Rcpp

Documenting Rcpp functions and classes in R packages

Artem Sokolov and Dirk Eddelbuettel — written Jan 2, 2020 — source

Introduction

Roxygen2 is a convenient way to document functions in R packages. Based on the Doxygen model, it parses relevant information from the comments and generates the corresponding man/*.Rd files. The major strength of this model – besides not having to write *.Rd files by hand – is that documentation ends up living right next to the functionality it describes, thus enabling easy maintenance and synchronization between the two.

When using Rcpp in package development, the R functions in RcppExports.R are generated automatically from the source .cpp files. Rcpp also faithfully transcribes comment blocks from .cpp to .R. We can take advantage of this fact to add documentation directly to the .cpp files and have it appear in the package reference manual.

This vignette demonstrates four different ways to document Rcpp functions and classes in R packages. We will create an R package from scratch, add some very basic functionality and show how Roxygen2 blocks appear in the final documentation. Throughout the vignette, we will focus on base R, Rcpp and roxygen2 with no additional dependencies. There are a number of popular add-on packages helping with package development (e.g. devtools, remotes, usethis as of January 2020), and these additional helpers may be reviewed in a follow-up vignette. In case Rcpp or roxygen2 are not yet installed, do

install.packages(c("Rcpp","roxygen2"))

Create a package

We begin by initializing a package skeleton. The following functions create a new directory and establish a barebones structure for an R package with Rcpp support:

Rcpp::Rcpp.package.skeleton("testpkg", path="~/test/")

Using your favorite text editor, create a new file ~/test/testpkg/R/zzz.R and add the following lines to it:

Rcpp::loadModule("double_cpp", TRUE)

This exposes the functionality of an Rcpp module that we will use to encapsulate our C++ class. Replace "double_cpp" with your desired module name, but note that the name has to match what appears in the .cpp file below.

Add C++ functionality and Roxygen2 comment blocks

All code blocks presented in this section are part of the same contiguous .cpp file. For the purposes of this tutorial, assume that the file lives in ~/test/testpkg/src/mult.cpp. Let’s review the four different ways to introduce Roxygen2 comment blocks inside .cpp files.

Approach 1: Standalone functions

The first approach is the most straightforward and mimics traditional usage of Roxygen2 in pure R packages. The comments are placed immediately before a stand-alone function and begin with //', which Rcpp will translate into #' in the corresponding RcppExports.R file:

#include <Rcpp.h>

//' Multiplies two doubles
//'
//' @param v1 First value
//' @param v2 Second value
//' @return Product of v1 and v2
// [[Rcpp::export]]
double mult( double v1, double v2 ) {return v1*v2;}

Approach 2: Nested field structure

Classes impose an additional layer of hierarchy by grouping multiple functions and variables. We need to decide how this hierarchy should be represented in the R help pages, which themselves follow a flat format. If a class is relatively small, a simple solution is to use a nested field structure to describe individual member functions. The entire class will then appear as a single entry in the final package reference manual.

//' @name Double
//' @title Encapsulates a double
//' @description Type the name of the class to see its methods
//' @field new Constructor
//' @field mult Multiply by another Double object \itemize{
//' \item Parameter: other - The other Double object
//' \item Returns: product of the values
//' }
class Double {
public:
  Double( double v ) : value(v) {}
  double mult( const Double& other ) {return value * other.value;}
private:
  double value;
};

Approach 3: Stand-alone pages for individual class methods

Occasionally, a member function may be complex enough to require its own ? reference entry. A major advantage of Roxygen2 is that such entries can be created with relative ease by placing the corresponding comment block at the top level in a file.

//' @name Double$new
//' @title Constructs a new Double object
//' @param v A value to encapsulate

The only disadvantage is that the documentation does not live directly next to the function it describes. Unforunately, this is due to a limitation that only the top-level comment blocks are exported into R by Rcpp.

Approach 4: Rcpp module docstrings

The final place for function documentation is inside the docstring feature provided by the Rcpp modules themselves. This works well for relatively simple classes. Unfortunately, the documentation becomes overly verbose, if a class makes heavy use of templates.

RCPP_EXPOSED_CLASS(Double)
RCPP_MODULE(double_cpp) {
  using namespace Rcpp;

  class_<Double>("Double")
    .constructor<double>("Wraps a double")
    .method("mult", &Double::mult, "Multiply by another Double object")
    ;
}

Compile, install and test

After finishing ~/test/testpkg/R/zzz.R and ~/test/testpkg/src/mult.cpp, run the following commands in an R session somewhere inside ~/test/testpkg:

Rcpp::compileAttributes()           # this updates the Rcpp layer from C++ to R
roxygen2::roxygenize(roclets="rd")  # this updates the documentation based on roxygen comments

followed by the usual R CMD build and R CMD install (or equivalent helper functions via RStudio, the usethis or devtools package or alike).

The first command compiles the .cpp code and generates R/RcppExports.R. You will notice that the roxygen comment blocks are faithfully transcribed from .cpp to .R. The second command then generates the man/*.Rd files based on these roxygen blocks. Having prepared the sources, we then build and install package as usual, making it available through the standard library(testpkg) interface.

To test the package and view its documentation, start a fresh R session and examine the help pages.

library( help=testpkg )     # Lists our functions: Double, Double$new and mult
                            #     along with those generated by Rcpp.package.skeleton()
?testpkg::mult              # Approach 1: stand-alone functions
?testpkg::Double            # Approach 2: nested field structure
?testpkg::`Double$new`      # Approach 3: individual class methods
testpkg::Double             # Approach 4: docstrings

We can also make sure that the package functions as expected.

testpkg::mult(2, 3)    
# [1] 6

d1 = testpkg::Double$new(5)
d2 = testpkg::Double$new(3)
d1$mult(d2)
# [1] 15

Going Further

As mentioned above, additional packages (or tools like the RStudio IDE) offer to help with package creation, documentation, build and more. As well, the roxygen2 can do more than we showed here by auto-generating the NAMESPACE file, collating R files as needed and more. However, we feel it helps to understand what each relevant tool offers in and by itself, and also appreciate the relative simplicity of the tools describe in the Writing R Extensions manual that is part of base R. A follow-up vignette may describe the additional tools.

tags: modules  basics 

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