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 the 'Shiny' web application framework from 'RStudio' 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).


News

Version 2.4.0

  • launch_shinystan is now an S3 generic with methods. This allows developers of packages that use shinystan to create their own launch_shinystan methods instead of using a different function name or creating a naming conflict.

Version 2.3.0

Fixes

  • Fix various issues resulting in errors for models fit using static HMC (thanks to Cole Monnahan).
  • Deprecate burnin argument to as.shinystan. Use warmup instead. Only relevant for models not fit using Stan.

New features

  • Add NUTS energy diagnostic plots to Diagnose page
  • Allowing passing sampler_params to as.shinystan. This makes it possible to display sampler diagnositcs for HMC/NUTS even if not using Stan's implementation of those algorithms (thanks to Cole Monnahan)

Version 2.2.1

  • Better compatibility with latest releases of 'shinyjs' and 'DT' packages
  • shinystan::launch_shinystan_demo() now works without first having to load the package with a call to library
  • Unless running on a server, the app now stops running when browser tab is closed

Version 2.2.0-1

  • Fix bug in deploy_shinystan preventing some ShinyStan apps from being deployed

Version 2.2.0

  • Add optional argument pars to the as.shinystan method for stanfit objects, allowing a subset of parameters to be selected for inclusion in the resulting shinystan object.
  • Introduce drop_parameters function for removing parameters from a shinystan object (useful for very large objects when you only want to look at a subset of parameters).
  • Add rstanarm to Suggests (in the DESCRIPTION file) so rstanarm::pp_check can be called.
  • Allow selecting yrep from global environment for PPcheck
  • Change as.shinystan to S4 generic with methods
  • Add rsconnect to Imports in DESCRIPTION.
  • Rename some of the slots in shinystan objects. The update_sso function can be used to ensure that old shinystan objects have an internal structure compatible with this release.
  • Improve line coverage of api tests

Version 2.1.0

  • Compatibility with recent ggplot2 update
  • Select parameters via regular expressions in parameters plot ('Estimate' page)
  • Fix error when selecting an entire parameter group in parameters plot ('Estimate' page)

Version 2.0.1

  • Fixes small bugs and typos
  • Adds support for stanreg objects
  • Moves ggplot2 from Depends to Imports

Version 2.0.0 (major update, initial CRAN release)

Version 2.0.0 has a new look, a new(ish) name, and a lot of new functionality. Many bugs have also been fixed (see GitHub issue tracker).

New names

  • The name of the R package is shinystan and the app/GUI is ShinyStan.

Deploy ShinyStan apps to shinyapps.io (RStudio's ShinyApps service)

  • The deploy_shinystan function lets you easily deploy ShinyStan apps to RStudio's shinyapps.io for any of your models. Each of your apps (i.e. each of your models) will have a unique url.

Some of the new features in ShinyStan app

  • Rebranding (new look to reflect changes to Stan logo and website)
  • HMC/NUTS diagnostic plots ('Diagnose' page, 'HMC/NUTS (plots)' tab)
  • Specify transformations (e.g. log, logit, sqrt, etc.) for density, histogram, bivariate, trivariate plots (on 'Explore' page) and HMC/NUTS diagnostics plots.
  • Many plots can now also be saved as pdf
  • Bivariate scatterplot plot also shows divergent transitions and max treedepth saturation (on 'Explore' page)
  • More detailed glossary entries
  • (Experimental) Introduce basic graphical posterior predictive checking ('Diagnose' page, 'PPcheck' tab) for limited class of models
  • Option to show partial autocorrelations ('Diagnose' page, 'Autocorrelation' tab)
  • Better customization of of posterior summary statistics table
  • Many improvements to GUI design

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("shinystan")

2.5.0 by Jonah Gabry, 2 months ago


http://mc-stan.org/, http://discourse.mc-stan.org


Report a bug at https://github.com/stan-dev/shinystan/issues/


Browse source code at https://github.com/cran/shinystan


Authors: 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]


Documentation:   PDF Manual  


GPL (>= 3) license


Imports bayesplot, colourpicker, DT, dygraphs, ggplot2, gridExtra, gtools, markdown, methods, reshape2, rsconnect, rstan, stats, shinyjs, shinythemes, threejs, utils, xtable, xts

Depends on shiny

Suggests coda, knitr, rmarkdown, rstanarm, testthat


Imported by brms, idealstan, rstanarm, walkr.

Suggested by adnuts, bayesplot, breathteststan, rstan, rstantools, survHE.


See at CRAN