Set and read options used in RStan. Some settings as options can be controlled by the user.




Arguments of the form opt = val set option opt to value val. Arguments of the form opt set the function to return option opt's value. Each argument must be a character string.


The available options are:

  1. plot_rhat_breaks: The cut off points for Rhat for which we would indicate using a different color. This is a numeric vector, defaulting to c(1.1, 1.2, 1.5, 2). The value for this option will be sorted in ascending order, so for example plot_rhat_breaks = c(1.2, 1.5) is equivalent to plot_rhat_breaks = c(1.5, 1.2).

  2. plot_rhat_cols: A vector of the same length as plot_rhat_breaks that indicates the colors for the breaks.

  3. plot_rhat_nan_col: The color for Rhat when it is Inf or NaN.

  4. plot_rhat_large_col: The color for Rhat when it is larger than the largest value of plot_rhat_breaks.

  5. rstan_alert_col: The color used in method plot of S4 class stanfit to show that the vector/array parameters are truncated.

  6. rstan_chain_cols: The colors used in methods plot and traceplot of S4 class stanfit for coloring different chains.

  7. rstan_warmup_bg_col: The background color for the warmup area in the traceplots.

  8. boost_lib: The path for the Boost C++ library used to compile Stan models. This option is valid for the whole R session if not changed again.

  9. eigen_lib: The path for the Eigen C++ library used to compile Stan models. This option is valid for the whole R session if not changed again.

  10. auto_write: A logical scalar (defaulting to FALSE) that controls whether a compiled instance of a stanmodel-class is written to the hard disk in the same directory as the .stan program.

  11. threads_per_chain: A positive integer (defaulting to 1). If the model was compiled with threading support, the number of threads to use in parallelized sections _within_ an MCMC chain (e.g., when using the Stan functions `reduce_sum()` or `map_rect()`). The actual number of CPU cores used is `chains * threads_per_chain` where `chains` is the number of parallel chains. For an example of using threading, see the Stan case study [Reduce Sum: A Minimal Example](


The values as a list for existing options and NA for non-existent options. When only one option is specified, its old value is returned.