├── .Rbuildignore ├── .gitattributes ├── .github ├── .gitignore └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── .travis.yml ├── BayesianTools.Rproj ├── BayesianTools ├── .Rbuildignore ├── .gitignore ├── CRAN.md ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R │ ├── BayesianSetupGenerateParallel.R │ ├── BayesianTools.R │ ├── DIC.R │ ├── GOF.R │ ├── MAP.R │ ├── RcppExports.R │ ├── SBC.R │ ├── SMC.R │ ├── VSEM.R │ ├── WAIC.R │ ├── benchmark.R │ ├── blockUpdate.R │ ├── classBayesianOutput.R │ ├── classBayesianSetup.R │ ├── classLikelihood.R │ ├── classMcmcSampler.R │ ├── classMcmcSamplerList.R │ ├── classPosterior.R │ ├── classPrior.R │ ├── classSMCSamplerList.R │ ├── classSmcSampler.R │ ├── codaFunctions.R │ ├── convertCoda.R │ ├── diagnosticsGelman.R │ ├── getVolume.R │ ├── importPackages.R │ ├── marginalLikelihood.R │ ├── mcmcConfidence.R │ ├── mcmcDE.R │ ├── mcmcDEzs.R │ ├── mcmcDREAM.R │ ├── mcmcDREAM_helperFunctions.R │ ├── mcmcDREAMzs.R │ ├── mcmcFrancesco.R │ ├── mcmcMetropolis.R │ ├── mcmcMultipleChains.R │ ├── mcmcRun.R │ ├── mcmcSamplerAutomatic.R │ ├── mcmcTwalk.R │ ├── mcmcTwalk_helperFunctions.R │ ├── plotCorrelationDensity.r │ ├── plotDiagnostic.R │ ├── plotMarginals.R │ ├── plotSensitivityOAT.R │ ├── plotTimeSeries.R │ ├── plotTrace.R │ ├── proposalGenerator.R │ ├── testFunctions.R │ ├── utils-Numerics.R │ ├── utils.R │ └── utilsFrancesco.R ├── _pkgdown.yml ├── inst │ └── examples │ │ ├── DEfamilyHelp.R │ │ ├── GOF.R │ │ ├── MetropolisHelp.R │ │ ├── SMCHelp.R │ │ ├── VSEMHelp.R │ │ ├── WAICHelp.R │ │ ├── bridgesampleHelp.R │ │ ├── classBayesianSetup.R │ │ ├── correlationPlotHelp.R │ │ ├── createPrior.R │ │ ├── generateParallelExecuter.R │ │ ├── generateTestDensityMultiNormalHelp.R │ │ ├── getSampleHelp.R │ │ ├── getVolume.R │ │ ├── marginalLikelihoodHelp.R │ │ ├── marginalPlotHelp.R │ │ ├── mcmcRun.R │ │ ├── plotDiagnosticHelp.R │ │ ├── plotSensitivityHelp.R │ │ ├── plotTimeSeriesHelp.R │ │ ├── plotTimeSeriesResultsHelp.R │ │ ├── proposalGeneratorHelp.R │ │ ├── testLinearModel.R │ │ └── tracePlotHelp.R ├── man │ ├── AM.Rd │ ├── AdaptpCR.Rd │ ├── BayesianTools.Rd │ ├── DE.Rd │ ├── DEzs.Rd │ ├── DIC.Rd │ ├── DR.Rd │ ├── DRAM.Rd │ ├── DREAM.Rd │ ├── DREAMzs.Rd │ ├── GOF.Rd │ ├── Gfun.Rd │ ├── M.Rd │ ├── MAP.Rd │ ├── Metropolis.Rd │ ├── Twalk.Rd │ ├── TwalkMove.Rd │ ├── Twalksteps.Rd │ ├── VSEM.Rd │ ├── VSEMcreateLikelihood.Rd │ ├── VSEMcreatePAR.Rd │ ├── VSEMgetDefaults.Rd │ ├── WAIC.Rd │ ├── applySettingsDefault.Rd │ ├── betaFun.Rd │ ├── bridgesample.Rd │ ├── calibrationTest.Rd │ ├── checkBayesianSetup.Rd │ ├── combineChains.Rd │ ├── convertCoda.Rd │ ├── correctThin.Rd │ ├── correlationPlot.Rd │ ├── createBayesianSetup.Rd │ ├── createBetaPrior.Rd │ ├── createLikelihood.Rd │ ├── createMcmcSamplerList.Rd │ ├── createPosterior.Rd │ ├── createPrior.Rd │ ├── createPriorDensity.Rd │ ├── createProposalGenerator.Rd │ ├── createSmcSamplerList.Rd │ ├── createTruncatedNormalPrior.Rd │ ├── createUniformPrior.Rd │ ├── factorMatrice.Rd │ ├── figures │ │ ├── betaDensity.png │ │ ├── normalDensity.png │ │ └── uniformDensity.png │ ├── gelmanDiagnostics.Rd │ ├── generateCRvalues.Rd │ ├── generateParallelExecuter.Rd │ ├── generateTestDensityMultiNormal.Rd │ ├── getBlock.Rd │ ├── getBlockSettings.Rd │ ├── getCredibleIntervals.Rd │ ├── getDharmaResiduals.Rd │ ├── getPanels.Rd │ ├── getPossibleSamplerTypes.Rd │ ├── getPredictiveDistribution.Rd │ ├── getPredictiveIntervals.Rd │ ├── getRmvnorm.Rd │ ├── getSample.Rd │ ├── getSetup.Rd │ ├── getVolume.Rd │ ├── likelihoodAR1.Rd │ ├── likelihoodIidNormal.Rd │ ├── logSumExp.Rd │ ├── makeObjectClassCodaMCMC.Rd │ ├── marginalLikelihood.Rd │ ├── marginalPlot.Rd │ ├── marginalPlotDensity.Rd │ ├── marginalPlotViolin.Rd │ ├── mcmcMultipleChains.Rd │ ├── mergeChains.Rd │ ├── metropolisRatio.Rd │ ├── package-deprecated.Rd │ ├── plotDiagnostic.Rd │ ├── plotSensitivity.Rd │ ├── plotTimeSeries.Rd │ ├── plotTimeSeriesResiduals.Rd │ ├── plotTimeSeriesResults.Rd │ ├── propFun.Rd │ ├── rescale.Rd │ ├── runMCMC.Rd │ ├── sampleEquallySpaced.Rd │ ├── sampleMetropolis.Rd │ ├── scaleMatrix.Rd │ ├── setupStartProposal.Rd │ ├── smcSampler.Rd │ ├── stopParallel.Rd │ ├── sumSquare.Rd │ ├── testDensityBanana.Rd │ ├── testDensityGelmanMeng.Rd │ ├── testDensityInfinity.Rd │ ├── testDensityMultiNormal.Rd │ ├── testDensityNormal.Rd │ ├── testLinearModel.Rd │ ├── thinMatrix.Rd │ ├── tracePlot.Rd │ ├── updateGroups.Rd │ ├── updateProposalGenerator.Rd │ └── vsemC.Rd ├── src │ ├── RcppExports.cpp │ ├── init.c │ └── vsem.cpp ├── tests │ ├── testthat.R │ └── testthat │ │ ├── test-correlationPlot.R │ │ ├── test-createBayesianSetup.R │ │ ├── test-getSample.R │ │ ├── test-infinity.R │ │ ├── test-marginalLikelihood.R │ │ ├── test-marginalPlot.R │ │ ├── test-plotDiagnostic.R │ │ ├── test-plotTimeSeriesResults.R │ │ ├── test-runMCMC.R │ │ ├── test-samplers.R │ │ ├── test-settingsDefault.R │ │ ├── test-startValues.R │ │ ├── test-tracePlot.R │ │ ├── test-utilities.R │ │ ├── test-utils-Numerics.R │ │ └── testFunctionalities.R └── vignettes │ ├── BayesianTools.Rmd │ ├── InterfacingAModel.Rmd │ ├── betaDensity.png │ ├── normalDensity.png │ └── uniformDensity.png ├── Development ├── BT-issues │ └── issue-222.R ├── BayesFactor.R ├── CreateData.R ├── DATASET.R ├── Figures │ └── figures.R ├── data.R ├── manualTests │ ├── BasicTests.Rmd │ ├── Defaults │ │ ├── defaults.Rdata │ │ └── saveDefaults.R │ ├── Effect_catchDuplicates.Rmd │ ├── MarginalLikelihoodTest.Rmd │ ├── MetropolisTest.Rmd │ ├── Sampler_testfile.Rmd │ ├── TestScalingAdaptive │ │ ├── Compare_adaptiveHighDimensionsPart1.Rmd │ │ └── Compare_adaptiveHighDimensionsPart2.Rmd │ ├── TestScalingForHighDimensions │ │ ├── Test_HighDimensions_DE.Rmd │ │ ├── Test_HighDimensions_DREAM.Rmd │ │ └── Test_HighDimensions_Metropolis.Rmd │ ├── test-getSample_coda.R │ └── test-workflow.R ├── t-walk.R ├── testSuite.R └── vignette │ └── Test.Rnw ├── Examples ├── 16-TG14 │ ├── TG14-v2.2.Rmd │ └── TG14-v2.3.Rmd ├── BayesFactor.Rmd ├── DEzsPriorRestart.R ├── Old │ ├── BT-MCMC-Auto-Demo.Rmd │ ├── BayesianToolsReference.Rmd │ ├── ForestModel.Rmd │ └── ForestModel.md ├── ParticleMCMC │ └── Untitled.R ├── PlotTimeSeriesResults.Rmd ├── PlotTimeSeriesResults.md ├── RandomEffectsModel.Rmd ├── RandomEffectsModel.md ├── RandomEffectsModel_files │ └── figure-html │ │ ├── unnamed-chunk-2-1.png │ │ ├── unnamed-chunk-3-1.png │ │ ├── unnamed-chunk-4-1.png │ │ ├── unnamed-chunk-6-1.png │ │ └── unnamed-chunk-7-1.png ├── Teaching │ └── Optimization.Rmd ├── VSEM-Extended.R ├── VSEM-Test-Stefan.R ├── VSEM-VaryingParameters │ └── Example.R ├── install.R └── postHocPrior.R ├── Publications ├── SpeichEtAl-SMCForModelCalibration │ ├── 1_reference_MCMC │ │ ├── VSEMa_gen_ref.r │ │ ├── VSEMb_gen_ref.r │ │ └── threePGN_gen_ref.r │ ├── 2_MCMC_runs │ │ ├── mcmcRef_VSEMa_np_mult.r │ │ ├── mcmcRef_VSEMb_np_mult.r │ │ ├── mcmcRef_np_mult.r │ │ └── mcmcRef_sleep_np_mult.r │ ├── 3_SMC_runs │ │ ├── VSEMa_SMC_mult.r │ │ ├── VSEMb_SMC_mult.r │ │ ├── multiNorm.r │ │ ├── threePGN_SMC_mult.r │ │ └── threePGN_sleep_SMC_mult_30.r │ ├── 4_parallelization │ │ ├── test_parallel_1_20ms.r │ │ ├── test_parallel_1_50ms.r │ │ ├── test_parallel_1_mult.r │ │ ├── test_parallel_2plus_20ms.r │ │ ├── test_parallel_2plus_50ms.r │ │ └── test_parallel_2plus_mult.r │ ├── 5_launch_scripts │ │ ├── compare_smc_threePGN_mult1.moab │ │ └── test_parallel_40_50ms_mult1.moab │ ├── 6_prior_posterior_plots │ │ ├── SMCruns.Rmd │ │ ├── readme.Rmd │ │ ├── readme.md │ │ └── readme_files │ │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── readme.Rmd │ ├── readme.md │ └── readme_files │ │ └── figure-html │ │ └── unnamed-chunk-3-1.png └── readme.md ├── README.md ├── Test ├── BasicBTTest.R ├── BasicNormalTest.R └── Distance.R ├── _pkgdown.yml ├── docs ├── articles │ ├── BayesianTools.R │ ├── BayesianTools.html │ ├── BayesianTools_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-20-2.png │ │ │ ├── unnamed-chunk-20-3.png │ │ │ ├── unnamed-chunk-20-4.png │ │ │ ├── unnamed-chunk-35-1.png │ │ │ ├── unnamed-chunk-38-1.png │ │ │ ├── unnamed-chunk-9-1.png │ │ │ ├── unnamed-chunk-9-2.png │ │ │ └── unnamed-chunk-9-3.png │ └── index.html ├── authors.html ├── index.html ├── jquery.sticky-kit.min.js ├── link.svg ├── pkgdown.css ├── pkgdown.js └── reference │ ├── AM.html │ ├── BayesianTools.html │ ├── DE.html │ ├── DEzs.html │ ├── DIC.html │ ├── DR.html │ ├── DRAM.html │ ├── DREAM.html │ ├── DREAMzs.html │ ├── GOF-5.png │ ├── GOF.html │ ├── M.html │ ├── MAP.html │ ├── Metropolis.html │ ├── Twalk.html │ ├── VSEM-10.png │ ├── VSEM-9.png │ ├── VSEM.html │ ├── VSEMcreateLikelihood.html │ ├── VSEMcreatePAR.html │ ├── VSEMgetDefaults.html │ ├── WAIC.html │ ├── applySettingsDefault.html │ ├── bridgesample.html │ ├── checkBayesianSetup.html │ ├── convertCoda.html │ ├── correctThin.html │ ├── correlationPlot-6.png │ ├── correlationPlot.html │ ├── createBayesianSetup.html │ ├── createBetaPrior.html │ ├── createBreakMat.html │ ├── createLikelihood.html │ ├── createMcmcSamplerList.html │ ├── createPosterior.html │ ├── createPrior.html │ ├── createPriorDensity.html │ ├── createProposalGenerator-21.png │ ├── createProposalGenerator-22.png │ ├── createProposalGenerator-23.png │ ├── createProposalGenerator-24.png │ ├── createProposalGenerator-25.png │ ├── createProposalGenerator.html │ ├── createSmcSamplerList.html │ ├── createTruncatedNormalPrior.html │ ├── createUniformPrior.html │ ├── gelmanDiagnostics.html │ ├── generateParallelExecuter.html │ ├── generateTestDensityMultiNormal-10.png │ ├── generateTestDensityMultiNormal-9.png │ ├── generateTestDensityMultiNormal.html │ ├── getCredibleIntervals.html │ ├── getDharmaResiduals.html │ ├── getMetropolisDefaultSettings.html │ ├── getPanels.html │ ├── getPossibleSamplerTypes.html │ ├── getPredictiveDistribution.html │ ├── getPredictiveIntervals.html │ ├── getSample-5.png │ ├── getSample.html │ ├── getVolume.html │ ├── histMarginal.html │ ├── index.html │ ├── likelihoodAR1.html │ ├── likelihoodIidNormal.html │ ├── logSumExp.html │ ├── marginalLikelihood-10.png │ ├── marginalLikelihood-9.png │ ├── marginalLikelihood.html │ ├── marginalPlot-5.png │ ├── marginalPlot.html │ ├── mcmcMultipleChains.html │ ├── metropolisRatio.html │ ├── package-deprecated.html │ ├── plotHist.html │ ├── plotSensitivity.html │ ├── plotTimeSeries-5.png │ ├── plotTimeSeries.html │ ├── plotTimeSeriesResiduals.html │ ├── plotTimeSeriesResults.html │ ├── rescale.html │ ├── runMCMC-13.png │ ├── runMCMC-14.png │ ├── runMCMC-15.png │ ├── runMCMC.html │ ├── sampleEquallySpaced.html │ ├── sampleMetropolis.html │ ├── setupStartProposal.html │ ├── smcSampler-73.png │ ├── smcSampler-74.png │ ├── 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