TreeBUGS: Hierarchical Multinomial Processing Tree Modeling

User-friendly analysis of hierarchical multinomial processing tree (MPT) models that are often used in cognitive psychology. Implements the latent-trait MPT approach (Klauer, 2010) <DOI:10.1007/s11336-009-9141-0> and the beta-MPT approach (Smith & Batchelder, 2010) <DOI:10.1016/j.jmp.2009.06.007> to model heterogeneity of participants. MPT models are conveniently specified by an .eqn-file as used by other MPT software and data are provided by a .csv-file or directly in R. Models are either fitted by calling JAGS or by an MPT-tailored Gibbs sampler in C++ (only for nonhierarchical and beta MPT models). Provides tests of heterogeneity and MPT-tailored summaries and plotting functions.

Install the latest version of this package by entering the following in R:
install.packages("TreeBUGS")
AuthorDaniel Heck [aut, cre], Nina Arnold [aut, dtc], Denis Arnold [aut], Alexander Ly [ctb]
Date of publication2017-04-01 15:40:29 UTC
MaintainerDaniel Heck <heck@uni-mannheim.de>
LicenseGPL-2
Version1.1.0
https://github.com/denis-arnold/TreeBUGS

View on CRAN

Man pages

arnold2013: Data of a Source-Monitoring Experiment

BayesFactorMPT: Bayes Factors for Simple (Nonhierarchical) MPT Models

betaMPT: Fit a Hierarchical Beta-MPT Model

betaMPTcpp: C++ Sampler for Hierarchical Beta-MPT Model

betweenSubjectMPT: Between-Subject Comparison of Parameters

correlationPosterior: Posterior Distribution for Correlations

extendMPT: Extend MCMC Sampling for MPT Model

genBetaMPT: Generate Data for Beta MPT Models

genMPT: Generate MPT Frequencies

genTraitMPT: Generate Data for Trait MPT Models

getGroupMeans: Get Mean Group Estimates

getParam: Get Parameter Posterior Statistics

marginalMPT: Marginal Likelihood for Simple MPT

plot: Plot Convergence for Hierarchical MPT Models

plotDistribution: Plot Distribution of Individual Estimates

plotFit: Plot Posterior Predictive Mean Frequencies

plotFreq: Plot Raw Frequencies

plotParam: Plot Parameter Estimates

plotPrior: Plot Prior Distributions

plotPriorPost: Plot Prior vs. Posterior Distribution

posteriorPredictive: Get Posterior Predictive Samples

PPP: Compute Posterior Predictive P-Values

priorPredictive: Prior Predictive Samples

probitInverse: Probit-Inverse of Group-Level Normal Distribution

readEQN: Read multiTree files

simpleMPT: C++ Sampler for Standard (Nonhierarchical) MPT Models

summarizeMCMC: MCMC Summary

summarizeMPT: Summarize JAGS Output for Hierarchical MPT Models

testHetChi: Chi-Square Test of Heterogeneity

testHetPerm: Permutation Test of Heterogeneity

traitMPT: Fit a Hierarchical Latent-trait MPT Model

transformedParameters: Get Transformed Parameters

TreeBUGS-package: TreeBUGS: Hierarchical Multinomial Processing Tree Modeling

withinSubjectEQN: Make Within-Subject EQN Files

Functions

arnold2013 Man page
BayesFactorMPT Man page
betaMPT Man page
betaMPTcpp Man page
betweenSubjectMPT Man page
correlationPosterior Man page
extendMPT Man page
genBetaMPT Man page
genMPT Man page
genTraitMPT Man page
getGroupMeans Man page
getParam Man page
marginalMPT Man page
plot.betaMPT Man page
plotDistribution Man page
plotFit Man page
plotFreq Man page
plotParam Man page
plotPrior Man page
plotPriorPost Man page
plot.simpleMPT Man page
plot.traitMPT Man page
posteriorPredictive Man page
PPP Man page
priorPredictive Man page
probitInverse Man page
readEQN Man page
simpleMPT Man page
summarizeMCMC Man page
summarizeMPT Man page
testHetChi Man page
testHetPerm Man page
traitMPT Man page
transformedParameters Man page
TreeBUGS Man page
TreeBUGS-package Man page
withinSubjectEQN Man page

Files

inst
inst/CITATION
inst/MPTmodels
inst/MPTmodels/2htm.eqn
inst/MPTmodels/winbugs_zero_trick.jags
inst/MPTmodels/2htsm.eqn
inst/doc
inst/doc/TreeBUGS_1_intro.Rmd
inst/doc/TreeBUGS_1_intro.R
inst/doc/TreeBUGS_2_extended.Rmd
inst/doc/TreeBUGS_1_intro.html
inst/doc/TreeBUGS_2_extended.R
inst/doc/TreeBUGS_2_extended.html
tests
tests/testthat.R
tests/testthat
tests/testthat/test_genMPT.R tests/testthat/test_readEQN.R
src
src/Makevars
src/loglikMPT.cpp
src/betaMPT.cpp
src/init.c
src/RcppExports.cpp
NAMESPACE
NEWS
data
data/arnold2013.RData
R
R/arnold2013.R R/covariateHandling.R R/plotPriorPost.R R/getGroupMeans.R R/parseRestrictions.R R/corSamples.R R/TreeBUGS-package.R R/checkFunctions.R R/covCorrelationString.R R/callingSampler.R R/sampleHyperprior.R R/posteriorPredictive.R R/printMPT.R R/thetaHandling.R R/genDataTrait.R R/renameBUGSoutput.R R/testHetChi.R R/genDataBeta.R R/covPredictorHandling.R R/genDataMPT.R R/T1perGroup.R R/getParam.R R/plotFit.R R/BF_likelihoods.R R/transformedParModelfile.R R/writeSummaryToFile.R R/BF_marginalMPT.R R/betweenSubjects.R R/testHetPerm.R R/summarizeMCMC.R R/fitSimpleMPT.R R/covDataRead.R R/covFactor.R R/fitBetaMPTcpp.R R/transformedParPosthoc.R R/fitModel.R R/plotPrior.R R/BF_auxiliary.R R/RcppExports.R R/extendMPT.R R/within_subject_EQN.R R/correlationBayes.R R/plotDistribution.R R/makeModelDescription.R R/fitModelCpp.R R/correlationBayesMCMC.R R/readEQN.R R/CollectionOfInputProcessingFunctions.R R/priorPredictive.R R/plotParameters.R R/fitBetaMPT.R R/BF_Rao_Blackwell.R R/fitTraitMPT.R R/parseEQN.R R/genDataCheck.R R/plotFrequencies.R R/summarizeMPT.R R/PPP.R R/probitInverse.R R/plotConvergence.R
vignettes
vignettes/TreeBUGS_1_intro.Rmd
vignettes/TreeBUGS_2_extended.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/marginalMPT.Rd man/summarizeMCMC.Rd man/priorPredictive.Rd man/TreeBUGS-package.Rd man/getGroupMeans.Rd man/withinSubjectEQN.Rd man/posteriorPredictive.Rd man/testHetChi.Rd man/plotDistribution.Rd man/summarizeMPT.Rd man/plotPrior.Rd man/simpleMPT.Rd man/plotPriorPost.Rd man/readEQN.Rd man/testHetPerm.Rd man/genTraitMPT.Rd man/correlationPosterior.Rd man/extendMPT.Rd man/plotParam.Rd man/betaMPTcpp.Rd man/genBetaMPT.Rd man/getParam.Rd man/traitMPT.Rd man/betaMPT.Rd man/transformedParameters.Rd man/arnold2013.Rd man/plotFit.Rd man/BayesFactorMPT.Rd man/genMPT.Rd man/betweenSubjectMPT.Rd man/probitInverse.Rd man/plot.Rd man/plotFreq.Rd man/PPP.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.