use_rstan: Add Stan infrastructure to an existing package

In rstantools: Tools for Developing R Packages Interfacing with 'Stan'

Add Stan infrastructure to an existing package

Description

Add Stan infrastructure to an existing R package. To create a new package containing Stan programs use rstan_create_package() instead.

Usage

use_rstan(pkgdir = ".", license = TRUE, auto_config = TRUE)

Arguments

pkgdir	Path to package root folder.
license	Logical or character; whether or not to paste the contents of a license.stan file at the top of all Stan code, or path to such a file. If TRUE (the default) adds the ⁠GPL (>= 3)⁠ license (see Details).
auto_config	Whether to automatically configure Stan functionality whenever the package gets installed (see Details). Defaults to TRUE.

Details

Prepares a package to compile and use Stan code by performing the following steps:

1. Create inst/stan folder where all .stan files defining Stan models should be stored.

2. Create inst/stan/include where optional license.stan file is stored.

3. Create inst/include/stan_meta_header.hpp to include optional header files used by Stan code.

4. Create src folder (if it doesn't exist) to contain the Stan C++ code.

5. Create R folder (if it doesn't exist) to contain wrapper code to expose Stan C++ classes to R.

6. Update DESCRIPTION file to contain all needed dependencies to compile Stan C++ code.

7. If NAMESPACE file is generic (i.e., created by rstan_create_package()), append import(Rcpp, methods), importFrom(rstan, sampling), importFrom(rstantools, rstan_config), importFrom(RcppParallel, RcppParallelLibs), and useDynLib directives. If NAMESPACE is not generic, display message telling user what to add to NAMESPACE for themselves.

When auto_config = TRUE, a configure[.win] file is added to the package, calling rstan_config() whenever the package is installed. Consequently, the package must list rstantools in the DESCRIPTION Imports field for this mechanism to work. Setting auto_config = FALSE removes the package's dependency on rstantools, but the package then must be manually configured by running rstan_config() whenever stanmodel files in inst/stan are added, removed, or modified.

Value

Invisibly, TRUE or FALSE indicating whether or not any files or folders where created or modified.

Using the pre-compiled Stan programs in your package

The stanmodel objects corresponding to the Stan programs included with your package are stored in a list called stanmodels. To run one of the Stan programs from within an R function in your package just pass the appropriate element of the stanmodels list to one of the rstan functions for model fitting (e.g., sampling()). For example, for a Stan program "foo.stan" you would use rstan::sampling(stanmodels$foo, ...).

rstantools documentation built on May 29, 2024, 4:02 a.m.