# Continuous Time Structural Equation Modelling

## Documentation for package ‘ctsem’ version 3.3.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

AnomAuth | AnomAuth
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
ctLongToWide | ctLongToWide Restructures time series / panel data from long format to wide format for ctsem analysis
ctLOO | K fold cross validation for ctStanFit objects
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
ctsem | ctsem
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
ctStanPlot | plot.ctStanFit
ctStanPlotPost | ctStanPlotPost
ctStanPostPredict | Compares model implied density and values to observed, for a ctStanFit object.
ctstantestdat | ctstantestdat
ctstantestfit | ctstantestfit
ctStanTIpredeffects | Get time independent predictor effect estimates
ctStanTIpredMarginal | Plot marginal relationships between covariates and parameters for a ctStanFit object.
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
datastructure | datastructure
extract | Extract samples from a ctStanFit object
inv_logit | Inverse logit
isdiag | Diagnostics for ctsem importance sampling
Kalman | Kalman
log1p_exp | log1p_exp
longexample | longexample
Oscillating | Oscillating
plot.ctKalmanDF | Plots Kalman filter output from ctKalman.
plot.ctsemFitMeasure | Misspecification plot using ctCheckFit output
plot.ctStanFit | plot.ctStanFit
plot.ctStanModel | Prior plotting
sdpcor2cov | sdcor2cov
standatact_specificsubjects | Adjust standata from ctsem to only use specific subjects
stanoptimis | Optimize / importance sample a stan or ctStan model.
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
summary.ctStanFit | summary.ctStanFit
w32chk | Check for non win32