",
      "topics": [
        "ctPlotPosterior",
        "ctStanPlotPost"
      ]
    },
    {
      "page": "ctPoly",
      "title": "Plots uncertainty bands with shading",
      "topics": [
        "ctPoly"
      ]
    },
    {
      "page": "ctPostPredData",
      "title": "Create a data.table to compare data generated from a ctsem fit with the original data.",
      "topics": [
        "ctPostPredData"
      ]
    },
    {
      "page": "ctPostPredict",
      "title": "Compares model implied density and values to observed, for a ctStanFit object.",
      "topics": [
        "ctPostPredict",
        "ctStanPostPredict"
      ]
    },
    {
      "page": "ctPostPredPlots",
      "title": "Create diagnostic plots to assess the goodness-of-fit for a ctsem model.",
      "topics": [
        "ctPostPredPlots"
      ]
    },
    {
      "page": "ctPredict",
      "title": "ctPredict",
      "topics": [
        "ctKalman",
        "ctPredict"
      ]
    },
    {
      "page": "ctPredictTIP",
      "title": "ctPredictTIP",
      "topics": [
        "ctPredictTIP"
      ]
    },
    {
      "page": "ctRawParnames",
      "title": "ctRawParnames",
      "topics": [
        "ctRawParnames",
        "ctStanParnames"
      ]
    },
    {
      "page": "ctResiduals",
      "title": "Extract Standardized Residuals from a ctsem Fit",
      "topics": [
        "ctResiduals"
      ]
    },
    {
      "page": "ctstantestdat",
      "title": "ctstantestdat",
      "topics": [
        "ctstantestdat"
      ]
    },
    {
      "page": "ctstantestfit",
      "title": "ctstantestfit",
      "topics": [
        "ctstantestfit"
      ]
    },
    {
      "page": "ctSubjectPars",
      "title": "Extract an array of subject specific parameters from a ctStanFit object.",
      "topics": [
        "ctStanSubjectPars",
        "ctSubjectPars"
      ]
    },
    {
      "page": "ctSummaryMatrices",
      "title": "ctSummaryMatrices",
      "topics": [
        "ctStanContinuousPars",
        "ctSummaryMatrices"
      ]
    },
    {
      "page": "ctTIpredEffects",
      "title": "Get time independent predictor effect estimates",
      "topics": [
        "ctStanTIpredeffects",
        "ctTIpredEffects"
      ]
    },
    {
      "page": "ctWideNames",
      "title": "ctWideNames sets default column names for wide ctsem datasets. Primarily intended for internal ctsem usage.",
      "topics": [
        "ctWideNames"
      ]
    },
    {
      "page": "ctWideToLong",
      "title": "ctWideToLong Convert ctsem wide to long format",
      "topics": [
        "ctWideToLong"
      ]
    },
    {
      "page": "datastructure",
      "title": "datastructure",
      "topics": [
        "datastructure"
      ]
    },
    {
      "page": "inv_logit",
      "title": "Inverse logit",
      "topics": [
        "inv_logit"
      ]
    },
    {
      "page": "log1p_exp",
      "title": "log1p_exp",
      "topics": [
        "log1p_exp"
      ]
    },
    {
      "page": "longexample",
      "title": "longexample",
      "topics": [
        "longexample"
      ]
    },
    {
      "page": "Oscillating",
      "title": "Oscillating",
      "topics": [
        "Oscillating"
      ]
    },
    {
      "page": "plot.ctKalmanDF",
      "title": "Plots prediction output from ctPredict.",
      "topics": [
        "plot.ctKalmanDF"
      ]
    },
    {
      "page": "plot.ctStanFit",
      "title": "plot.ctStanFit",
      "topics": [
        "ctStanPlot",
        "plot.ctStanFit"
      ]
    },
    {
      "page": "plot.ctStanModel",
      "title": "Prior plotting",
      "topics": [
        "plot.ctStanModel"
      ]
    },
    {
      "page": "plotctACF",
      "title": "Plot an approximate continuous-time ACF object from ctACF",
      "topics": [
        "plotctACF"
      ]
    },
    {
      "page": "print.summary.ctStanFit",
      "title": "Print ctStanFit summaries",
      "topics": [
        "print.summary.ctStanFit"
      ]
    },
    {
      "page": "sdpcor2cov",
      "title": "sdcor2cov",
      "topics": [
        "sdpcor2cov"
      ]
    },
    {
      "page": "stan_reinitsf",
      "title": "Quickly initialise stanfit object from model and data",
      "topics": [
        "stan_reinitsf"
      ]
    },
    {
      "page": "stan_unconstrainsamples",
      "title": "Convert samples from a stanfit object to the unconstrained scale",
      "topics": [
        "stan_unconstrainsamples"
      ]
    },
    {
      "page": "standatact_specificsubjects",
      "title": "Adjust standata from ctsem to only use specific subjects",
      "topics": [
        "standatact_specificsubjects"
      ]
    },
    {
      "page": "stanoptimis",
      "title": "Optimize / importance sample a stan or ctStan model.",
      "topics": [
        "stanoptimis"
      ]
    },
    {
      "page": "stanWplot",
      "title": "Runs stan, and plots sampling information while sampling.",
      "topics": [
        "stanWplot"
      ]
    },
    {
      "page": "summary.ctEmpiricalBayesFit",
      "title": "Summarise empirical Bayes subject-wise ctsem fits",
      "topics": [
        "summary.ctEmpiricalBayesFit"
      ]
    },
    {
      "page": "summary.ctStanFit",
      "title": "summary.ctStanFit",
      "topics": [
        "summary.ctStanFit"
      ]
    },
    {
      "page": "test_isclose",
      "title": "Tests if 2 values are close to each other",
      "topics": [
        "test_isclose"
      ]
    }
  ],
  "_readme": "https://github.com/cdriveraus/ctsem/raw/HEAD/README.md",
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  "_sysdeps": [
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      "version": "2022.3.0-2",
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