ctsem: Continuous Time Structural Equation Modelling
Version 2.4.0

A multivariate continuous (and discrete) time dynamic modelling package for panel and time series data, using linear stochastic differential equations. Contains a faster frequentist set of functions using OpenMx for single subject and mixed-effects (random intercepts only) structural equation models, or a hierarchical Bayesian implementation using Stan that allows for random effects over all model parameters. Allows for modelling of multiple noisy measurements of multiple stochastic processes, time varying input / event covariates, and time invariant covariates used to predict the parameters.

AuthorCharles Driver [aut, cre, cph], Manuel Voelkle [aut, cph], Han Oud [aut, cph]
Date of publication2017-05-17 19:48:56 UTC
MaintainerCharles Driver <driver@mpib-berlin.mpg.de>
LicenseGPL-3
Version2.4.0
URL https://github.com/cdriveraus/ctsem
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ctsem")

Getting started

README.md

Popular man pages

ctCollapse: ctCollapse Easily collapse an array margin using a specified...
ctDiscretePars: ctDiscretePars
ctFit: Fit a ctsem object
ctModel: Define a ctsem model
ctPlot: ctPlot
ctPoly: Plots uncertainty bands with shading
plot.ctsemMultigroupFit: Plot function for ctsemMultigroupFit object
See all...

All man pages Function index File listing

Man pages

AnomAuth: AnomAuth
ctCI: ctCI Computes confidence intervals on specified parameters /...
ctCollapse: ctCollapse Easily collapse an array margin using a specified...
ctCompareExpected: ctCompareExpected Compares model implied to observed means...
ctDeintervalise: ctDeintervalise
ctDensity: ctDensity
ctDiscretePars: ctDiscretePars
ctDiscretiseData: Discretise long format continuous time (ctsem) data to...
ctExample1: ctExample1
ctExample1TIpred: ctExample1TIpred
ctExample2: ctExample2
ctExample2level: ctExample2level
ctExample3: ctExample3
ctExample4: ctExample4
ctFit: Fit a ctsem object
ctGenerate: ctGenerate
ctGenerateFromFit: Generates data according to the model estimated in a ctsemFit...
ctIndplot: ctIndplot
ctIntervalise: Converts absolute times to intervals for wide format ctsem...
ctKalman: ctKalman
ctLongToWide: ctLongToWide Restructures time series / panel data from long...
ctModel: Define a ctsem model
ctMultigroupFit: Fits a multiple group continuous time model.
ctPlot: ctPlot
ctPlotArray: Plots a three dimensional array
ctPoly: Plots uncertainty bands with shading
ctPostPredict: Posterior predictive type check for ctsemFit.
ctRefineTo: ctRefineTo
ctsem: ctsem
ctStanContinuousPars: ctStanContinuousPars
ctStanDiscretePars: ctStanDiscretePars
ctStanDiscreteParsPlot: ctStanDiscreteParsPlot
ctStanFit: ctStanFit
ctStanFitTV: ctStanFit
ctStanKalman: ctStanKalman
ctStanKalmanPlot: ctStanKalmanPlot
ctStanModel: Convert a frequentist (omx) ctsem model specification to...
ctStanParnames: ctStanParnames
ctStanPlotPost: ctStanPlotPost
ctstantestdat: ctstantestdat
ctstantestfit: ctstantestfit
ctStanTIpredeffects: Get time independent predictor effect estimates
ctWideNames: ctWideNames sets default column names for wide ctsem...
ctWideToLong: ctWideToLong Convert ctsem wide to long format
datastructure: datastructure
inv_logit: Inverse logit
longexample: longexample
Oscillating: Oscillating
plot.ctsemFit: Plotting function for object class ctsemFit
plot.ctsemMultigroupFit: Plot function for ctsemMultigroupFit object
plot.ctStanFit: plot.ctStanFit
plot.ctStanModel: Prior plotting
sdpcor2cov: sdcor2cov
stanWplot: Runs stan, and plots sampling information while sampling.
summary.ctsemFit: Summary function for ctsemFit object
summary.ctsemMultigroupFit: Summary function for ctsemMultigroupFit object
summary.ctStanFit: summary.ctStanFit

Functions

AnomAuth Man page
Oscillating Man page
carefulFit Source code
cseq Source code
ctCI Man page Source code
ctCollapse Man page Source code
ctCompareExpected Man page Source code
ctDeintervalise Man page Source code
ctDensity Man page Source code
ctDiscretePars Man page Source code
ctDiscretiseData Man page Source code
ctExample1 Man page
ctExample1TIpred Man page
ctExample2 Man page
ctExample2level Man page
ctExample3 Man page
ctExample4 Man page
ctFit Man page Source code
ctGenerate Man page Source code
ctGenerateFromFit Man page Source code
ctIndplot Man page Source code
ctIntervalise Man page Source code
ctKalman Man page Source code
ctLabel Source code
ctLongToWide Man page Source code
ctModel Man page Source code
ctMultigroupFit Man page Source code
ctParamsSummary Source code
ctPlot Man page Source code
ctPlotArray Man page Source code
ctPoly Man page Source code
ctPostPredict Man page Source code
ctRefineTo Man page Source code
ctStanContinuousPars Man page Source code
ctStanDiscretePars Man page Source code
ctStanDiscreteParsPlot Man page Source code
ctStanFit Man page Source code
ctStanFitTV Man page Source code
ctStanKalman Man page Source code
ctStanKalmanPlot Man page Source code
ctStanModel Man page Source code
ctStanParnames Man page Source code
ctStanPlot Man page
ctStanPlotPost Man page Source code
ctStanTIpredeffects Man page Source code
ctSummaryMatrices Source code
ctWideNames Man page Source code
ctWideToLong Man page Source code
ctsem Man page
ctsem-package Man page
ctstantestdat Man page
ctstantestfit Man page
datastructure Man page
get_stan_massmat Source code
get_stan_params Source code
indexMatrix Source code
inv_logit Man page Source code
longexample Man page
omxSummary Source code
plot.ctStanFit Man page Source code
plot.ctStanModel Man page Source code
plot.ctsemFit Man page Source code
plot.ctsemMultigroupFit Man page Source code
rl Source code
sdpcor2cov Man page Source code
stanWplot Man page Source code
summary.ctStanFit Man page Source code
summary.ctsemFit Man page Source code
summary.ctsemMultigroupFit Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/ctsem.R
inst/doc/ctsem.rnw
inst/doc/hierarchical.R
inst/doc/hierarchical.rnw
inst/doc/hierarchical.pdf
inst/doc/ctsem.pdf
tests
tests/testthat
tests/testthat/kalmanVram.R
tests/testthat/bayesvsfreqtrait.R
tests/testthat/test-reshaping.R
tests/testthat/differenttraits.R
tests/testthat/test-knownFits.R
tests/testthat/bayesvsfreqtraitdual.R
tests/testthat/test-intervalise.R
tests/testthat/singleprocess.R
tests/testthat/test-objectiveEquiv.R
tests/testthat/ctStanFitTests.R
tests/testthat/bayesvsfreq.R
tests/testthat/bayesvsfreqtraitdualoptim.R
NAMESPACE
NEWS
data
data/longexample.rda
data/ctstantestdat.rda
data/AnomAuth.rda
data/ctExample1.rda
data/ctExample1TIpred.rda
data/ctstantestfit.rda
data/Oscillating.rda
data/ctExample2.rda
data/ctExample4.rda
data/ctExample3.rda
data/datastructure.rda
R
R/ctsem.R
R/ctDeintervalise.R
R/ctDataHelp.R
R/ctStanKalman.R
R/ctLongtowide.r
R/ctModel.R
R/ctGenerateFromFit.R
R/ctDiscretiseData.R
R/ctWideToLong.R
R/ctStanModel.R
R/plot.ctStanFit.R
R/ctDiscretePars.R
R/plot.ctsemFit.R
R/ctPlotArray.R
R/ctRefineTo.R
R/summary.ctsemFit.R
R/carefulFit.R
R/plot.ctStanModel.R
R/ctsemUtils.R
R/ctCompareExpectation.R
R/stanWplot.R
R/ctStanPlotPost.R
R/ctStanFitTV.R
R/sdpcor2cov.R
R/ctIntervalise.R
R/ctLabel.R
R/ctCI.R
R/ctStanSummary.R
R/ctKalman.R
R/ctStanTIpredeffects.R
R/ctFit.R
R/ctGenerate.R
R/ctStanFit.R
R/ctIndplot.R
R/ctPostPredict.R
R/ctMultigroupFit.R
vignettes
vignettes/ctsem.rnw
vignettes/pathdiagramtwoprocessbasic.pdf
vignettes/hierarchical.rnw
vignettes/pathdiagramdiscretecomparison.png
vignettes/hierarchicalreferences.bib
vignettes/references.bib
vignettes/pathdiagramtwoprocessfull2.pdf
vignettes/ctsemrefs.bib
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/ctPoly.Rd
man/ctPostPredict.Rd
man/plot.ctStanFit.Rd
man/plot.ctStanModel.Rd
man/ctPlot.Rd
man/ctLongToWide.Rd
man/ctStanDiscreteParsPlot.Rd
man/ctStanKalman.Rd
man/ctStanPlotPost.Rd
man/ctstantestfit.Rd
man/ctIntervalise.Rd
man/ctDeintervalise.Rd
man/ctStanDiscretePars.Rd
man/ctWideNames.Rd
man/ctMultigroupFit.Rd
man/plot.ctsemMultigroupFit.Rd
man/ctStanContinuousPars.Rd
man/ctPlotArray.Rd
man/ctCI.Rd
man/ctFit.Rd
man/ctExample2.Rd
man/ctStanModel.Rd
man/ctKalman.Rd
man/sdpcor2cov.Rd
man/ctExample2level.Rd
man/summary.ctStanFit.Rd
man/ctModel.Rd
man/ctIndplot.Rd
man/stanWplot.Rd
man/ctDiscretiseData.Rd
man/ctDensity.Rd
man/ctStanFitTV.Rd
man/ctStanParnames.Rd
man/ctDiscretePars.Rd
man/ctsem.Rd
man/ctExample1TIpred.Rd
man/inv_logit.Rd
man/ctExample1.Rd
man/ctWideToLong.Rd
man/ctGenerateFromFit.Rd
man/summary.ctsemMultigroupFit.Rd
man/ctStanKalmanPlot.Rd
man/plot.ctsemFit.Rd
man/ctGenerate.Rd
man/datastructure.Rd
man/ctStanFit.Rd
man/ctExample4.Rd
man/ctCollapse.Rd
man/ctstantestdat.Rd
man/summary.ctsemFit.Rd
man/ctStanTIpredeffects.Rd
man/ctExample3.Rd
man/longexample.Rd
man/ctRefineTo.Rd
man/ctCompareExpected.Rd
man/AnomAuth.Rd
man/Oscillating.Rd
ctsem documentation built on May 19, 2017, 3:53 p.m.

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