Catching things up

Author: medewitt

DESCRIPTION

@@ -13,14 +13,14 @@ Description: This package provides helper functions that can be used for integra
     need for Rcpp and RStan packages(and their dependencies). Using CmdStanR
     will also afford users the opportunity to use the latest developments
     within CmdStan. However, building these packages requires some work and this
-    package provides tools to assist with that,
+    package provides tools to assist with that process.
 License: MIT + file LICENSE
 URL: https://github.com/medewitt/staninside, https://michaeldewittjr.com/staninside/
 BugReports: https://github.com/medewitt/staninside/issues
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2
 Depends: 
     R (>= 3.1)
 Suggests: 

Makefile

@@ -1,2 +1,8 @@
 push:
 	Rscript --vanilla _push.R
+
+docs:
+	Rscript -e "pkgdown::build_docs()"
+
+check:
+	Rscript -e "devtools::check()"

R/copy_models.R

@@ -11,48 +11,52 @@
 #'
 #' @examples
 #' local_location <- tempdir()
-#' copy_models(pkgname = "staninside", local_location  = local_location)
+#' copy_models(pkgname = "staninside", local_location = local_location)
+copy_models <- function(pkgname = "staninside", local_location = NULL) {
+  if (is.null(local_location)) {
+    local_location <- rappdirs::user_cache_dir(appname = pkgname)
+    cli::cli_alert("`{local_location}` will be used")
+  }
 
-copy_models <- function(pkgname = "staninside", local_location  = NULL){
+  stan_code_to_copy <- find_stan_code(pkgname)
 
-	if(is.null(local_location)){
-		local_location <- rappdirs::user_cache_dir(appname = pkgname)
-		cli::cli_alert("`{local_location}` will be used")
-	}
+  pkg_location <- names(stan_code_to_copy$base_stan_location)
 
-	stan_code_to_copy <- find_stan_code(pkgname)
+  new_locations_base <- gsub(pattern = ".+/stan/", "", pkg_location)
 
-	pkg_location <- names(stan_code_to_copy$base_stan_location)
+  new_locations <- file.path(local_location, new_locations_base)
 
-	new_locations_base <- gsub(pattern = ".+/stan/","",pkg_location)
+  dirs_needed <- unique(dirname(new_locations_base))
 
-	new_locations <- file.path(local_location,new_locations_base)
+  dirs_needed <- dirs_needed[dirs_needed != "."]
 
-	dirs_needed <- unique(dirname(new_locations_base))
+  dirs_needed <- dirs_needed[!grepl(dirs_needed, pattern = ".stan")]
 
-	dirs_needed <- dirs_needed[dirs_needed!="."]
 
-	dirs_needed <- dirs_needed[!grepl(dirs_needed, pattern = ".stan")]
+  dirs_needed <- dirs_needed[!vapply(file.path(local_location, dirs_needed),
+    function(x) fs::dir_exists(path = x),
+    FUN.VALUE = logical(1)
+  )]
 
+  if (!fs::dir_exists(local_location)) {
+    fs::dir_create(local_location)
+  }
 
-	dirs_needed <- dirs_needed[!vapply(file.path(local_location,dirs_needed),
-				 function(x) fs::dir_exists(path = x), FUN.VALUE = logical(1))]
 
-	if(!fs::dir_exists(local_location)){
-		fs::dir_create(local_location)
-	}
+  if (length(dirs_needed) > 0) {
+    lapply(
+      file.path(local_location, dirs_needed),
+      function(x) fs::dir_create(path = x, recurse = TRUE)
+    )
+  }
 
+  fs::file_copy(
+    path = pkg_location,
+    new_path = new_locations,
+    overwrite = TRUE
+  )
 
-	if(length(dirs_needed)>0){
-	lapply(file.path(local_location,dirs_needed),
-				 function(x) fs::dir_create(path = x, recurse = TRUE))
-	}
+  cli::cli_alert_success("All models have been copied to your specified location")
 
-	fs::file_copy(path = pkg_location,
-								new_path =new_locations,
-								overwrite = TRUE)
-
-	cli::cli_alert_success("All models have been copied to your specified location")
-
-	invisible(new_locations)
+  invisible(new_locations)
 }

R/find_stan_code.R

@@ -6,39 +6,48 @@
 #'
 #' @param pkgname a string, the name of the package in which to
 #'     look for the Stan code.
+#' @return a list with the Stan code location within the package
+#'     and the text of the code,
 #' @export
 #' @examples
 #' find_stan_code(pkgname = "staninside")
-
-find_stan_code <- function(pkgname = "staninside"){
-
-	if(!pkgname %in% rownames(installed.packages())){
-		stop(sprintf("`%s` is not an installed package.\n", pkgname))
-	}
-
-	stan_pkg_location <- fs::dir_ls(system.file(package = pkgname),
-						 glob = "*.stan", recurse = TRUE)
-
-	stan_pkg_contents <- lapply(stan_pkg_location, readLines)
-
-	cleaner_regex <- paste(".+",pkgname,"stan", "(.+\\.stan)", sep = "/")
-	base_stan_location <- vapply(X = stan_pkg_location,
-															 function(x) gsub(pattern = cleaner_regex,
-															 								 replacement =  "\\1",
-															 								 x),
-															 FUN.VALUE = character(1))
-
-	names(stan_pkg_contents) <- base_stan_location
-
-	for(i in seq_along(stan_pkg_contents)){
-		class(stan_pkg_contents[[i]]) <- c("character", "stancode")
-	}
-
-	return(list(base_stan_location=base_stan_location,
-							stan_pkg_contents = stan_pkg_contents))
+find_stan_code <- function(pkgname = "staninside") {
+  if (!pkgname %in% rownames(installed.packages())) {
+    stop(sprintf("`%s` is not an installed package.\n", pkgname))
+  }
+
+  stan_pkg_location <- fs::dir_ls(system.file(package = pkgname),
+    glob = "*.stan", recurse = TRUE
+  )
+
+  stan_pkg_contents <- lapply(stan_pkg_location, readLines)
+
+  cleaner_regex <- paste(".+", pkgname, "stan", "(.+\\.stan)", sep = "/")
+  base_stan_location <- vapply(
+    X = stan_pkg_location,
+    function(x) {
+      gsub(
+        pattern = cleaner_regex,
+        replacement = "\\1",
+        x
+      )
+    },
+    FUN.VALUE = character(1)
+  )
+
+  names(stan_pkg_contents) <- base_stan_location
+
+  for (i in seq_along(stan_pkg_contents)) {
+    class(stan_pkg_contents[[i]]) <- c("character", "stancode")
+  }
+
+  return(list(
+    base_stan_location = base_stan_location,
+    stan_pkg_contents = stan_pkg_contents
+  ))
 }
 
-#'@export
-print.stancode <- function(x, ...){
-	cat(x, sep = "\n")
+#' @export
+print.stancode <- function(x, ...) {
+  cat(x, sep = "\n")
 }

man/copy_models.Rd

@@ -20,19 +20,19 @@ library(staninside)
 
 # Motivation
 
-Stan is a powerful language and using R (and specifically rstan) as glue to allow R users to easily interface existing models.
-Sometimes a user might wish to use a different backend (CmdStanR) or examine and modify the written Stan code directly.
+Stan is a powerful language and using R (and specifically `rstan`) as glue to allow R users to easily interface existing models.
+Sometimes a user might wish to use a different backend (`CmdStanR`) or examine and modify the written Stan code directly.
 This package seeks to allow users the ability to:
 
-* Build R packages that are not pre-compiled by rstan
+* Build R packages that are not pre-compiled by `rstan`
 * Allow users to use CmdStanR in their R packages
 * Allow users to easily see the Stan code within packages
 
 ## Building a Stan Package
 
 ### Package Infrastructure
 
-If a package developer were to build a package with stanside, they first could create the package directory in the usual ways.
+If a package developer were to build a package with `staninside`, they first could create the package directory in the usual ways.
 
 Next, to build the appropriate structure the author could call
 
@@ -62,7 +62,7 @@ These separate `.stan` files can then be accessed within the Stan code with the
 ### Model Fitting
 
 Generally speaking, there will be some function in an R package that will fit the data to a model. 
-In order to faciliate this fitting with a CmdStanR backend, a process like that below could be used.
+In order to facilitate this fitting with a CmdStanR backend, a process like that below could be used.
 
 ```r