Cite Stan packages in a project/files — stan

stan_cite() generates the correct citations for Stan packages in a directory or set of files. The {knitr} package is required to parse Quarto (.qmd) or RMarkdown (.Rmd) documents. stan_cite() uses some simple heuristics to guess which packages export functions, and also attempts to map re-exports to their origin package. Calls to library(), require(), requireNamespace(), or use() are all recognized as attaching a package.

Usage

stan_cite(
  path = ".",
  strict = TRUE,
  format = c("bibtex", "bibentry"),
  skip_dirs = .scan_skip_dirs,
  ignore_unqualified_functions = .stdlib_funs,
  quiet = getOption("stanflow.quiet", FALSE)
)

Arguments

path: A single project directory (searched recursively) or a vector of files (.R/.Rmd/.qmd).
strict: If TRUE (default), only count unqualified function calls that resolve to a single Stan package.
format: One of "bibtex" or "bibentry", specifying the return format.
skip_dirs: Defaults to directories listed in scan_skip_dirs. Character vector of directory names to skip when scanning a directory.
ignore_unqualified_functions: Defaults to exports from base R packages listed in stdlib_funs(). Character vector of function names to ignore when attributing (unqualified) calls to Stan packages. Calls like rstan::plot() will NOT be ignored even if plot is in ignore_unqualified_functions, since they are namespaced.
quiet: Logical. If TRUE, suppresses status messages.

Value

A BibTeX character vector or a bibentry object.

Details

The parsing is handled by scan_usage(); stan_cite() owns the citation lookups.