# Continuous Time Structural Equation Modelling

## Documentation for package ‘ctsem’ version 3.11.0

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

## Help Pages

ctsem-package | ctsem
AnomAuth | AnomAuth
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
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
ctFitCovCheck | Visual lagged covariance or correlation diagnostics for ctsem fits.
ctFitCovCheckPlot | ctFitCovCheckPlot
ctFitUpdate | Update a ctStanFit object
ctGenerate | ctGenerate
ctGenerateFromFit | Add a '$generated' object to ctstanfit object, with random data generated from posterior of ctstanfit object
ctGenerateFromPriors | Generate data from a ctstanmodel object
ctIntervalise | Converts absolute times to intervals for wide format ctsem panel data
ctKalman | ctKalman
ctKalmanArray | Get Kalman filter estimates from a ctStanFit object
ctLongToWide | ctLongToWide Restructures time series / panel data from long format to wide format for ctsem analysis
ctLOO | K fold cross validation for ctStanFit objects
ctModel | Define a ctsem model
ctModelConvertOMX | Convert an old OpenMx-style ctsem model to the modern ctsem model format.
ctModelCoverage_check | Coverage Check Function
ctModelHigherOrder | Raise the order of a ctsem type ='omx' model object.
ctModelLatex | Generate and optionally compile latex equation of subject level ctsem model.
ctModelMatrices | Matrix view for ctStanModel objects
ctModelMatrices<- | Matrix view for ctStanModel objects
ctOptimUncertainty | Update optimized ctsem uncertainty estimates
ctPlotArray | Plots three dimensional y values for quantile plots
ctPlotPosterior | ctPlotPosterior
ctPoly | Plots uncertainty bands with shading
ctPostPredData | Create a data.table to compare data generated from a ctsem fit with the original data.
ctPostPredict | Compares model implied density and values to observed, for a ctStanFit object.
ctPostPredPlots | Create diagnostic plots to assess the goodness-of-fit for a ctsem model.
ctPredictTIP | ctPredictTIP
ctRawParnames | ctRawParnames
ctResiduals | Extract Standardized Residuals from a ctsem Fit
ctsem | ctsem
ctStanContinuousPars | ctSummaryMatrices
ctStanDiscretePars | ctDiscretePars
ctStanDiscreteParsPlot | ctDiscreteParsPlot
ctStanFit | Fit a ctsem model
ctStanFitUpdate | Update a ctStanFit object
ctStanGenerate | Generate data from a ctstanmodel object
ctStanGenerateFromFit | Add a '$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 an old OpenMx-style ctsem model to the modern ctsem model format.
ctStanParnames | ctRawParnames
ctStanPlot | plot.ctStanFit
ctStanPlotPost | ctPlotPosterior
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.
ctstantestdat | ctstantestdat
ctstantestfit | ctstantestfit
ctStanTIpredeffects | Get time independent predictor effect estimates
ctStanUpdModel | Update an already compiled and fit ctStanFit object
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
datastructure | datastructure
extract | Extract samples from a ctStanFit object
inv_logit | Inverse logit
log1p_exp | log1p_exp
longexample | longexample
Oscillating | Oscillating
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
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_reinitsf | Quickly initialise stanfit object from model and data
stan_unconstrainsamples | Convert samples from a stanfit object to the unconstrained scale
summary.ctEmpiricalBayesFit | Summarise empirical Bayes subject-wise ctsem fits
summary.ctStanFit | summary.ctStanFit
test_isclose | Tests if 2 values are close to each other