From 3ec6d57287faa14185c5627cf423e74b798edcfb Mon Sep 17 00:00:00 2001
From: Sam <s.e.abbott12@gmail.com>
Date: Wed, 28 Aug 2024 19:58:11 +0100
Subject: [PATCH] add input for stan r functions

---
 R/pcd-stan-tools.R             | 14 ++++++++++----
 man/pcd_load_stan_functions.Rd |  4 ++++
 man/pcd_stan_functions.Rd      |  6 +++++-
 3 files changed, 19 insertions(+), 5 deletions(-)

diff --git a/R/pcd-stan-tools.R b/R/pcd-stan-tools.R
index 20e06f9..5250dac 100644
--- a/R/pcd-stan-tools.R
+++ b/R/pcd-stan-tools.R
@@ -9,12 +9,14 @@ pcd_stan_path <- function() {
 
 #' List available Stan functions
 #'
+#' @inheritParams pcd_load_stan_functions
 #' @return A character vector of available Stan function names
 #' @export
 #' @aliases pcd_stan_functions
-pcd_stan_functions <- function() {
+pcd_stan_functions <- function(
+    stan_path = primarycensoreddist::pcd_stan_path()) {
   stan_files <- list.files(
-    pcd_stan_path(),
+    stan_path,
     pattern = "\\.stan$", full.names = TRUE,
     recursive = TRUE
   )
@@ -37,6 +39,9 @@ pcd_stan_functions <- function() {
 #' @param functions Character vector of function names to load. Defaults to all
 #' functions.
 #'
+#' @param stan_path Character string, the path to the Stan code. Defaults to the
+#' path to the Stan code in the primarycensoreddist package.
+#'
 #' @param wrap_in_block Logical, whether to wrap the functions in a
 #' `functions{}` block. Default is FALSE.
 #'
@@ -50,10 +55,11 @@ pcd_stan_functions <- function() {
 #' @export
 #' @aliases pcd_load_stan_functions
 pcd_load_stan_functions <- function(
-    functions = NULL, wrap_in_block = FALSE, write_to_file = FALSE,
+    functions = NULL, stan_path = primarycensoreddist::pcd_stan_path(),
+    wrap_in_block = FALSE, write_to_file = FALSE,
     output_file = "pcd_stan_functions.stan") {
   stan_files <- list.files(
-    pcd_stan_path(),
+    stan_paths,
     pattern = "\\.stan$", full.names = TRUE,
     recursive = TRUE
   )
diff --git a/man/pcd_load_stan_functions.Rd b/man/pcd_load_stan_functions.Rd
index 633e24b..d4c256f 100644
--- a/man/pcd_load_stan_functions.Rd
+++ b/man/pcd_load_stan_functions.Rd
@@ -6,6 +6,7 @@
 \usage{
 pcd_load_stan_functions(
   functions = NULL,
+  stan_path = primarycensoreddist::pcd_stan_path(),
   wrap_in_block = FALSE,
   write_to_file = FALSE,
   output_file = "pcd_stan_functions.stan"
@@ -15,6 +16,9 @@ pcd_load_stan_functions(
 \item{functions}{Character vector of function names to load. Defaults to all
 functions.}
 
+\item{stan_path}{Character string, the path to the Stan code. Defaults to the
+path to the Stan code in the primarycensoreddist package.}
+
 \item{wrap_in_block}{Logical, whether to wrap the functions in a
 \verb{functions\{\}} block. Default is FALSE.}
 
diff --git a/man/pcd_stan_functions.Rd b/man/pcd_stan_functions.Rd
index 42b991e..6cc0b77 100644
--- a/man/pcd_stan_functions.Rd
+++ b/man/pcd_stan_functions.Rd
@@ -4,7 +4,11 @@
 \alias{pcd_stan_functions}
 \title{List available Stan functions}
 \usage{
-pcd_stan_functions()
+pcd_stan_functions(stan_path = primarycensoreddist::pcd_stan_path())
+}
+\arguments{
+\item{stan_path}{Character string, the path to the Stan code. Defaults to the
+path to the Stan code in the primarycensoreddist package.}
 }
 \value{
 A character vector of available Stan function names