ctsem: Continuous Time Structural Equation Modelling

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 publication2017-01-24 00:38:42
MaintainerCharles Driver <driver@mpib-berlin.mpg.de>
LicenseGPL-3
Version2.2.0
https://github.com/cdriveraus/ctsem

View on CRAN

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

ctExample1: ctExample1

ctExample1TIpred: ctExample1TIpred

ctExample2: ctExample2

ctExample2level: ctExample2level

ctExample3: ctExample3

ctExample4: ctExample4

ctFit: Fit a ctsem object

ctGenerate: ctGenerate

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

ctRefineTo: ctRefineTo

ctsem: ctsem

ctStanContinuousPars: ctStanContinuousPars

ctStanDiscretePars: ctStanDiscretePars

ctStanDiscreteParsPlot: ctStanDiscreteParsPlot

ctStanFit: 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

summary.ctsemFit: Summary function for ctsemFit object

summary.ctsemMultigroupFit: Summary function for ctsemMultigroupFit object

summary.ctStanFit: summary.ctStanFit

Functions

AnomAuth Man page
ctCI Man page
ctCollapse Man page
ctCompareExpected Man page
ctDeintervalise Man page
ctDensity Man page
ctDiscretePars Man page
ctExample1 Man page
ctExample1TIpred Man page
ctExample2 Man page
ctExample2level Man page
ctExample3 Man page
ctExample4 Man page
ctFit Man page
ctGenerate Man page
ctIndplot Man page
ctIntervalise Man page
ctKalman Man page
ctLongToWide Man page
ctModel Man page
ctMultigroupFit Man page
ctPlot Man page
ctPlotArray Man page
ctPoly Man page
ctRefineTo Man page
ctsem Man page
ctsem-package Man page
ctStanContinuousPars Man page
ctStanDiscretePars Man page
ctStanDiscreteParsPlot Man page
ctStanFit Man page
ctStanKalman Man page
ctStanKalmanPlot Man page
ctStanModel Man page
ctStanParnames Man page
ctStanPlot Man page
ctStanPlotPost Man page
ctstantestdat Man page
ctstantestfit Man page
ctStanTIpredeffects Man page
ctWideNames Man page
ctWideToLong Man page
datastructure Man page
inv_logit Man page
longexample Man page
Oscillating Man page
plot.ctsemFit Man page
plot.ctsemMultigroupFit Man page
plot.ctStanFit Man page
plot.ctStanModel Man page
sdpcor2cov Man page
summary.ctsemFit Man page
summary.ctsemMultigroupFit Man page
summary.ctStanFit Man page

Files

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

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