Continuous Time Structural Equation Modelling

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Documentation for package ‘ctsem’ version 3.8.1

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

Help Pages

ctsem-package	ctsem
AnomAuth	AnomAuth
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
ctFitMultiModel	Fit and summarise a list of ctsem models
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).
ctStanParnames	ctStanParnames
ctStanPlot	plot.ctStanFit
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.
ctstantestdat	ctstantestdat
ctstantestfit	ctstantestfit
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
datastructure	datastructure
extract	Extract samples from a ctStanFit object
inv_logit	Inverse logit
isdiag	Diagnostics for ctsem importance sampling
log1p_exp	log1p_exp
longexample	longexample
Oscillating	Oscillating
plot.ctKalmanDF	Plots Kalman filter output from ctKalman.
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