Rcpp 0.9.0 announcement

December 25, 2010
By

(This article was first published on Thinking inside the box , and kindly contributed to R-bloggers)

The text below went out as a post to the r-packages list a few days ago, but I thought it would make sense to post it on the blog too. So with a little html markup...

Summary

Version 0.9.0 of the Rcpp package is now on CRAN and its mirrors. This release marks another step in the development of the package, and a few key points are highlighted below. More details are in the NEWS and ChangeLog files included in the package.

Overview

Rcpp is an R package and associated C++ library that facilitates integration of C++ code in R packages. The package features a complete set of C++ classes (Rcpp::IntegerVector, Rcpp:NumericVector, Rcpp::Function, Rcpp::Environment, ...) that makes it easier to manipulate R objects of matching types (integer vectors, functions, environments, etc ...). Rcpp takes advantage of C++ language features such as the explicit constructor / destructor lifecycle of objects to manage garbage collection automatically and transparently. We believe this is a major improvement over use of PROTECT / UNPROTECT. When an Rcpp object is created, it protects the underlying SEXP so that the garbage collector does not attempt to reclaim the memory. This protection is withdrawn when the object goes out of scope. Moreover, users generally do not need to manage memory directly (via calls to new / delete or malloc / free) as this is done by the Rcpp classes or the corresponding STL containers. A few key points about Rcpp:
  • a rich API covering all core R data types including vectors, matrices, functions, environments, ... (with the exeception of factors which are less useful in C++)
  • seamless (bi-directional) data interchange between R and C++
  • possibility of inline use permitting definition, compilation, linking and loading of C++ functions directly from R
  • extensive documentation now covering eight vignettes
  • exception handling and error propagation back to R
  • extensive test suite using RUnit covering over 700 tests
  • extension packages RcppArmadillo and RcppGSL provide easy-to-use integration with the Armadillo (linear algebra) and GNU GSL librasries
  • increasing adoption among R users and package developers with now twenty packages from CRAN or BioConductor depending on Rcpp
  • support for the legacy 'classic' Rcpp is now provided by the RcppClassic package which is being released concurrently with Rcpp 0.9.0
Several key features were added during the 0.8.* cycles and are described below.

Rcpp sugar

Rcpp now provides syntactic sugar: vectorised expressions at the C++ level which are motivated by the corresponding R expressions. This covers operators (binary arithmetic, binary logical, unary), functions (producing single logical results, mathematical functions and d/p/q/r statistical functions). Examples comprises anything from ifelse() to pmin()/pmax() or A really simply example is a function
    SEXP foo( SEXP xx, SEXP yy){
        NumericVector x(xx), y(yy) ;
        return ifelse( x < y, x*x, -(y*y) ) ;
    }
which deploys the sugar 'ifelse' function modeled after the corresponding R function. Another simple example is
    double square( double x){
        return x*x ;
    }

    SEXP foo( SEXP xx ){
        NumericVector x(xx) ;
        return sapply( x, square ) ;
    }
where use the sugar function 'sapply' to sweep a simple C++ function which operates elementwise across the supplied vector. The Rcpp-sugar vignette describes sugar in more detail.

Rcpp modules

Rcpp modules are inspired by Boost.Python and make exposing C++ functions or classes to R even easier. A first illustration is provided by this simple C++ code snippet
    const char* hello( const std::string& who ){
        std::string result( "hello " ) ;
        result += who ;
        return result.c_str() ;
    }

    RCPP_MODULE(yada){
        using namespace Rcpp ;
        function( "hello", &hello ) ;
    }
which (after compiling and loading) we can access in R as
    yada <- Module( "yada" )
    yada$hello( "world" )
In a similar way, C++ classes can be exposed very easily. Rcpp modules are also described in more detail in their own vignette.

Reference Classes

R release 2.12.0 introduced Reference Classes. These are formal S4 classes with the corresponding dispatch method, but passed by reference and easy to use. Reference Classes can also be exposed to R by using Rcpp modules.

Extension packackages

The RcppArmadillo package permits use of the advanced C++ library 'Armadillo, a C++ linear algebra library aiming towards a good balance between speed and ease of use, providing integer, floating point and complex matrices and vectors with lapack / blas support via R. Armadillo uses templates for a delayed evaluation approach is employed (during compile time) to combine several operations into one and reduce (or eliminate) the need for temporaries. Armadillo is useful if C++ has been decided as the language of choice, rather than another language like Matlab ® or Octave, and aims to be as expressive as the former. Via Rcpp and RcppArmadillo, R users now have easy access to this functionality. Examples are provided in the RcppArmadillo package.

The RcppGSL package permits easy use of the GNU Scientific Library (GSL), a collection of numerical routines for scientifc computing. It is particularly useful for C and C++ programs as it provides a standard C interface to a wide range of mathematical routines such as special functions, permutations, combinations, fast fourier transforms, eigensystems, random numbers, quadrature, random distributions, quasi-random sequences, Monte Carlo integration, N-tuples, differential equations, simulated annealing, numerical differentiation, interpolation, series acceleration, Chebyshev approximations, root-finding, discrete Hankel transforms physical constants, basis splines and wavelets. There are over 1000 functions in total with an extensive test suite. The RcppGSL package provides an easy-to-use interface between GSL data structures and R using concepts from Rcpp. The RcppGSL package also contains a vignette with more documentation.

Legacy 'classic' API

Packages still using code interfacing the initial 'classic' Rcpp API are encouraged to migrate to the new API. Should a code transition not be possible, backwards compatibility is provided by the RcppClassic package released alongside Rcpp 0.9.0. By including RcppClassic.h and building against the RcppClassic package and library, vintage code can remain operational using the classic API. The short vignette in the RcppClassic package has more details.

Documentation

The package contains a total of eight vignettes the first of which provides a short and succinct introduction to the Rcpp package along with several motivating examples.

Links

Support

Questions about Rcpp should be directed to the Rcpp-devel mailing list https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel

Dirk Eddelbuettel, Romain Francois, Doug Bates and John Chambers
December 2010

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