AnomAuth                AnomAuth
Oscillating             Oscillating
ctACF                   Continuous Time Autocorrelation Function
                        (ctACF)
ctACFresiduals          Calculate Continuous Time Autocorrelation
                        Function (ACF) for Standardized Residuals of
                        ctsem fit.
ctAddSamples            Sample more values from an optimized ctstanfit
                        object
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
ctDensity               ctDensity
ctDiscretiseData        Discretise long format continuous time (ctsem)
                        data to specific timestep.
ctDocs                  Get documentation pdf for ctsem
ctExample1              ctExample1
ctExample1TIpred        ctExample1TIpred
ctExample2              ctExample2
ctExample2level         ctExample2level
ctExample3              ctExample3
ctExample4              ctExample4
ctExtract               Extract samples from a ctStanFit object
ctFit                   ctFit function placeholder
ctFitAuto               ctFitAuto
ctFitAutoGroupModel     ctFitAutoGroupModel
ctFitCovCheck           Visual model-fit diagnostics for ctsem fits,
                        optionally split by the mean of a chosen
                        observed variable.
ctFitCovCheckPlot       ctFitCovCheckPlot
ctFitMultiModel         Fit and summarise a list of ctsem models
ctGenerate              ctGenerate
ctIntervalise           Converts absolute times to intervals for wide
                        format ctsem panel data
ctKalman                ctKalman
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
ctModelCoverage_check   Coverage Check Function
ctModelHigherOrder      Raise the order of a ctsem model object of type
                        'omx'.
ctModelLatex            Generate and optionally compile latex equation
                        of subject level ctsem model.
ctPlotArray             Plots three dimensional y values for quantile
                        plots
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.
ctPredictTIP            ctPredictTIP
ctResiduals             Extract Standardized Residuals from a ctsem Fit
ctStanContinuousPars    ctStanContinuousPars
ctStanDiscretePars      ctStanDiscretePars
ctStanDiscreteParsPlot
                        ctStanDiscreteParsPlot
ctStanFit               ctStanFit
ctStanFitUpdate         Update a ctStanFit object
ctStanGenerate          Generate data from a ctstanmodel object
ctStanGenerateFromFit   Add a '$generated' object to ctstanfit object,
                        with random data generated from posterior of
                        ctstanfit object
ctStanKalman            Get Kalman filter estimates from a ctStanFit
                        object
ctStanModel             Convert a frequentist (omx) ctsem model
                        specification to Bayesian (Stan).
ctStanParnames          ctStanParnames
ctStanPlotPost          ctStanPlotPost
ctStanPostPredict       Compares model implied density and values to
                        observed, for a ctStanFit object.
ctStanSubjectPars       Extract an array of subject specific parameters
                        from a ctStanFit object.
ctStanTIpredeffects     Get time independent predictor effect estimates
ctStanUpdModel          Update an already compiled and fit ctStanFit
                        object
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 Kalman filter output from ctKalman.
plot.ctStanFit          plot.ctStanFit
plot.ctStanModel        Prior plotting
plotctACF               Plot an approximate continuous-time ACF object
                        from ctACF
sdpcor2cov              sdcor2cov
stanWplot               Runs stan, and plots sampling information while
                        sampling.
stan_checkdivergences   Analyse divergences in a stanfit object
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.ctStanFit       summary.ctStanFit
test_isclose            Tests if 2 values are close to each other
