Introducing shinyStan

As a project for Andrew’s Statistical Communication and Graphics graduate course at Columbia, a few of us (Michael Andreae, Yuanjun Gao, Dongying Song, and I) had the goal of giving RStan’s print and plot functions a makeover. We ended up getting a bit carried away and instead we designed a graphical user interface for interactively exploring virtually any Bayesian model fit using a Markov chain Monte Carlo algorithm.

The result is shinyStan, a package for R and an app powered by Shiny. The full version of shinyStan v1.0.0 can be downloaded as an R package from the Stan Development Team GitHub page here, and we have a demo uponline here.  If you’re not an R user, we’re working on a full online version of shinyStan too.

 

For me, there are two primary motivations behind shinyStan:

1) Interactive visual model exploration

• Immediate, informative, customizable visual and numerical summaries of model parameters and convergence diagnostics for MCMC simulations.
• Good defaults with many opportunities for customization.

2) Convenient saving and sharing

• Store the basic components of an entire project (code, posterior samples, graphs, tables, notes) in a single object.
• Export graphics into R session as ggplot2 objects for further customization and easy integration in reports or post-processing for publication.

There’s also a third thing that has me excited at the moment. That online demo I mentioned above… well, since you’ll be able to upload your own data soon enough and even add your own plots if we haven’t included something you want, imagine an interactive library of your models hosted online. I’m imaginingsomething like this except, you know, finite, useful, and for statistical models instead of books. (Quite possibly with fewer paradoxes too.) So it won’t be anything like Borges’ library, but I couldn’t resist the chance to give him a shout-out.

Finally, for those of you who haven’t converted to Stan quite yet, shinyStan is agnostic when it comes to inputs, which is to say that you don’t need to use Stan to use shinyStan (though we like it when you do). If you’re a Jags or Bugs user, or if you write your own MCMC algorithms, as long as you have some simulations in an array, matrix, mcmc.list, etc., you can take advantage of shinyStan.

If you haven’t stopped reading yet and want a more detailed list of features, release notes are below. But why read the notes when you can try it out right now! And if you do try it out, we’d love your feedback.

How to Get It

• Installation instructions for the full shinyStan R package
• shinyStan demo online

Release Notes

shinyStan v1.0.0======================================================================Interactive and customizable plots:----------------------------------------* Parameter estimates * Traceplots for individual or multiple parameters* Dynamic trace plots for individual parameters with dygraphs (JavaScript) charting library* Autocorrelation for individual or multiple parameters * Bivariate scatterplots* (New) Trivariate scatter plots (using three.js library)* (New) Distributions of Rhat, effective sample size / total sample size, monte carlo error / posterior sdCustomizable tables (via jQuery DataTables)----------------------------------------* Posterior summary statistics (can now search table with regular expressions for easier filtering)* Average, max and min of sampler parameters (for NUTS and HMC algorithms)Other features:----------------------------------------* In addition to stanfit objects, you can also use arrays of simulations and mcmc.lists with shinyStan* Model code is viewable in the shinyStan GUI* Save notes about your model* Save plots as ggplot2 objects (i.e. not just the image but an object that can be edited with functions from the ggplot2 package)* Glossaries with definitions of terms used in the tables* Generate new quantities as a function of one or two existing parametersComing soon to your local shinyStan:----------------------------------------* Graphical posterior predictive checks* shinyStan online* Deploy a shinyStan app for each of your models online to shinyapps.io (Start an online library of your models)  * Add your own custom plots to a shinystan objects so you can really store everything in one object