AnomAuth                AnomAuth
Kalman                  Kalman
Oscillating             Oscillating
ctCheckFit              Check absolute fit of ctFit or ctStanFit
                        object.
ctCollapse              ctCollapse Easily collapse an array margin
                        using a specified function.
ctDeintervalise         ctDeintervalise
ctDensity               ctDensity
ctDiscretePars          ctDiscretePars
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
ctGenerate              ctGenerate
ctIndplot               ctIndplot
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
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
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).
ctStanParMatrices       Returns population system matrices from a
                        ctStanFit object, and vector of values for free
                        parameters.
ctStanParnames          ctStanParnames
ctStanPlotPost          ctStanPlotPost
ctStanPostPredict       Compares model implied density and values to
                        observed, for a ctStanFit object.
ctStanTIpredMarginal    Plot marginal relationships between covariates
                        and parameters for 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                   ctsem
ctstantestdat           ctstantestdat
ctstantestfit           ctstantestfit
datastructure           datastructure
inv_logit               Inverse logit
isdiag                  Diagnostics for ctsem importance sampling
log1p_exp               log1p_exp
longexample             longexample
plot.ctKalmanDF         Plots Kalman filter output from ctKalman.
plot.ctStanFit          plot.ctStanFit
plot.ctStanModel        Prior plotting
plot.ctsemFitMeasure    Misspecification plot using ctCheckFit output
sdpcor2cov              sdcor2cov
stanWplot               Runs stan, and plots sampling information while
                        sampling.
stan_checkdivergences   Analyse divergences in a stanfit object
stan_postcalc           Compute functions of matrices from samples of 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
w32chk                  Check for non win32
