Compile a stan model while pointing at the package default include directory (stan) for #include statements

This function reads in and optionally compiles a Stan model. It is written to search the installed package stan directory for additional source files to include. Within each stan file, use #include {path to your file with the stan directory}.stan

Usage

compile_model(
  model_filepath = system.file("stan", "wwinference.stan", package = "wwinference"),
  include_paths = system.file("stan", package = "wwinference"),
  threads = FALSE,
  target_dir = tempdir(),
  stanc_options = list(),
  cpp_options = list(),
  verbose = TRUE,
  ...
)

Arguments

model_filepath: path to .stan file defining the model, default is `system.file("stan", "wwinference.stan", package = "wwinference")
include_paths: path(s) to directories to search for files specified in #include statements. Passed to cmdstanr::cmdstan_model(). Defaults to the stan subdirectory of the installed wwinference package.
threads: Number of threads to use in model compilation, as an integer. Passed to cmdstanr::cmdstan_model(). Default FALSE (use single-threaded compilation).
target_dir: Directory in which to save the compiled stan model binary. Passed as the dir keyword argument to cmdstanr::cmdstan_model(). Defaults to a temporary directory for the R session (the output of tempdir()).
stanc_options: Options for the stan compiler passed to cmdstanr::cmdstan_model(), as a list. See that function's documentation for more details. Default list() (use default options).
cpp_options: Options for the C++ compiler passed to cmdstanr::cmdstan_model(), as a list. See that function's documentation for more details. Default list() (use default options).
verbose: Write detailed output to the terminal while executing the function? Boolean, default TRUE.
...: Additional keyword arguments passed to cmdstanr::cmdstan_model().

Value

The resulting cmdstanr model object, as the output of cmdstanr::cmdstan_model().

Details

The code for this function has been adapted from code written (under an MIT license) as part of the epinowcast R package.