Continuous Time Structural Equation Modelling

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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