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

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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).

Author
Jonah 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 publication
2016-08-31 20:47:31
Maintainer
Jonah Gabry <jsg2201@columbia.edu>
License
GPL (>= 3)
Version
2.2.1
URLs

View on CRAN

Man pages

as.shinystan
Create and test shinystan objects
deploy_shinystan
Deploy a ShinyStan app on the web using shinyapps.io by...
drop_parameters
Drop parameters from a shinystan object
generate_quantity
Add new quantity to shinystan object
launch_shinystan
Launch the ShinyStan app
launch_shinystan_demo
ShinyStan demo
rename_model
rename_model (deprecated)
retrieve
Get summary statistics from shinystan object
shinystan-class
S4 shinystan objects
shinystan-metadata
View or change metadata associated with a shinystan object
shinystan-package
ShinyStan interface and shinystan R package
update_sso
Update an object created by the previous version of shinystan

Files in this package

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