AnomAuth                AnomAuth
Oscillating             Oscillating
ctACF                   Continuous Time Autocorrelation Function
                        (ctACF)
ctACFresiduals          Calculate Continuous Time Autocorrelation
                        Function (ACF) for Standardized Residuals of
                        ctsem fit.
ctCheckFit              Visual model fit diagnostics for ctsem fit
                        objects.
ctChisqTest             Chi Square test wrapper for ctStanFit objects.
ctCollapse              ctCollapse Easily collapse an array margin
                        using a specified function.
ctDeintervalise         ctDeintervalise
ctDiscretePars          ctDiscretePars
ctDiscreteParsPlot      ctDiscreteParsPlot
ctDiscretiseData        Discretise long format continuous time (ctsem)
                        data to specific timestep.
ctDocs                  Get documentation pdf for ctsem
ctEmpiricalBayesFit     Empirical Bayes subject-wise ctsem fits
ctExample1              ctExample1
ctExample1TIpred        ctExample1TIpred
ctExample2              ctExample2
ctExample2level         ctExample2level
ctExample3              ctExample3
ctExample4              ctExample4
ctExtract               Extract samples from a ctStanFit object
ctFit                   Fit a ctsem model
ctFitAddSamples         Sample more values from an optimized ctstanfit
                        object
ctFitCovCheck           Visual lagged covariance or correlation
                        diagnostics for ctsem fits.
ctFitCovCheckPlot       ctFitCovCheckPlot
ctFitUpdate             Update a ctStanFit object
ctFitUpdateModel        Update model/data for an already compiled and
                        fit ctsem object
ctGenerate              ctGenerate
ctGenerateFromFit       Add a '$generated' object to ctstanfit object,
                        with random data generated from posterior of
                        ctstanfit object
ctGenerateFromPriors    Generate data from a ctstanmodel object
ctIntervalise           Converts absolute times to intervals for wide
                        format ctsem panel data
ctKalmanArray           Get Kalman filter estimates from a ctStanFit
                        object
ctLOO                   K fold cross validation for ctStanFit objects
ctLongToWide            ctLongToWide Restructures time series / panel
                        data from long format to wide format for ctsem
                        analysis
ctModel                 Define a ctsem model
ctModelConvertOMX       Convert an old OpenMx-style ctsem model to the
                        modern ctsem model format.
ctModelCoverage_check   Coverage Check Function
ctModelHigherOrder      Raise the order of a ctsem type ='omx' model
                        object.
ctModelLatex            Generate and optionally compile latex equation
                        of subject level ctsem model.
ctModelMatrices         Matrix view for ctStanModel objects
ctOptimUncertainty      Update optimized ctsem uncertainty estimates
ctPlotArray             Plots three dimensional y values for quantile
                        plots
ctPlotPosterior         ctPlotPosterior
ctPoly                  Plots uncertainty bands with shading
ctPostPredData          Create a data.table to compare data generated
                        from a ctsem fit with the original data.
ctPostPredPlots         Create diagnostic plots to assess the
                        goodness-of-fit for a ctsem model.
ctPostPredict           Compares model implied density and values to
                        observed, for a ctStanFit object.
ctPredict               ctPredict
ctPredictTIP            ctPredictTIP
ctRawParnames           ctRawParnames
ctResiduals             Extract Standardized Residuals from a ctsem Fit
ctSubjectPars           Extract an array of subject specific parameters
                        from a ctStanFit object.
ctSummaryMatrices       ctSummaryMatrices
ctTIpredEffects         Get time independent predictor effect estimates
ctWideNames             ctWideNames sets default column names for wide
                        ctsem datasets. Primarily intended for internal
                        ctsem usage.
ctWideToLong            ctWideToLong Convert ctsem wide to long format
ctsem-package           ctsem
ctstantestdat           ctstantestdat
ctstantestfit           ctstantestfit
datastructure           datastructure
inv_logit               Inverse logit
log1p_exp               log1p_exp
longexample             longexample
plot.ctKalmanDF         Plots prediction output from ctPredict.
plot.ctStanFit          plot.ctStanFit
plot.ctStanModel        Prior plotting
plotctACF               Plot an approximate continuous-time ACF object
                        from ctACF
print.summary.ctStanFit
                        Print ctStanFit summaries
sdpcor2cov              sdcor2cov
stanWplot               Runs stan, and plots sampling information while
                        sampling.
stan_reinitsf           Quickly initialise stanfit object from model
                        and data
stan_unconstrainsamples
                        Convert samples from a stanfit object to the
                        unconstrained scale
standatact_specificsubjects
                        Adjust standata from ctsem to only use specific
                        subjects
stanoptimis             Optimize / importance sample a stan or ctStan
                        model.
summary.ctEmpiricalBayesFit
                        Summarise empirical Bayes subject-wise ctsem
                        fits
summary.ctStanFit       summary.ctStanFit
test_isclose            Tests if 2 values are close to each other
