Clean up R doc

WardBrian · Feb 27, 2025 · 2e91a8b · 2e91a8b
1 parent 9a32d85
commit 2e91a8b
Show file tree

Hide file tree

Showing 12 changed files with 64 additions and 12 deletions.
diff --git a/clients/R/convert_docs.R b/clients/R/convert_docs.R
@@ -13,12 +13,9 @@ for (f in files) {
 
     # read .Rd file and convert to markdown
     rd <- rd2markdown::get_rd(file = file.path(".", "man", f))
-    md <- rd2markdown::rd2markdown(rd, fragments = c())
-    # replaces the headers with more appropriate levels for embedding
-    md_indented <- gsub("(#+)", "\\1##", md)
+    md <- rd2markdown::rd2markdown(rd, fragments = c(), level=3)
 
     # write it to the docs folder
-    writeLines(md_indented, file.path("..", "..", "docs", "languages", "_r",
-        paste0(name, ".md")))
+    writeLines(md, file.path("..", "..", "docs", "languages", "_r", paste0(name, ".md")))
 
 }
diff --git a/docs/languages/_r/HMCMetric.md b/docs/languages/_r/HMCMetric.md
@@ -1,4 +1,4 @@
-data
+ data
 
 ### Enumeration `HMCMetric`
 
@@ -10,4 +10,9 @@ An object of class `list` of length 3.
 HMCMetric
 ```
 
+#### Description
+
 Choices of metric for HMC. Can select from `$UNIT`, `$DENSE`, and `$DIAGONAL`.
+
+
+
diff --git a/docs/languages/_r/OptimizationAlgorithm.md b/docs/languages/_r/OptimizationAlgorithm.md
@@ -1,4 +1,4 @@
-data
+ data
 
 ### Enumeration `OptimizationAlgorithm`
 
@@ -10,4 +10,9 @@ An object of class `list` of length 3.
 OptimizationAlgorithm
 ```
 
+#### Description
+
 Choices of optimization algorithm. Can select from `$NEWTON`, `$BFGS`, and `$LBFGS`.
+
+
+
diff --git a/docs/languages/_r/compile_model.md b/docs/languages/_r/compile_model.md
@@ -14,6 +14,8 @@ compile_model(stan_file, stanc_args = NULL, make_args = NULL)
 
 Path to the compiled model.
 
+#### Description
+
 Compiles a Stan model.
 
 #### Details
@@ -23,3 +25,6 @@ Run TinyStan's Makefile on a `.stan` file, creating the `.so` used by the StanMo
 #### See Also
 
 `set_tinystan_path()`
+
+
+
diff --git a/docs/languages/_r/get_tinystan_path.md b/docs/languages/_r/get_tinystan_path.md
@@ -4,6 +4,8 @@
 get_tinystan_path()
 ```
 
+#### Description
+
 By default this is set to the value of the environment variable `TINYSTAN`.
 
 #### Details
@@ -13,3 +15,6 @@ If there is no path set, this function will download a matching version of TinyS
 #### See Also
 
 set_tinystan_path
+
+
+
diff --git a/docs/languages/_r/laplace_sampler.tinystan_model.md b/docs/languages/_r/laplace_sampler.tinystan_model.md
@@ -1,7 +1,7 @@
 ### Generic function `laplace_sampler`
 
 ```r
-#### S3 method for class 'tinystan_model'
+## S3 method for class 'tinystan_model'
 laplace_sampler(
   model,
   mode,
@@ -16,4 +16,9 @@ laplace_sampler(
 )
 ```
 
+#### Description
+
 Run Stan's Laplace approximation algorithm
+
+
+
diff --git a/docs/languages/_r/optimizer.tinystan_model.md b/docs/languages/_r/optimizer.tinystan_model.md
@@ -1,7 +1,7 @@
 ### Generic function `optimizer`
 
 ```r
-#### S3 method for class 'tinystan_model'
+## S3 method for class 'tinystan_model'
 optimizer(
   model,
   data = "",
@@ -24,4 +24,9 @@ optimizer(
 )
 ```
 
+#### Description
+
 Run Stan's Optimization algorithms
+
+
+
diff --git a/docs/languages/_r/pathfinder.tinystan_model.md b/docs/languages/_r/pathfinder.tinystan_model.md
@@ -1,7 +1,7 @@
 ### Generic function `pathfinder`
 
 ```r
-#### S3 method for class 'tinystan_model'
+## S3 method for class 'tinystan_model'
 pathfinder(
   model,
   data = "",
@@ -28,4 +28,9 @@ pathfinder(
 )
 ```
 
+#### Description
+
 Run Stan's pathfinder algorithm
+
+
+
diff --git a/docs/languages/_r/sampler.tinystan_model.md b/docs/languages/_r/sampler.tinystan_model.md
@@ -1,7 +1,7 @@
 ### Generic function `sampler`
 
 ```r
-#### S3 method for class 'tinystan_model'
+## S3 method for class 'tinystan_model'
 sampler(
   model,
   data = "",
@@ -32,6 +32,8 @@ sampler(
 )
 ```
 
+#### Description
+
 Run Stan's NUTS sampler
 
 #### Examples
@@ -42,3 +44,6 @@ mod <- tinystan_model(system.file('bernoulli.stan', package = 'tinystan'))
 fit = sampler(model = mod, data = data_file)
 fit
 ```
+
+
+
diff --git a/docs/languages/_r/set_tinystan_path.md b/docs/languages/_r/set_tinystan_path.md
@@ -4,8 +4,13 @@
 set_tinystan_path(path)
 ```
 
+#### Description
+
 Set the path to TinyStan.
 
 #### Details
 
 This should point to the top-level folder of the repository.
+
+
+
diff --git a/docs/languages/_r/tinystan-package.md b/docs/languages/_r/tinystan-package.md
@@ -1,7 +1,9 @@
-package
+ package
 
 ### tinystan: A tiny interface to Stan algorithms
 
+#### Description
+
  `tinystan`: A tiny interface to Stan algorithms.
 
 #### Details
@@ -11,3 +13,6 @@ tinystan (`tinystan` package) is an interface to Stan ([mc-stan.org](https://mc-
 #### Author(s)
 
 Maintainer : Brian Ward [email protected]
+
+
+
diff --git a/docs/languages/_r/tinystan_model.md b/docs/languages/_r/tinystan_model.md
@@ -4,6 +4,8 @@
 tinystan_model(lib, stanc_args = NULL, make_args = NULL, warn = TRUE)
 ```
 
+#### Description
+
 Load a Stan model, compiling if necessary.
 
 #### Examples
@@ -14,3 +16,6 @@ mod <- tinystan_model(system.file('bernoulli.stan', package = 'tinystan'))
 fit = sampler(model = mod, data = data_file)
 fit
 ```
+
+
+