Compile a Stan program

The $compile() method of a CmdStanModel object checks the syntax of the Stan program, translates the program to C++, and creates a compiled executable. To just check the syntax of a Stan program without compiling it use the $check_syntax() method instead.

In most cases the user does not need to explicitly call the $compile() method as compilation will occur when calling cmdstan_model(). However it is possible to set compile=FALSE in the call to cmdstan_model() and subsequently call the $compile() method directly.

After compilation, the paths to the executable and the .hpp file containing the generated C++ code are available via the $exe_file() and $hpp_file() methods. The default is to create the executable in the same directory as the Stan program and to write the generated C++ code in a temporary directory. To save the C++ code to a non-temporary location use $save_hpp_file(dir).

compile(
  quiet = TRUE,
  dir = NULL,
  pedantic = FALSE,
  include_paths = NULL,
  user_header = NULL,
  cpp_options = list(),
  stanc_options = list(),
  force_recompile = getOption("cmdstanr_force_recompile", default = FALSE),
  compile_model_methods = FALSE,
  compile_hessian_method = FALSE,
  compile_standalone = FALSE,
  dry_run = FALSE,
  threads = FALSE
)

Arguments

quiet: (logical) Should the verbose output from CmdStan during compilation be suppressed? The default is TRUE, but if you encounter an error we recommend trying again with quiet=FALSE to see more of the output.
dir: (string) The path to the directory in which to store the CmdStan executable (or .hpp file if using $save_hpp_file()). The default is the same location as the Stan program.
pedantic: (logical) Should pedantic mode be turned on? The default is FALSE. Pedantic mode attempts to warn you about potential issues in your Stan program beyond syntax errors. For details see the Pedantic mode chapter in the Stan Reference Manual. Note: to do a pedantic check for a model without compiling it or for a model that is already compiled the $check_syntax() method can be used instead.
include_paths: (character vector) Paths to directories where Stan should look for files specified in #include directives in the Stan program.
user_header: (string) The path to a C++ file (with a .hpp extension) to compile with the Stan model.
cpp_options: (list) Any makefile options to be used when compiling the model (STAN_THREADS, STAN_MPI, STAN_OPENCL, etc.). Anything you would otherwise write in the make/local file. For an example of using threading see the Stan case study Reduce Sum: A Minimal Example.
stanc_options: (list) Any Stan-to-C++ transpiler options to be used when compiling the model. See the Examples section below as well as the stanc chapter of the CmdStan Guide for more details on available options: https://mc-stan.org/docs/cmdstan-guide/stanc.html.
force_recompile: (logical) Should the model be recompiled even if was not modified since last compiled. The default is FALSE. Can also be set via a global cmdstanr_force_recompile option.
compile_model_methods: (logical) Compile additional model methods (log_prob(), grad_log_prob(), constrain_variables(), unconstrain_variables()).
compile_hessian_method: (logical) Should the (experimental) hessian() method be be compiled with the model methods?
compile_standalone: (logical) Should functions in the Stan model be compiled for use in R? If TRUE the functions will be available via the functions field in the compiled model object. This can also be done after compilation using the $expose_functions() method.
dry_run: (logical) If TRUE, the code will do all checks before compilation, but skip the actual C++ compilation. Used to speedup tests.
threads: Deprecated and will be removed in a future release. Please turn on threading via cpp_options = list(stan_threads = TRUE) instead.

Value

The $compile() method is called for its side effect of creating the executable and adding its path to the CmdStanModel object, but it also returns the CmdStanModel object invisibly.

After compilation, the $exe_file(), $hpp_file(), and $save_hpp_file()

methods can be used and return file paths.

Examples

# \dontrun{
file <- file.path(cmdstan_path(), "examples/bernoulli/bernoulli.stan")

# by default compilation happens when cmdstan_model() is called.
# to delay compilation until calling the $compile() method set compile=FALSE
mod <- cmdstan_model(file, compile = FALSE)
mod$compile()
mod$exe_file()
#> [1] "/Users/jgabry/.cmdstan/cmdstan-2.33.1/examples/bernoulli/bernoulli"

# turn on threading support (for using functions that support within-chain parallelization)
mod$compile(force_recompile = TRUE, cpp_options = list(stan_threads = TRUE))
mod$exe_file()
#> [1] "/Users/jgabry/.cmdstan/cmdstan-2.33.1/examples/bernoulli/bernoulli"

# turn on pedantic mode (new in Stan v2.24)
file_pedantic <- write_stan_file("
parameters {
  real sigma;  // pedantic mode will warn about missing <lower=0>
}
model {
  sigma ~ exponential(1);
}
")
mod <- cmdstan_model(file_pedantic, pedantic = TRUE)
#> Warning in '/var/folders/s0/zfzm55px2nd2v__zlw5xfj2h0000gn/T/RtmpAMFHpW/model-5f0d242e1d46.stan', line 6, column 2: Parameter
#>     sigma is given a exponential distribution, which has strictly positive
#>     support, but sigma was not constrained to be strictly positive.

# }

Arguments

Value

See also

Examples