Using expose_stan_functions in a package

[stijn]

Based on this thread

Saving the dso from expose_stan_functions

I have a workflow where I write unit test for my Stan functions in R, but run my test scripts through Makefiles. Often the test code changes faster than the Stan code and if there was a convenient way to save the functions that expose_stan_functions() exposes (like you can save the stanmodel object it would avoid needless recompilations and speed up testing. Does anyone have any experiences or ideas with this? Just saving the object returned by Rcpp::sourceCpp() using saveRDS() does not keep d…

and this one

Moving from sourceCpp to a package w/Rcpp

and this very sage advice in a third thread

@sakrejda

3. if you want to make your life easier with the package, rely on expose_stan_functions directly in your code, don’t try to compile it yourself.

I settled on adding the following bit of code in the automatically generated stanmodels.R before rm(MODELS_HOME). I also added an extra folder src/stan/stan_functions.

# Start Addition Stijn
stan_function_files <-dir(file.path(MODELS_HOME, "stan_functions"),
                      pattern = "stan$", full.names = TRUE)
lapply(stan_function_files, function(f) {
  file_name <- sub("\\.stan$", "", basename(f))
  stan_model <- rstan::stanc(f, allow_undefined = TRUE,
                             obfuscate_model_name = FALSE)
  rstan::expose_stan_functions(stan_model,
                               cacheDir = file.path(MODELS_HOME,
                                                    "stan_functions",
                                                    file_name),
                               cleanupCacheDir = TRUE)
  }
)
Rcpp::compileAttributes()
# End Addition Stijn

The code is very much modelled after what is already in stanmodels.R. That is, it loops over all files in the new folder, exposes the functions in a separate subfolder for each file, and cleans up any old .cpp (hence the separate folders). Finally, compileAttributes gathers and links all the functions.

If I figure out how stanmodels.R gets called at installation, I make a separate file with this bit of code to keep the original file pristine.