Continuous Time Structural Equation Modelling


[Up] [Top]

Documentation for package ‘ctsem’ version 3.9.1

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
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
ctPostPredData Create a data.table to compare data generated from a ctsem fit with the original data.
ctPostPredPlots Create diagnostic plots to assess the goodness-of-fit for a ctsem model.
ctResiduals Extract Standardized Residuals from a ctsem Fit
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_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