├── .Rbuildignore ├── .github ├── .gitignore ├── FUNDING.yml ├── ISSUE_TEMPLATE.md ├── dependabot.yml └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── as.matrix.stanreg.R ├── bayes_R2.R ├── data_block.R ├── doc-QR.R ├── doc-adapt_delta.R ├── doc-algorithms.R ├── doc-datasets.R ├── doc-example_jm.R ├── doc-example_model.R ├── doc-modeling-functions.R ├── doc-rstanarm-deprecated.R ├── doc-rstanarm-package.R ├── draws.R ├── jm_data_block.R ├── jm_make_assoc_parts.R ├── jm_make_assoc_terms.R ├── launch_shinystan.R ├── log_lik.R ├── loo-kfold.R ├── loo-prediction.R ├── loo.R ├── misc.R ├── neg_binomial_2.R ├── plots.R ├── posterior_interval.R ├── posterior_linpred.R ├── posterior_predict.R ├── posterior_survfit.R ├── posterior_traj.R ├── posterior_vs_prior.R ├── pp_check.R ├── pp_data.R ├── pp_validate.R ├── predict.R ├── predictive_error.R ├── predictive_interval.R ├── print-and-summary.R ├── prior_summary.R ├── priors.R ├── ps_check.R ├── simulate_b_pars.R ├── stan_aov.R ├── stan_betareg.R ├── stan_betareg.fit.R ├── stan_biglm.R ├── stan_biglm.fit.R ├── stan_clogit.R ├── stan_gamm4.R ├── stan_glm.R ├── stan_glm.fit.R ├── stan_glmer.R ├── stan_jm.R ├── stan_jm.fit.R ├── stan_lm.R ├── stan_lm.fit.R ├── stan_mvmer.R ├── stan_nlmer.R ├── stan_polr.R ├── stan_polr.fit.R ├── stanmvreg-methods.R ├── stanmvreg.R ├── stanreg-methods.R ├── stanreg-objects.R ├── stanreg.R ├── stanreg_list.R └── zzz.R ├── README.md ├── configure ├── configure.win ├── data ├── bball1970.rda ├── bball2006.rda ├── kidiq.rda ├── mortality.rda ├── pbcLong.rda ├── pbcSurv.rda ├── radon.rda ├── roaches.rda ├── tumors.rda └── wells.rda ├── demo ├── 00Index ├── ARM_Ch03.R ├── ARM_Ch04.R ├── ARM_Ch05.R ├── ARM_Ch07.R ├── ARM_Ch08.R ├── ARM_Ch09.R ├── ARM_Ch12_13.R ├── ARM_Ch14.R ├── CLEANUP.R └── SETUP.R ├── dev-notes ├── frost.css ├── rstanarm_dev_notes.html └── rstanarm_dev_notes.md ├── inst ├── CITATION ├── include │ ├── CODOLS.hpp │ ├── stan_meta_header.hpp │ └── tests.cpp └── stan │ ├── bernoulli.stan │ ├── binomial.stan │ ├── continuous.stan │ ├── count.stan │ ├── data │ ├── NKX.stan │ ├── data_assoc.stan │ ├── data_betareg.stan │ ├── data_event.stan │ ├── data_glm.stan │ ├── data_mvmer.stan │ ├── dimensions_mvmer.stan │ ├── glmer_stuff.stan │ ├── glmer_stuff2.stan │ ├── hyperparameters.stan │ ├── hyperparameters_assoc.stan │ ├── hyperparameters_event.stan │ ├── hyperparameters_mvmer.stan │ └── weights_offset.stan │ ├── functions │ ├── SSfunctions.stan │ ├── bernoulli_likelihoods.stan │ ├── binomial_likelihoods.stan │ ├── common_functions.stan │ ├── continuous_likelihoods.stan │ ├── count_likelihoods.stan │ ├── jm_functions.stan │ └── mvmer_functions.stan │ ├── gqs │ └── gen_quantities_mvmer.stan │ ├── include │ ├── Brilleman_copyright.stan │ ├── Columbia_copyright.stan │ └── license.stan │ ├── jm.stan │ ├── lm.stan │ ├── model │ ├── assoc_evaluate.stan │ ├── eta_add_Zb.stan │ ├── eta_no_intercept.stan │ ├── eta_z_no_intercept.stan │ ├── event_lp.stan │ ├── make_eta.stan │ ├── make_eta_bern.stan │ ├── make_eta_tmp.stan │ ├── make_eta_tmp2.stan │ ├── make_eta_z.stan │ ├── mvmer_lp.stan │ ├── priors_betareg.stan │ ├── priors_glm.stan │ └── priors_mvmer.stan │ ├── mvmer.stan │ ├── parameters │ ├── parameters_assoc.stan │ ├── parameters_betareg.stan │ ├── parameters_event.stan │ ├── parameters_glm.stan │ └── parameters_mvmer.stan │ ├── polr.stan │ ├── tdata │ ├── tdata_betareg.stan │ ├── tdata_glm.stan │ └── tdata_mvmer.stan │ └── tparameters │ ├── tparameters_betareg.stan │ ├── tparameters_glm.stan │ └── tparameters_mvmer.stan ├── man-roxygen ├── args-QR.R ├── args-adapt_delta.R ├── args-algorithm.R ├── args-ci-geom-args.R ├── args-dots-ignored.R ├── args-dots.R ├── args-formula-data-subset.R ├── args-ids.R ├── args-labs.R ├── args-m.R ├── args-max_treedepth.R ├── args-pars.R ├── args-prior_PD.R ├── args-prior_aux.R ├── args-prior_covariance.R ├── args-prior_intercept.R ├── args-prior_smooth.R ├── args-priors.R ├── args-regex-pars.R ├── args-remove-stub.R ├── args-same-as-2.R ├── args-same-as-rarely-2.R ├── args-same-as-rarely.R ├── args-same-as.R ├── args-scales.R ├── args-sparse.R ├── args-stanjm-object.R ├── args-stanmvreg-object.R ├── args-stanreg-object.R ├── args-x-y.R ├── reference-bayesvis.R ├── reference-bda.R ├── reference-gelman-carlin.R ├── reference-gelman-hill.R ├── reference-lme4.R ├── reference-loo.R ├── reference-morey.R ├── reference-muth.R ├── reference-piironen-vehtari.R ├── reference-stan-manual.R ├── return-stanfit-object.R ├── return-stanreg-object.R └── see-also.R ├── man ├── QR-argument.Rd ├── adapt_delta.Rd ├── as.matrix.stanreg.Rd ├── available-algorithms.Rd ├── available-models.Rd ├── bayes_R2.stanreg.Rd ├── example_jm.Rd ├── example_model.Rd ├── family.stanmvreg.Rd ├── family.stanreg.Rd ├── figures │ ├── logo.svg │ └── stanlogo.png ├── formula.stanreg.Rd ├── get_y.Rd ├── kfold.stanreg.Rd ├── launch_shinystan.stanreg.Rd ├── log_lik.stanreg.Rd ├── logit.Rd ├── loo.stanreg.Rd ├── loo_predict.stanreg.Rd ├── model.frame.stanmvreg.Rd ├── model.frame.stanreg.Rd ├── model.matrix.stanreg.Rd ├── neg_binomial_2.Rd ├── pairs.stanreg.Rd ├── plot.predict.stanjm.Rd ├── plot.stanreg.Rd ├── plot.survfit.stanjm.Rd ├── posterior_interval.stanreg.Rd ├── posterior_linpred.stanreg.Rd ├── posterior_predict.stanreg.Rd ├── posterior_survfit.Rd ├── posterior_traj.Rd ├── posterior_vs_prior.Rd ├── pp_check.stanreg.Rd ├── pp_validate.Rd ├── predict.stanreg.Rd ├── predictive_error.stanreg.Rd ├── predictive_interval.stanreg.Rd ├── print.stanreg.Rd ├── print.survfit.stanjm.Rd ├── prior_summary.stanreg.Rd ├── priors.Rd ├── ps_check.Rd ├── reexports.Rd ├── rstanarm-datasets.Rd ├── rstanarm-deprecated.Rd ├── rstanarm-package.Rd ├── se.Rd ├── stan_betareg.Rd ├── stan_biglm.Rd ├── stan_clogit.Rd ├── stan_gamm4.Rd ├── stan_glm.Rd ├── stan_glmer.Rd ├── stan_jm.Rd ├── stan_lm.Rd ├── stan_mvmer.Rd ├── stan_nlmer.Rd ├── stan_polr.Rd ├── stanmvreg-methods.Rd ├── stanreg-draws-formats.Rd ├── stanreg-methods.Rd ├── stanreg-objects.Rd ├── stanreg_list.Rd ├── summary.stanreg.Rd ├── terms.stanmvreg.Rd └── terms.stanreg.Rd ├── rstanarm.Rproj ├── src └── init.cpp ├── tests ├── testthat.R └── testthat │ ├── Rplots.pdf │ ├── helper.R │ ├── test_loo.R │ ├── test_methods.R │ ├── test_misc.R │ ├── test_plots.R │ ├── test_posterior_predict.R │ ├── test_pp_check.R │ ├── test_pp_validate.R │ ├── test_predict.R │ ├── test_stan_betareg.R │ ├── test_stan_clogit.R │ ├── test_stan_functions.R │ ├── test_stan_glm.R │ ├── test_stan_glmer.R │ ├── test_stan_jm.R │ ├── test_stan_lm.R │ ├── test_stan_mvmer.R │ ├── test_stan_nlmer.R │ └── test_stan_polr.R └── vignettes ├── .install_extras ├── ab-testing.Rmd ├── aov.Rmd ├── betareg.Rmd ├── binomial.Rmd ├── children ├── SETTINGS-gg.txt ├── SETTINGS-knitr.txt ├── four_steps.txt └── stan_glm_priors.txt ├── continuous.Rmd ├── count.Rmd ├── glmer.Rmd ├── jm.Rmd ├── lm.Rmd ├── mrp-files ├── 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