targets R package Stan model example

The goal of this workflow is to validate a small Bayesian model using an interval-based method similar to simulation-based calibration (SBC; Cook, Gelman, and Rubin 2006; Talts et al. 2020). We simulate multiple datasets from the model and fit the model on each dataset. For each model fit, we determine if the 50% credible interval of the regression coefficient beta contains the true value of beta used to generate the data. If we implemented the model correctly, roughly 50% of the models should recapture the true beta in 50% credible intervals.

Consider stantargets

The stantargets R package is an extension to targets and cmdstanr for Bayesian data analysis, and it makes the latter two packages easier to use together. The pipeline in this repo can be written far more concisely using the tar_stan_mcmc_rep_summary() function (see this vignette). https://github.com/wlandau/stantargets-example-validation is a version of this example project that uses stantargets, and the pipeline in the _targets.R file is much simpler and easier to define.

The model

y_i ~ iid Normal(alpha + x_i * beta, sigma^2)
alpha ~ Normal(0, 1)
beta ~ Normal(0, 1)
sigma ~ HalfCauchy(0, 1)

The targets pipeline

The targets R package manages the workflow. It automatically skips steps of the pipeline when the results are already up to date, which is critical for Bayesian data analysis because it usually takes a long time to run Markov chain Monte Carlo. It also helps users understand and communicate this work with tools like the interactive dependency graph below.

library(targets)
tar_visnetwork()

How to access

You can try out this example project as long as you have a browser and an internet connection. Click here to navigate your browser to an RStudio Cloud instance. Alternatively, you can clone or download this code repository and install the R packages listed here.

How to run

In the R console, call the tar_make() function to run the pipeline. Then, call tar_read(hist) to retrieve the histogram. Experiment with other functions such as tar_visnetwork() to learn how they work.

File structure

The files in this example are organized as follows.

├── run.sh
├── run.R
├── _targets.R
├── _targets/
├── sge.tmpl
├── R
│   ├── functions.R
│   └── utils.R
├── stan
│   └── model.stan
└── report.Rmd

File	Purpose
run.sh	Shell script to run run.R in a persistent background process. Works on Unix-like systems. Helpful for long computations on servers.
run.R	R script to run tar_make() or tar_make_clustermq() (uncomment the function of your choice.)
_targets.R	The special R script that declares the targets pipeline. See tar_script() for details.
sge.tmpl	A clustermq template file to deploy targets in parallel to a Sun Grid Engine cluster. The comments in this file explain some of the choices behind the pipeline construction and arguments to tar_target().
R/functions.R	A custom R script with the most important user-defined functions.
R/utils.R	A custom R script with helper functions.
stan/model.stan	The specification of our Stan model.
report.Rmd	An R Markdown report summarizing the results of the analysis. For more information on how to include R Markdown reports as reproducible components of the pipeline, see the tar_render() function from the tarchetypes package and the literate programming chapter of the manual.

Scaling out

This computation is currently downsized for pedagogical purposes. To scale it up, open the _targets.R script and increase the number of simulations (the number inside seq_len() in the index target).

High-performance computing

You can run this project locally on your laptop or remotely on a cluster. You have several choices, and they each require modifications to run.R and _targets.R.

Mode	When to use	Instructions for run.R	Instructions for _targets.R
Sequential	Low-spec local machine or Windows.	Uncomment tar_make()	No action required.
Local multicore	Local machine with a Unix-like OS.	Uncomment tar_make_clustermq()	Uncomment options(clustermq.scheduler = "multicore")
Sun Grid Engine	Sun Grid Engine cluster.	Uncomment tar_make_clustermq()	Uncomment options(clustermq.scheduler = "sge", clustermq.template = "sge.tmpl")

References

Cook, Samantha R., Andrew Gelman, and Donald B. Rubin. 2006. “Validation of Software for Bayesian Models Using Posterior Quantiles.” Journal of Computational and Graphical Statistics 15 (3): 675–92. http://www.jstor.org/stable/27594203.

Talts, Sean, Michael Betancourt, Daniel Simpson, Aki Vehtari, and Andrew Gelman. 2020. “Validating Bayesian Inference Algorithms with Simulation-Based Calibration.” http://arxiv.org/abs/1804.06788.