clean up documents and documentation

Author: medewitt

.Rbuildignore

@@ -12,3 +12,5 @@
 ^_push\.R$
 ^Makefile$
 ^\.pre-commit-config\.yaml$
+^doc$
+^Meta$

.gitignore

@@ -4,3 +4,5 @@
 .httr-oauth
 .DS_Store
 inst/doc
+/doc/
+/Meta/

NAMESPACE

@@ -5,4 +5,8 @@ export(clear_stan_cache)
 export(copy_models)
 export(find_stan_code)
 export(setup_stan_package)
+importFrom(fs,dir_create)
+importFrom(fs,dir_exists)
+importFrom(fs,file_copy)
+importFrom(rappdirs,user_cache_dir)
 importFrom(utils,installed.packages)

R/clear_stan_cache.R

@@ -7,11 +7,12 @@
 #' @section Warning:
 #' This will removed cached models and requires that `rappdirs` is installed
 #' @returns invisible null
+#' @importFrom rappdirs user_cache_dir
 #' @export
 
-clear_stan_cache <- function(pkgname){
-	requireNamespace(pkgname)
-	app_loc <- rappdirs::user_cache_dir(pkgname)
-	unlink(app_loc, recursive = TRUE)
-	invisible(NULL)
+clear_stan_cache <- function(pkgname) {
+  requireNamespace(pkgname)
+  app_loc <- rappdirs::user_cache_dir(pkgname)
+  unlink(app_loc, recursive = TRUE)
+  invisible(NULL)
 }

R/copy_models.R

@@ -7,6 +7,7 @@
 #' @param local_location a file path representing the desired location
 #'   of the local copy.
 #' @returns file path of newly created files
+#' @importFrom fs dir_create dir_exists file_copy
 #' @export
 #'
 #' @examples

README.md

@@ -10,6 +10,7 @@
 coverage](https://codecov.io/gh/medewitt/staninside/branch/main/graph/badge.svg)](https://codecov.io/gh/medewitt/staninside?branch=main)
 [![CRAN
 status](https://www.r-pkg.org/badges/version/staninside)](https://CRAN.R-project.org/package=staninside)
+[![R-CMD-check](https://github.com/medewitt/staninside/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/medewitt/staninside/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 The goal of staninside is to facilitate the use of

_push.R

@@ -1,3 +1,8 @@
+devtools::document()
+devtools::build_readme()
+devtools::build_vignettes()
+devtools::check()
+
 rmarkdown::render("README.Rmd", output_file = "README.md")
 pkgdown::build_site()
 codemetar::write_codemeta()

vignettes/using-staninside.Rmd

@@ -63,6 +63,7 @@ These separate `.stan` files can then be accessed within the Stan code with the
 
 Generally speaking, there will be some function in an R package that will fit the data to a model. 
 In order to facilitate this fitting with a CmdStanR backend, a process like that below could be used.
+Note that this model assumes that cmdstanr is installed, though this could be replaced with other ways of calling Stan (e.g., `rstan`).
 
 ```r
 
@@ -73,22 +74,30 @@ fit_my_data <- function(my_data){
     if (length(list.files(local_location, pattern = ".stan")) > 1) {
         cli::cli_alert_info("Using cached Stan models")
         cli::cli_alert_info(
-        "Use `intervalcalc::clear_cache` if you need to refresh")
+        "Use `staninside::clear_stan_cache('mypackage')` if you need to refresh")
     } else {
         cli::cli_alert_info("Copying Stan models to cache")
         staninside::copy_models(this_pkg())
         cli::cli_alert_success("Models copied!")
     }
 
     model_file_path <- file.path(local_location, paste0("base", ".stan"))
-        mod <- cmdstanr::cmdstan_model(model_file_path)
+    mod <- cmdstanr::cmdstan_model(model_file_path)
 
-   fit <- mod$sample(data = my_data)
+    fit <- mod$sample(data = my_data)
 
-   return(fit)
+    return(fit)
 }
 
 ```
 
+You now can call `fit_my_data` to fit your model.
+The underlying Stan code is stored in the user cache directory and will be compiled on the first model fitting operation.
+
+
+
+
+
+