shinystan: Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models

A graphical user interface for interactive Markov chain Monte Carlo (MCMC) diagnostics and plots and tables helpful for analyzing a posterior sample. The interface is powered by RStudio's Shiny web application framework and works with the output of MCMC programs written in any programming language (and has extended functionality for Stan models fit using the rstan and rstanarm packages).

Install the latest version of this package by entering the following in R:
install.packages("shinystan")
AuthorJonah Gabry [aut, cre], Stan Development Team [ctb], Michael Andreae [ctb], Michael Betancourt [ctb], Bob Carpenter [ctb], Yuanjun Gao [ctb], Andrew Gelman [ctb], Ben Goodrich [ctb], Daniel Lee [ctb], Dongying Song [ctb], Rob Trangucci [ctb]
Date of publication2017-02-01 08:34:48
MaintainerJonah Gabry <jsg2201@columbia.edu>
LicenseGPL (>= 3)
Version2.3.0
https://github.com/stan-dev/shinystan/
http://mc-stan.org/

View on CRAN

Files

inst
inst/CITATION
inst/ShinyStan
inst/ShinyStan/ui.R inst/ShinyStan/server.R
inst/ShinyStan/server_files
inst/ShinyStan/server_files/tooltips
inst/ShinyStan/server_files/tooltips/tooltips.R inst/ShinyStan/server_files/debounce.R
inst/ShinyStan/server_files/pages
inst/ShinyStan/server_files/pages/explore
inst/ShinyStan/server_files/pages/explore/ui
inst/ShinyStan/server_files/pages/explore/ui/ui_trivariate_select_x.R
inst/ShinyStan/server_files/pages/explore/server
inst/ShinyStan/server_files/pages/explore/server/multiview.R inst/ShinyStan/server_files/pages/explore/server/histogram.R inst/ShinyStan/server_files/pages/explore/server/density.R inst/ShinyStan/server_files/pages/explore/server/bivariate.R inst/ShinyStan/server_files/pages/explore/server/summary_stats_param.R inst/ShinyStan/server_files/pages/explore/server/trivariate.R
inst/ShinyStan/server_files/pages/more
inst/ShinyStan/server_files/pages/more/notes_and_code.R
inst/ShinyStan/server_files/pages/diagnose
inst/ShinyStan/server_files/pages/diagnose/ui
inst/ShinyStan/server_files/pages/diagnose/ui/multitrace_customize.R
inst/ShinyStan/server_files/pages/diagnose/server
inst/ShinyStan/server_files/pages/diagnose/server/summary_stats_sampler.R inst/ShinyStan/server_files/pages/diagnose/server/autocorr.R inst/ShinyStan/server_files/pages/diagnose/server/diagnostics.R inst/ShinyStan/server_files/pages/diagnose/server/rhat_neff_mcse.R inst/ShinyStan/server_files/pages/diagnose/server/multitrace.R
inst/ShinyStan/server_files/pages/diagnose/ppcheck
inst/ShinyStan/server_files/pages/diagnose/ppcheck/ui
inst/ShinyStan/server_files/pages/diagnose/ppcheck/ui/pp_get_y_and_yrep.R
inst/ShinyStan/server_files/pages/diagnose/ppcheck/server
inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/hists_test_statistics.R inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/hists_rep_vs_obs.R inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/y_vs_avg_rep.R inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/rep_vs_resid_rep.R inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/rstanarm.R inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/pp_utils.R inst/ShinyStan/server_files/pages/diagnose/ppcheck/server/hists_resids.R inst/ShinyStan/server_files/pages/diagnose/ppcheck/ppcheck_helpers.R
inst/ShinyStan/server_files/pages/estimate
inst/ShinyStan/server_files/pages/estimate/ui
inst/ShinyStan/server_files/pages/estimate/ui/multiparam_selectize.R
inst/ShinyStan/server_files/pages/estimate/server
inst/ShinyStan/server_files/pages/estimate/server/summary_stats_latex.R inst/ShinyStan/server_files/pages/estimate/server/summary_stats.R inst/ShinyStan/server_files/pages/estimate/server/multiparameter_plot.R
inst/ShinyStan/server_files/utilities
inst/ShinyStan/server_files/utilities/par_samps_reactive.R inst/ShinyStan/server_files/utilities/extract_sso.R inst/ShinyStan/server_files/utilities/make_param_list_with_groups_sort.R
inst/ShinyStan/markdown
inst/ShinyStan/markdown/pp_check_tutorial.md
inst/ShinyStan/www
inst/ShinyStan/www/wide_ensemble.png
inst/ShinyStan/www/stan_logo.png
inst/ShinyStan/www/wide_funnel.png
inst/ShinyStan/global_utils.R
inst/ShinyStan/css
inst/ShinyStan/css/ShinyStan_dygraphs.css
inst/ShinyStan/css/ShinyStan.css
inst/ShinyStan/css/ShinyStan_datatables.css
inst/ShinyStan/ui_utils.R
inst/ShinyStan/ggplot_fns.rda
inst/ShinyStan/helper_functions
inst/ShinyStan/helper_functions/shinystan_helpers.R inst/ShinyStan/helper_functions/summary_stats_helpers.R inst/ShinyStan/helper_functions/hmc_diagnostics_helpers.R inst/ShinyStan/helper_functions/gg_theme_elements.R
inst/ShinyStan/ui_files
inst/ShinyStan/ui_files/hist_customize.R inst/ShinyStan/ui_files/rhat_neff_mcse_layout.R inst/ShinyStan/ui_files/table_latex_sidebar.R inst/ShinyStan/ui_files/diagnostics_sample.R inst/ShinyStan/ui_files/trivariate_select.R inst/ShinyStan/ui_files/multiparam_customize.R inst/ShinyStan/ui_files/PAGE_more_menu.R inst/ShinyStan/ui_files/sampler_stats_customize.R inst/ShinyStan/ui_files/diagnostics_stepsize.R inst/ShinyStan/ui_files/diagnostics_customize.R inst/ShinyStan/ui_files/PAGE_explore.R inst/ShinyStan/ui_files/diagnostics_by_parameter.R inst/ShinyStan/ui_files/diagnostics_ndivergent.R inst/ShinyStan/ui_files/about.R inst/ShinyStan/ui_files/table_customize.R inst/ShinyStan/ui_files/trivariate_customize.R inst/ShinyStan/ui_files/model_code.R inst/ShinyStan/ui_files/diagnostics_energy.R inst/ShinyStan/ui_files/PAGE_diagnose.R inst/ShinyStan/ui_files/density_customize.R inst/ShinyStan/ui_files/glossary.R inst/ShinyStan/ui_files/help.R inst/ShinyStan/ui_files/autocorr_customize.R inst/ShinyStan/ui_files/PAGE_home.R inst/ShinyStan/ui_files/PAGE_estimate.R inst/ShinyStan/ui_files/diagnostics_treedepth.R inst/ShinyStan/ui_files/pp_navlist.R inst/ShinyStan/ui_files/pp_about.R inst/ShinyStan/ui_files/dynamic_trace_helptext.R inst/ShinyStan/ui_files/table_latex_main.R inst/ShinyStan/ui_files/bivariate_customize.R inst/ShinyStan/ui_files/diagnostics_help.R inst/ShinyStan/ui_files/notepad.R inst/ShinyStan/ui_files/pp_navlist_rstanarm.R inst/ShinyStan/global.R
inst/ShinyStan/html
inst/ShinyStan/html/energy.html
inst/ShinyStan/html/neff.html
inst/ShinyStan/html/ndivergent.html
inst/ShinyStan/html/rhat.html
inst/ShinyStan/html/treedepth.html
inst/ShinyStan/html/accept_stat.html
inst/ShinyStan/html/citation.html
inst/ShinyStan/html/home_page_links.html
inst/ShinyStan/html/mcse.html
inst/ShinyStan/html/nleapfrog.html
inst/ShinyStan/html/contribs.html
inst/ShinyStan/html/nuts.html
inst/ShinyStan/html/stepsize.html
inst/ShinyStan/text
inst/ShinyStan/text/quick_mcse.txt
inst/ShinyStan/text/quick_neff.txt
inst/ShinyStan/text/quick_rhat.txt
inst/ShinyStan/server_utils.R
inst/doc
inst/doc/deploy_shinystan.html
inst/doc/shinystan-package.html
inst/doc/deploy_shinystan.Rmd
inst/doc/shinystan-package.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test_misc.R tests/testthat/test_creating_sso.R
tests/testthat/stanfit2_for_tests.rda
tests/testthat/test_using_sso.R
tests/testthat/retrieve_sso_answers
tests/testthat/retrieve_sso_answers/test_answer_quantiles.rds
tests/testthat/retrieve_sso_answers/test_answer_accept_stat.rds
tests/testthat/retrieve_sso_answers/test_answer_median.rds
tests/testthat/retrieve_sso_answers/test_answer_treedepth.rds
tests/testthat/retrieve_sso_answers/test_answer_mcse.rds
tests/testthat/retrieve_sso_answers/test_answer_divergent.rds
tests/testthat/retrieve_sso_answers/test_answer_ess.rds
tests/testthat/retrieve_sso_answers/test_answer_rhat.rds
tests/testthat/retrieve_sso_answers/test_answer_sd.rds
tests/testthat/retrieve_sso_answers/test_answer_stepsize.rds
tests/testthat/retrieve_sso_answers/test_answer_mean.rds
tests/testthat/old_sso_for_tests.rda
tests/testthat/data_for_retrieve_tests.R tests/testthat/test_deploy_shinystan.R
NAMESPACE
NEWS.md
data
data/eight_schools.rda
R
R/retrieve.R R/shinystan-objects.R R/update_sso.R R/sso-metadata.R R/rhat_ess_monitor_fns.R R/drop_parameters.R R/generate_quantity.R R/launch_shinystan.R R/misc.R R/zzz.R R/deploy_shinystan.R R/shinystan-package.R
vignettes
vignettes/deploy_shinystan.Rmd
vignettes/shinystan-package.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/figures
man/figures/stanlogo.png
man/as.shinystan.Rd man/launch_shinystan.Rd man/update_sso.Rd man/launch_shinystan_demo.Rd man/retrieve.Rd man/rename_model.Rd man/drop_parameters.Rd man/deploy_shinystan.Rd man/shinystan-class.Rd man/shinystan-metadata.Rd man/shinystan-package.Rd man/generate_quantity.Rd

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