├── .gitattributes ├── .gitignore ├── Miscellaneous-R-Code.Rproj ├── ModelFitting ├── Bayesian │ ├── StanBugsJags │ │ ├── BetaMixedModel.stan │ │ ├── IRT_models │ │ │ ├── IRT_2PM.stan │ │ │ ├── IRT_3PM.stan │ │ │ ├── IRT_4PM.stan │ │ │ ├── IRT_rasch.stan │ │ │ ├── ReadMe.md │ │ │ └── test_stan_irt.R │ │ ├── MixedModelGeneric.stan │ │ ├── MixedModelSleepstudy_withREcorrelation.stan │ │ ├── ReadMe.md │ │ ├── cfa │ │ ├── jags_MixedModelBetaRegression.jags │ │ ├── linregwithprior.stan │ │ ├── lmbugs.bugs │ │ ├── lmjags.jags │ │ ├── multilevelmediation.stan │ │ ├── multilevelmediationYuanMacKinnon2009.bugs │ │ └── singlelevelmediationYuanMacKinnon2009.bugs │ ├── bugs_linreg.R │ ├── horseshoe │ │ ├── README.md │ │ ├── example.R │ │ ├── wei_bg.stan │ │ ├── wei_bg_joint.stan │ │ ├── wei_gau.stan │ │ ├── wei_gau_joint.stan │ │ ├── wei_hs.stan │ │ ├── wei_hs_joint.stan │ │ ├── wei_lap.stan │ │ └── wei_lap_joint.stan │ ├── jags_MixedModelBetaRegression.R │ ├── jags_linreg.R │ ├── multinomial │ │ ├── README.md │ │ ├── mnl_1.stan │ │ ├── mnl_2.stan │ │ ├── mnl_3.stan │ │ ├── mnl_4.stan │ │ ├── multinomial_stan_comparisons.R │ │ ├── stan_basic_mnl_conceptual.stan │ │ └── stan_mnl_altspecific.stan │ ├── r2bugs.distributions.R │ ├── rstanBetaRegression.R │ ├── rstan_MixedModelBetaRegression.R │ ├── rstan_MixedModelSleepstudy.R │ ├── rstan_MixedModelSleepstudy_withREcorrelation.R │ ├── rstan_MixtureModel.R │ ├── rstan_linregwithprior.R │ ├── rstan_multilevelMediation.R │ ├── rstan_topicModels0.R │ ├── rstant_testBEST.R │ ├── stochasticVolatility.R │ ├── topicModelgibbs.R │ ├── variationalBayesRegression.R │ └── variationalBayesRegression.Rmd ├── EM Examples │ ├── EM Mixture MV.R │ ├── EM Mixture.R │ ├── EM algorithm for ppca with missing.R │ ├── EM algorithm for ppca.R │ ├── EM algorithm for probit example.R │ ├── EM for pca.R │ └── EM for state space unobserved components.R ├── Mixed Models │ ├── mixedModelML │ │ ├── mixedModelML.R │ │ ├── mixedModelML.Rmd │ │ ├── mixedModelML.html │ │ ├── mixedModelML.md │ │ ├── mixedModelML.pdf │ │ └── mixedModelML_files │ │ │ ├── figure-html │ │ │ ├── diag.html │ │ │ ├── fitCSgam-1.png │ │ │ ├── gamSleepStudy-1.png │ │ │ ├── gammSleepStudy-1.png │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ └── unnamed-chunk-3-2.png │ │ │ └── figure-latex │ │ │ ├── fitCSgam-1.pdf │ │ │ └── gammSleepStudy-1.pdf │ ├── mixedModels │ │ ├── anovamixed.Rmd │ │ ├── anovamixed.html │ │ ├── anovamixed.pdf │ │ ├── growthCurvevsMixedModel.R │ │ ├── growth_vs_mixed.Rmd │ │ ├── growth_vs_mixed.html │ │ ├── growth_vs_mixed_files │ │ │ ├── figure-html │ │ │ │ ├── lavaanmod-1.png │ │ │ │ ├── randomIntsSlopesMods-1.png │ │ │ │ └── visualizeTrends-1.png │ │ │ └── growthvsMixed_EstResults.RData │ │ ├── growth_vs_mixed_sim.Rmd │ │ ├── growth_vs_mixed_sim.html │ │ ├── growth_vs_mixed_sim.md │ │ ├── mixedModels.Rmd │ │ ├── mixedModels.md │ │ ├── mixedModels.pdf │ │ └── mixedModels_files │ │ │ ├── figure-html │ │ │ ├── sleepModFits-1.png │ │ │ ├── sleepModFitsReduced-1.png │ │ │ └── sleepstudyPlot-1.png │ │ │ ├── figure-latex │ │ │ ├── sleepModFits-1.pdf │ │ │ ├── sleepModFitsReduced-1.pdf │ │ │ └── sleepstudyPlot-1.pdf │ │ │ └── figure-markdown_github │ │ │ ├── sleepModFits-1.png │ │ │ ├── sleepModFitsReduced-1.png │ │ │ └── sleepstudyPlot-1.png │ ├── one_factor_RE.R │ ├── one_factor_RE.jl │ ├── one_factor_RE.m │ ├── twofactorRE.R │ ├── twofactorRE.jl │ └── twofactorRE.m ├── NBzeroinfl.R ├── RKHSReg │ ├── RKHSReg.R │ ├── RKHSReg.md │ └── update.Rmd ├── bivariateProbit.R ├── cfa_ml.R ├── convert_code_to_html.R ├── crp.R ├── cubicsplines.R ├── elm.R ├── gp Examples │ ├── README.md │ ├── gaussSample.m │ ├── gaussianProcessStan.R │ ├── gaussianProcessStan.Rmd │ ├── gaussianprocessNoiseFree.R │ ├── gaussianprocessNoisy.R │ ├── gpStanModelCode.stan │ ├── gpStanModelCode_gammaExponential.stan │ ├── gpStanModelCode_generalizedSquaredExponential.stan │ ├── gpStanModelCode_rationalQuadratic.stan │ ├── gpStan_squaredExponentialFactorAnalysis.R │ ├── gpStan_squaredExponentialFactorAnalysis.stan │ ├── gprDemoChangeHparams.m │ ├── gprDemoNoiseFree.m │ └── stangp.RData ├── gradient_descent.R ├── heckman_selection.R ├── hmm_viterbi.R ├── hmm_viterbi.py ├── hurdle.R ├── ipw.R ├── lasso.R ├── markov_model.R ├── multinomial.R ├── naivebayes.R ├── nelder_mead.R ├── nelder_mead.ipynb ├── nelder_mead.py ├── newton_irls.R ├── one_line_models.R ├── ordinal_regression.R ├── penalized_ML.R ├── poiszeroinfl.R ├── quantile_regression.Rmd ├── quantile_regression.html ├── ridge.R ├── standard_lm.R ├── standard_logistic.R ├── stochastic_gradient_descent.R ├── survivalCox.R └── tobit.R ├── Other ├── Programming_Shenanigans │ ├── compoundInterest.R │ ├── fillbyLastRecursive.R │ ├── fizzbuzz.R │ ├── fizzbuzz.jl │ ├── fizzbuzz.py │ ├── matrixOperations.Rmd │ ├── matrixOperations.html │ ├── matrixOperations.md │ ├── matrixOperations_files │ │ └── figure-html │ │ │ └── unnamed-chunk-16-1.png │ ├── stringReverseRecursively.R │ ├── stringReverseRecursively.py │ ├── wordWrap.R │ └── wordWrap.py ├── Python Startup │ ├── mixedModel.py │ └── regressionExamples.py ├── getRollCall.R ├── ggtheme.R ├── shakespeareanInsulter.R ├── spurriousCorrelationwithRatios.R ├── xkcdscrape.R └── xkcdscrape.py ├── README.md ├── SC and TR ├── GAMS.R ├── MLcode.R ├── coursecode.r ├── mixedModelML │ ├── mixedModelML.R │ ├── mixedModelML.Rmd │ ├── mixedModelML.html │ ├── mixedModelML.md │ ├── mixedModelML.pdf │ └── mixedModelML_files │ │ ├── figure-html │ │ ├── diag.html │ │ ├── fitCSgam-1.png │ │ ├── gamSleepStudy-1.png │ │ ├── gammSleepStudy-1.png │ │ ├── unnamed-chunk-1-1.png │ │ ├── unnamed-chunk-3-1.png │ │ └── unnamed-chunk-3-2.png │ │ └── figure-latex │ │ ├── fitCSgam-1.pdf │ │ └── gammSleepStudy-1.pdf └── mixedModels │ ├── anovamixed.Rmd │ ├── anovamixed.html │ ├── anovamixed.pdf │ ├── growthCurvevsMixedModel.R │ ├── growth_vs_mixed.Rmd │ ├── growth_vs_mixed.html │ ├── growth_vs_mixed_files │ ├── 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