Merge pull request #4 from onnela-lab/cran-rev1

Address comments from CRAN review.

.Rbuildignore

@@ -10,3 +10,4 @@ Makefile
 ^LICENSE\.md$
 ^gptoolsStan\.Rcheck$
 ^.*?\.tar\.gz$
+^playground$

.gitignore

@@ -10,3 +10,4 @@ build
 .DS_Store
 CRAN-SUBMISSION
 .Rhistory
+playground

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: gptoolsStan
-Title: Gaussian Processes on Graphs and Lattices in Stan
+Title: Gaussian Processes on Graphs and Lattices in 'Stan'
 Version: 0.1.0
 Authors@R: c(
     person("Till", "Hoffmann", , "[email protected]", role = c("aut", "cre"),
@@ -8,9 +8,11 @@ Authors@R: c(
            comment = c(ORCID = "0000-0001-6613-8668")))
 Description: Gaussian processes are flexible distributions to model functional data. Whilst
     theoretically appealing, they are computationally cumbersome except for small datasets.
-    This package implements two methods for scaling GP inference in Stan. First, a sparse
-    approximation of the likelihood that is generally applicable and, second, an exact method for
-    regularly spaced data modeled by stationary kernels using fast Fourier methods.
+    This package implements two methods for scaling Gaussian process inference in 'Stan'. First, a
+    sparse approximation of the likelihood that is generally applicable and, second, an exact method
+    for regularly spaced data modeled by stationary kernels using fast Fourier methods. Utility
+    functions are provided to compile and fit 'Stan' models using the 'cmdstanr' interface.
+    References: Hoffmann and Onnela (2022) <arXiv:2301.08836>.
 License: MIT + file LICENSE
 Encoding: UTF-8
 Language: en-US

R/model.R

@@ -1,6 +1,18 @@
-#' Get the gptools include path for compiling Stan programs with `cmdstanr`.
+#' Get the 'gptoolsStan' include path for compiling 'Stan' programs.
 #'
 #' @export
+#' @return Path to the directory containing source files for 'gptoolsStan' as characters.
+#' @examples
+#' \dontrun{
+#' library(cmdstanr)
+#' library(gptoolsStan)
+#'
+#' # Compile the model with paths set up to include 'Stan' sources from 'gptoolsStan'.
+#' model <- cmdstan_model(
+#'   stan_file="/path/to/your/model.stan",
+#'   include_paths=gptools_include_path(),
+#' )
+#' }
 gptools_include_path <- function() {
     system.file("extdata", package="gptoolsStan")
 }

cran-comments.md

@@ -1,4 +1,36 @@
-## R CMD check results
+# Revisions in response to comments from 2023-12-18 for resubmission of 0.1.0.
+
+Thank you for the comments. Please find point-by-point responses below. Code changes are available at https://github.com/onnela-lab/gptoolsStan/pull/4.
+
+> Please always write package names, software names and API (application programming interface) names in single quotes in title and description. e.g: --> 'Stan' Please note that package names are case sensitive.
+
+We have wrapped 'Stan' and 'cmdstanr' in single quotes.
+
+> Please always explain all acronyms in the description text. -> 'GP'
+
+We have expanded acronyms.
+
+> If there are references describing the methods in your package, please add these in the description field of your DESCRIPTION file in the form
+> authors (year) <doi:...>
+> authors (year) <arXiv:...>
+> authors (year, ISBN:...)
+> or if those are not available: <https:...>
+> with no space after 'doi:', 'arXiv:', 'https:' and angle brackets for auto-linking. (If you want to add a title as well please put it in quotes: "Title")
+
+We have added a reference.
+
+> Please add `\value` to `.Rd` files regarding exported methods and explain the functions results in the documentation. Please write about the structure of the output (class) and also what the output means. (If a function does not return a value, please document that too, e.g. `\value{No return value, called for side effects}` or similar)
+> Missing Rd-tags:
+>
+>    - `gptools_include_path.Rd: \value`
+
+We have added a `\value` tag.
+
+> Please add small executable examples in your Rd-files to illustrate the use of the exported function but also enable automatic testing.
+
+We have added an example to the `.Rd` files. It is however wrapped in `\dontrun` because running the example requires that 'cmdstan' and 'cmdstanr' are installed.
+
+# R CMD check results for first submission 0.1.0.
 
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