reorg and add a test

.Rbuildignore

@@ -22,4 +22,5 @@
 ^Meta$
 ^\.vscode$
 ^CITATION\.cff$
-^stan\.Rmd$
+^using-stan-tools\.Rmd$
+^fitting-dists-with-stan\.Rmd$

NEWS.md

@@ -4,11 +4,12 @@
 
 * Added support for `swindow = 0` to `rprimarycensoreddist` to allow for non-secondary event censored distributions.
 * Adapted `rprimarycensoreddist` so that truncation is based on the primary censored distribution before secondary events are censored. This better matches the generative process.
+* Added a new Stan interface tool to enable finding which files functions are implemented in the Stan code.
 
 ## Documentation
 
 * Added a getting started vignette.
-* Added a vignette showcasing how to use the package Stan code in a modeling workflow.
+* Added a vignette showcasing how to use the package Stan code with `cmdstanr`.
 
 # primarycensoreddist 0.1.0
 

_pkgdown.yml

@@ -21,10 +21,12 @@ navbar:
     articles:
       text: Articles
       menu:
+      - text: How to use primarycensoreddist with Stan
+        href: articles/using-stan-tools.html
       - text: Fitting distributions using primarycensorseddist and cmdstan
-        href: articles/stan.html
+        href: articles/fitting-dists-with-stan.html
       - text: Fitting distributions using primarycensorseddist and fitdistr
-        href: articles/fitdistr.html
+        href: articles/fitting-dists-with-fitdistr.html
 
 authors:
   Sam Abbott:

tests/testthat/test-pcd-stan-tools.R

@@ -114,3 +114,31 @@ test_that("pcd_load_stan_functions loads functions from specific files", {
   }
   expect_false(grepl("expgrowth_pdf", stan_code, fixed = TRUE))
 })
+
+test_that("pcd_stan_files returns correct files", {
+  # Test with no functions specified
+  all_files <- pcd_stan_files()
+  expect_type(all_files, "character")
+  expect_gt(length(all_files), 0)
+  expect_true(all(grepl("\\.stan$", all_files)))
+
+  # Test with specific functions
+  expgrowth_functions <- c("expgrowth_pdf", "expgrowth_lpdf")
+  expgrowth_files <- pcd_stan_files(functions = expgrowth_functions)
+  expect_type(expgrowth_files, "character")
+  expect_gt(length(expgrowth_files), 0)
+  expect_true(all(grepl("expgrowth", expgrowth_files)))
+
+  # Test with functions from different files
+  mixed_functions <- c("expgrowth_pdf", "primary_censored_integrand")
+  mixed_files <- pcd_stan_files(functions = mixed_functions)
+  expect_type(mixed_files, "character")
+  expect_gt(length(mixed_files), 1)
+  expect_true(any(grepl("expgrowth", mixed_files)))
+  expect_true(any(grepl("primary_censored", mixed_files)))
+
+  # Test with non-existent function
+  non_existent <- pcd_stan_files(functions = "non_existent_function")
+  expect_type(non_existent, "character")
+  expect_length(non_existent, 0)
+})

vignettes/fitting-dists-with-stan.Rmd

@@ -0,0 +1,18 @@
+---
+title: "Fitting distributions using primarycensorseddist and cmdstan"
+description: "A guide on how to use primarycensoreddist with Stan for Bayesian inference of epidemiological delay distributions."
+author: Sam Abbott
+output:
+  bookdown::html_document2:
+    fig_caption: yes
+    code_folding: show
+pkgdown:
+  as_is: true
+bibliography: library.bib
+csl: https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl
+link-citations: true
+vignette: >
+  %\VignetteIndexEntry{Fitting distributions using primarycensorseddist and cmdstan}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---

vignettes/stan.Rmd → vignettes/using-stan-tools.Rmd

@@ -1,6 +1,6 @@
 ---
-title: "Fitting distributions using primarycensorseddist and cmdstan"
-description: "A guide on how to use primarycensoreddist with Stan for Bayesian inference."
+title: "How to use primarycensoreddist with Stan"
+description: "A guide on how to use primarycensoreddist with Stan."
 author: Sam Abbott
 output:
   bookdown::html_document2:
@@ -12,7 +12,7 @@ bibliography: library.bib
 csl: https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl
 link-citations: true
 vignette: >
-  %\VignetteIndexEntry{Fitting distributions using primarycensorseddist and cmdstan}
+  %\VignetteIndexEntry{How to use primarycensoreddist with Stan}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -22,13 +22,12 @@ vignette: >
 
 ## What are we going to do in this Vignette
 
-In this vignette, we'll explore how to use the `primarycensoreddist` package in conjunction with Stan for Bayesian inference on censored data. We'll cover the following key points:
+In this vignette, we'll explore how to use the `primarycensoreddist` package in conjunction with Stan. We'll cover the following key points:
 
 1. Introduction to Stan and its relevance for our analysis
 2. Overview of the packages we'll be using
 3. How to access and use Stan functions provided by `primarycensoreddist`
 4. Methods for integrating these Stan functions into your workflow
-5. Practical examples of fitting distributions to censored data using Stan
 
 ## What is Stan and why are we using it
 
@@ -137,31 +136,3 @@ We can now use the function in R. Note that this may get slightly more complicat
 ```{r}
 expgrowth_rng(0, 1, 0.4)
 ```
-
-# Fitting a delay estimation model
-
-## Simulating data in R
-
-## Writing a naive model in Stan
-
-## Fitting the model using cmdstan
-
-## Comparing posterior estimates with true values
-
-## Writing a model using primarycensoreddist Stan functions
-
-## Comparing posterior estimates with true values
-
-# Fitting a convolution model
-
-## Simulating data in R
-
-## Writing a model using primarycensoreddist Stan functions
-
-## Fitting the model using cmdstan
-
-## Comparing posterior estimates with true values
-
-# Other options for fitting primarycensoreddist models with Stan
-
-## Future support for other packages