Using the Blitz library

blitz++ is a C library for high dimensional maths.

Need to add explanation here:

library(Rcpp)
library(inline)

## Loading required package: methods

inc = '
#include <blitz/array.h>
'

src = '
using namespace blitz;
Rcpp::NumericVector A(A_);
Rcpp::NumericVector A2(A2_);

// read dimension attribute of R arrays
Rcpp::IntegerVector d1 = A.attr("dim");
Rcpp::IntegerVector d2 = A2.attr("dim");

// create 2 blitz cubes B and B2
// supply contents of dim vectors manually
blitz::Array<double,3> B(A.begin(), shape(d1(0),d1(1),d1(2)), neverDeleteData);
blitz::Array<double,3> B2(A2.begin(), shape(d2(0),d2(1),d2(2)), neverDeleteData);

// do some blitz arithmethic
blitz::Array<double,3> C(d1(0),d1(1),d1(2));
C = B + B2;

// copy the result back to B (which is a view of A, i.e. will contain the same data)
B = C;

// return array
return wrap(A);
'

Result:

A = array(1:60,c(2,5,6))
A2 = array(120:60,c(2,5,6))

f = cxxfunction(signature(A_="numeric",A2_="numeric"),body=src,plugin="Rcpp",includes=inc)

## Warning: running command '/Library/Frameworks/R.framework/Resources/bin/R
## CMD SHLIB file58337ad31da0.cpp 2> file58337ad31da0.cpp.err.txt' had status
## 1

## clang: warning: argument unused during compilation: '-rdynamic'
## In file included from file58337ad31da0.cpp:4:
## In file included from /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include/Rcpp.h:27:
## /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include/RcppCommon.h:145:10: fatal error: 'tr1/unordered_map' file not found
## #include <tr1/unordered_map>
##          ^
## 1 error generated.
## make: *** [file58337ad31da0.o] Error 1
## 
## ERROR(s) during compilation: source code errors or compiler configuration errors!
## 
## Program source:
##   1: 
##   2: // includes from the plugin
##   3: 
##   4: #include <Rcpp.h>
##   5: 
##   6: 
##   7: #ifndef BEGIN_RCPP
##   8: #define BEGIN_RCPP
##   9: #endif
##  10: 
##  11: #ifndef END_RCPP
##  12: #define END_RCPP
##  13: #endif
##  14: 
##  15: using namespace Rcpp;
##  16: 
##  17: 
##  18: // user includes
##  19: 
##  20: #include <blitz/array.h>
##  21: 
##  22: 
##  23: // declarations
##  24: extern "C" {
##  25: SEXP file58337ad31da0( SEXP A_, SEXP A2_) ;
##  26: }
##  27: 
##  28: // definition
##  29: 
##  30: SEXP file58337ad31da0( SEXP A_, SEXP A2_ ){
##  31: BEGIN_RCPP
##  32: 
##  33: using namespace blitz;
##  34: Rcpp::NumericVector A(A_);
##  35: Rcpp::NumericVector A2(A2_);
##  36: 
##  37: // read dimension attribute of R arrays
##  38: Rcpp::IntegerVector d1 = A.attr("dim");
##  39: Rcpp::IntegerVector d2 = A2.attr("dim");
##  40: 
##  41: // create 2 blitz cubes B and B2
##  42: // supply contents of dim vectors manually
##  43: blitz::Array<double,3> B(A.begin(), shape(d1(0),d1(1),d1(2)), neverDeleteData);
##  44: blitz::Array<double,3> B2(A2.begin(), shape(d2(0),d2(1),d2(2)), neverDeleteData);
##  45: 
##  46: // do some blitz arithmethic
##  47: blitz::Array<double,3> C(d1(0),d1(1),d1(2));
##  48: C = B + B2;
##  49: 
##  50: // copy the result back to B (which is a view of A, i.e. will contain the same data)
##  51: B = C;
##  52: 
##  53: // return array
##  54: return wrap(A);
##  55: 
##  56: END_RCPP
##  57: }
##  58: 
##  59:

## Error: Compilation ERROR, function(s)/method(s) not created! clang:
## warning: argument unused during compilation: '-rdynamic' In file included
## from file58337ad31da0.cpp:4: In file included from
## /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include/Rcpp.h:27:
## /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include/RcppCommon.h:145:10:
## fatal error: 'tr1/unordered_map' file not found #include
## <tr1/unordered_map> ^ 1 error generated. make: *** [file58337ad31da0.o]
## Error 1

all.equal(f(A,A2),A+A2)

## Error: could not find function "f"

======================================================== Using the RcppArmadillo library ========================================================

The Armadillo C++ library provides vector, matrix and cube types. We convert an R array to a cube in RcppArmadillo.

First in the "arma.cpp" file

// [[Rcpp::depends(RcppArmadillo)]]
#include <RcppArmadillo.h>

using namespace Rcpp;

// [[Rcpp::export]]
SEXP f(SEXP A_, SEXP A2_){  
  NumericVector A(A_);
  NumericVector A2(A2_);

// read dimension attribute of R arrays
  IntegerVector d1 = A.attr("dim");
  IntegerVector d2 = A2.attr("dim");

// create 2 cubes B and B2
// supply contents of dim vectors manually
  arma::cube B(A.begin(), d1[0], d1[1], d1[2], false);
  arma::cube B2(A2.begin(),  d2[0], d2[1], d2[2], false);

// do some arithmethic
  arma::cube C(d1[0], d1[1], d1[2]);
  C = B + B2;

// copy the result back to B (which is a view of A, i.e. will contain the same data)
  B = C;

// return array
  return wrap(A);
} 

Then in the "arma.r" file

require(Rcpp)
require(RcppArmadillo)
sourceCpp("arma.cpp")

A = array(1:60,c(2,5,6))
A2 = array(120:60,c(2,5,6))
all.equal(f(A,A2),A+A2)