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Preparing Statistical Software with the srr package

Mark Padgham

2023-03-08

Source: vignettes/srr-stats.Rmd
srr-stats.Rmd

srr stands for Software Review Roclets, and is an R package containing roclets for general use in helping those developing and reviewing packages submitted to rOpenSci. At present, the srr package only contains roclets and associated functions to help those developing and reviewing packages submitted to rOpenSci’s system for Statistical Software Review. This vignette demonstrates how developers are intended to use this package to document the alignment of their software with rOpenSci’s standards for statistical software.

The main functions of the package are constructed as roxygen2 “roclets”, meaning that these functions are called each time package documentation is updated by calling devtools::document() or equivalently roxygen2::roxygenise(). The former is just a wrapper around the latter, to enable documentation to updated by a single call from within the devtools package. From here on, this stage of updating documentation and triggering the srr roclets will be referred to as “running roxygenise.”

1. The package skeleton

The srr_stats_pkg_skeleton() function included with this package differs from other package skeleton functions. Rather than providing a skeleton from which you can construct your own package, the srr_stats_pkg_skeleton() function generates a skeleton to help developers understand this package works. This skeleton of a package is intended to be modified to help you understand which kinds of modifications are allowed, and which generate errors. The package is by default called "demo", is constructed in R’s tempdir(), and looks like this:

library (srr)
d <- srr_stats_pkg_skeleton (pkg_name = "package")
fs::dir_tree (d)
## /tmp/Rtmp92BmFc/package
## ├── DESCRIPTION
## ├── NAMESPACE
## ├── R
## │   ├── RcppExports.R
## │   ├── package-package.R
## │   ├── srr-stats-standards.R
## │   └── test.R
## ├── README.Rmd
## ├── src
## │   ├── RcppExports.cpp
## │   └── cpptest.cpp
## └── tests
##     ├── testthat
##     │   └── test-a.R
##     └── testthat.R

The files listed there mostly exist to illustrate how standards can be included within code. The format of standards can be seen by examining any of those files. For example, the test.R file looks like this:

readLines (file.path (d, "R", "test.R"))
##  [1] "#' test_fn"                                                
##  [2] "#'"                                                        
##  [3] "#' A test funtion"                                         
##  [4] "#'"                                                        
##  [5] "#' @srrstats {G1.1, G1.2, G1.3} with some text"            
##  [6] "#' @srrstats Text can appear before standards {G2.0, G2.1}"
##  [7] "#' @srrstatsTODO {RE1.1} standards which are still to be"  
##  [8] "#' addressed are tagged 'srrstatsTODO'"                    
##  [9] "#'"                                                        
## [10] "#' @export"                                                
## [11] "test_fn <- function() {"                                   
## [12] "  message(\"This function does nothing\")"                 
## [13] "}"

That file illustrates some of the roxygen2 tags defined by this package, and described in detail below. These tags are parsed whenever package documentation is updated with roxygenise(), which will produce output like the following:

roxygen2::roxygenise (d)
## Setting `RoxygenNote` to "7.2.3"
## ℹ Loading package
## Writing NAMESPACE
## ──────────────────── rOpenSci Statistical Software Standards ───────────────────
## 
## 
## 
## ── @srrstats standards (8 / 12): 
## 
##   * [G1.1, G1.2, G1.3, G2.0, G2.1] in function 'test_fn()' on line#11 of file [R/test.R]
##   * [RE2.2] on line#2 of file [tests/testthat/test-a.R]
##   * [G2.3] in function 'test()' on line#6 of file [src/cpptest.cpp]
##   * [G1.4] on line#17 of file [./README.Rmd]
## 
## 
## 
## ── @srrstatsNA standards (1 / 12): 
## 
##   * [RE3.3] on line#5 of file [R/srr-stats-standards.R]
## 
## 
## 
## ── @srrstatsTODO standards (3 / 12): 
## 
##   * [RE4.4] on line#14 of file [R/srr-stats-standards.R]
##   * [RE1.1] on line#11 of file [R/test.R]
##   * [G1.5] on line#17 of file [./README.Rmd]
## 
## ────────────────────────────────────────────────────────────────────────────────
## 
## Writing package-package.Rd
## Writing test_fn.Rd
## Writing NAMESPACE

The “roclets” contained within this package parse any instances of the package-specified tags described below, and summarise the output by listing all locations of each kind of tag. Locations are given as file and line numbers, and where appropriate, the names of associated functions. We recommend that developers familiarise themselves with the system by simply modifying any roxygen2 block in any of the files of this package skeleton, and running roxygenise() to see what happens.

2. Enabling srr roclets for a package

The “roclets” can be enabled for a package by modifying the DESCRIPTION file so that the Roxygen line looks like this:

Roxygen: list (markdown = TRUE, roclets = c ("namespace", "rd", "srr::srr_stats_roclet"))

That will load the “roclets” used by this package to process standards as documented within your actual code. Note that you do not need to add, import, or depend upon the srr package anywhere else within the DESCRIPTION file. See the DESCRIPTION file of the package skeleton for an example.

3. roxygen2 tags

The srr packages recognises and uses the following three tags, each of which may be inserted into roxygen2 documentation blocks anywhere in your code. The tags are:

  1. @srrstats tags to indicate standards which have been addressed. These should be placed at the locations within your code where specific standards have been addressed, and should include a brief textual description of how the code at that location addresses the nominated standard.
  2. @srrstatsTODO tags to indicate standards which have not yet been addressed. The srr_stats_roxygen() function described below will place all standards for your nominated categories in an initial file in the /R directory of your project. Each of these will have a tag of @srrstatsTODO. As you address each standard, you’ll need to move it from that initial location to that point in your code where that standard is addressed, and change the tag from @srrstatsTODO to @srrstats. It may help to break the initial, commonly very long, single list of standards into smaller groups, and to move each of these into the approximate location within your code where these are likely to be addressed. For example, all standards which pertain to tests can be moved into the /tests (or /tests/testthat) directory.
  3. @srrstatsNA tags to indicate standards which you deem not applicable to your package. These need to be grouped together in a single block with a title of NA_standards. Such a block is both included in the package skeleton, and also in the output of srr_stats_roxygen() function. The numbers of any non-applicable standards can then be moved to this block, with a note explaining why these standards have been deemed not to apply to your package.

The output illustrated above shows how the srr package groups these three tags together, first collecting the output of standards which have been addressed (via @srrstats tags), then showing output of non-applicable standards (via @srrstatsNA tags), and finally standards which are still to be addressed (via @srrstatsTODO tags).

3.1 Format of srr documentation

The tags shown above from the skeleton package function test.R indicates the expected format of standards within roxygen2 documentation blocks. The package is designed to error on attempting to run roxygenise() with any inappropriately formatted entries, and so should provide informative messages to help rectify any problems. srr documentation must adhere to the following formatting requirements:

  1. The tags must appear immediately after the roxygen2-style comment symbols. This will almost always mean #' @srrstats (but see details below, under Locations of srrstats documentation).

  2. The standards number(s) must be enclosed within curly braces, such as #' @srrstats {G1.0}. Multiple standards may be associated with a single tag by including them within the same single pair of curly braces, and separating each by a comma, such as #' @srrstats {G1.0, G1.1}.

  3. Explanatory text may be placed anywhere before or after curly braces enclosing standards, such that #' @srrstats some text {G1.0} is entirely equivalent to #' @srrstats {G1.0} some text.

  4. Only the first pair of curly braces is parsed to determine standards numbers; any subsequent curly braces within one expression will be ignored. (Where an expression is everything that comes after one roxygen2 tag, and extends until the start of the next tag.) The following will accordingly only refer to G1.0, and not G1.1:

       #' @srrstats {G1.0} as well as {G1.1}.

    The appropriate way to refer to multiple tags is to include them in the one set of curly braces, as shown above, or to use separate tags, like this:

    #' @srrstats {G1.0} as well as
#' @srrstats {G1.1}

  5. Any standard may occur arbitrarily many times in any file(s) within a package. The only requirement is that any one standard should only be associated with one single kind of tag; thus should only be @srrstats (a standard which has been addressed), or @srrstatsNA (a standard which is not applicable), or @srrstatsTODO (a standard which has not yet been addressed).

In almost all cases, all tags for a package will be generated by the initial call to srr_stats_roxygen(), and should simply be moved to appropriate locations within a package’s code without modifying the format.

3.2 Locations of srrstats documentation

@srrstats tags and accompanying text can be placed almost anywhere within a package, especially in any file in the main /R, /tests, or src/ directories. Within the /R directory, tags should be placed only in roxygen2 blocks. These tags, and all associated text, will be ignored by the roclets used by roxygen2 to generate package documentation, and will only appear on screen output like that shown above, and generated when running roxygenise(). If tags need to be inserted where there is no roxygen2 block, then a new block will need to be created, the minimal requirement for which is that it then have an additional #' @noRd tag to suppress generation of documentation (.Rd) files. If that block is associated with a function, the following two lines will suffice:

#' @srrstats G1.0 This standard belongs here
#' @noRd
myfunction <- function (...) {
    # ...
}

If that block is not associated with a function, the documentation can be followed by a NULL, like this:

#' @srrstats G1.0 This standard belongs here
#' @noRd
NULL

Unlike roxygen2, which only processes blocks from within the main R/ directory, the srr package process blocks from within other directories too. As these blocks will never be passed through to the main roxygenise() function, they need neither #' @noRd tags, nor NULL definitions where none otherwise exist. An example is in the tests/ directory of the package skeleton:

readLines (file.path (d, "tests", "testthat", "test-a.R"))
## [1] "#' @srrstats {RE2.2} is addressed here"
## [2] "test_that(\"dummy test\", {"           
## [3] "    expect_true (TRUE)"                
## [4] "})"

While @srrstats tags can also be placed in the src/ directory, the package currently only parses doxygen-style blocks for code written in C or C++. (Note that srr is currently further restricted to C++ code compiled with Rcpp, but will soon be adapted to work with other C++ interfaces such as cpp11.) These blocks are converted by Rcpp into roxygen2 blocks in a file called R/RcppExports.R, and so need to include an additional @noRd tag to (optionally) suppress generation of .Rd documentation. The skeleton package again gives an example:

readLines (file.path (d, "src", "cpptest.cpp"))
##  [1] "#include <Rcpp.h>"                    
##  [2] ""                                     
##  [3] "//' src_fn"                           
##  [4] "//'"                                  
##  [5] "//' A test C++ function"              
##  [6] "//' @srrstats {G2.3} in src directory"
##  [7] "//' @noRd"                            
##  [8] "// [[Rcpp::export]]"                  
##  [9] "int test () {"                        
## [10] "    return 1L; }"

3.3 Documenting standards for documentation

Many standards refer to general package documentation, particularly in a README document, or in package vignettes. All such documents are presumed to be written in .Rmd format, for which @srrstats tags must be included within distinct code chunks. Again, the skeleton package has an example as follows:

readLines (file.path (d, "README.Rmd"))
##  [1] "# package"                                                                                
##  [2] ""                                                                                         
##  [3] "This is a skeleton of an [`srr` statistics](https://github.com/ropensci-review-tools/srr)"
##  [4] "package, intended developers to tweak as they like, in order to understand "              
##  [5] "how the package's roclets work."                                                          
##  [6] ""                                                                                         
##  [7] "This `README.Rmd` file is here to demonstrate how to embed `srr` roclet tags."            
##  [8] "These tags need to be within dedicated *code chunks*, like the following:"                
##  [9] ""                                                                                         
## [10] "```{r srr-tags, eval = FALSE, echo = FALSE}"                                              
## [11] "#' roxygen_block_name"                                                                    
## [12] "#'"                                                                                       
## [13] "#' (Add some text if you like)"                                                           
## [14] "#'"                                                                                       
## [15] "#' @srrstats {G1.4} Here is a reference to a standard"                                    
## [16] "#' @srrstatsTODO {G1.5} And here is a reference to a standard yet to be addressed"        
## [17] "```"                                                                                      
## [18] ""                                                                                         
## [19] "Note the chunk contains only [`roxygen2`](https://roxygen2.r-lib.org) lines,"             
## [20] "and nothing else at all. Please change the `eval` and `echo` parameters to"               
## [21] "see what happens when you knit the document."

Those lines illustrate the expected form. @srrstats tags should be within a single block contained within a dedicated code chunk. @srrstats chunks within .Rmd files will generally use echo = FALSE to prevent them appearing in the rendered documents. The roxygen2 lines do not need to be followed by a NULL (or any other non- roxygen2 statement), although if additional R code is necessary for any reason, you may also need to add eval = FALSE.

3.4 @srrstatsNA tags for non-applicable standards

While @srrstatsTODO and @srrstats tags may be placed anywhere within a package, @srrstatsNA tags used to denote non-applicable standards must be placed within a dedicated roxygen2 block with a title of NA_standards. As described above, both the package skeleton and the file produced by calling srr_stats_roxygen() include templates for this block. The following illustrates a minimal form:

#' NA_standards
#'
#' @srrstatsNA {S3.3} is not applicable
#' @noRd
NULL

An NA_standards block must end with NULL, rather than be associated with a function definition. There can be multiple NA_standards blocks in any location, enabling these standards to be moved to approximate locations where they might otherwise have been addressed. (For example, non-applicable standards referring to tests might all be grouped together in a single NA_standards block in the tests/ directory.)

4. The srr workflow

The first step for any developer intending to use this package on the way to a submission to rOpenSci’s project for peer-reviewing statistical software is to generate the package skeleton described above, and to try any and all conceivable ways to modify locations, formats, and other properties of the roxygen2 tags defined in this package, in order to understand how these tags are used to generate the summary results when running roxygenise. Following that initial familiarisation, a typical workflow will involve the following general steps:

  1. Automatically download and insert lists of general and category-specific standards in your package by running srr_stats_roxygen() (in the main package directory). This will by default generate a file in the R/ directory called srr-stats-standards.R, although any alternative name can also be passed to the function (or the file can be renamed after it has initially been created).
  2. Change your package’s DESCRIPTION file to use the srr roclets by adding roclets = "srr::srr_stats_roclet") to the Roxygen line, as demonstrated at the outset, as well as in the package skeleton.
  3. Run roxygenise to confirm that the roclets work on your package. You should initially see only a single list of @srrstatsTODO standards.
  4. We recommend as a first step cutting-and-pasting standards to approximate locations within your package’s code where you anticipate these standards being addressed. Multiple copies of any one standard may exist in multiple locations, so you may also repeat standards which you anticipate will be addressed in multiple locations. This should reduce a potentially very long initial list of standards down to several distinct groups of hopefully more manageable size.
  5. Begin addressing the standards by:
    • Ensuring your code conforms;
    • Moving each standard to the one or more location(s) where you think your code most directly addresses them;
    • Modifying the @srrstatsTODO tag to @srrstats
    • Changing the initial text describing the standard itself to a brief description of how your code addresses that standard.
  6. Standards which you deem not to be applicable to your package should be grouped together in a single roxygen2 block with the title NA_standards (as described above, and as generated by the srr_stats_roxygen() function).
  7. Update your documentation as frequently as you like or need, and use the output of the roclets to inform and guide the process of converting all @srrstatsTODO tags into either @srrstats or @srrstatsNA tags.

Note that we do not recommend copying files from the package skeleton into your own package for you srr documentation. The following lines demonstrate what happens if you insert actual standards into the package skeleton:

srr_stats_roxygen (category = "regression", # for example
                   filename = file.path (d, "R", "srr-stats-standards.R"),
                   overwrite = TRUE)
## ✔ Downloaded general standards
## ✔ Downloaded regression standards
## ℹ Roxygen2-formatted standards written to [srr-stats-standards.R]
roxygen2::roxygenise (d)
## ℹ Loading package
## Error: Standards [G1.1, G1.2, G1.3, G2.0, G2.1, RE2.2, G2.3, G1.4] are listed with both @srrstats and @srrstatsTODO tags.
## Please rectify to ensure these standards are only associated with one tag.

To ensure all standards are first inserted with @srrstatsTODO tags, and that there are no duplicates with other tags, please use only the srr_stats_roxygen() function.