![.C
Step 1. Put function in file (foo.c)
void foo(int *nin, double *x)
{
int n = nin[0];
int i;
for (i=0; i<n; i++)
x[i] = x[i] * x[i];
}
Rob Zinkov () Turbocharge your R July 12th, 2011 6 / 23](https://image.slidesharecdn.com/talk2-110714165345-phpapp02/85/Los-Angeles-R-users-group-July-12-2011-Part-2-6-320.jpg)
![.Call
.Call code
#include <R.h>
#include <Rinternals.h>
#include <Rmath.h>
SEXP vecSum(SEXP Rvec){
int i, n;
double *vec, value = 0;
vec = REAL(Rvec);
n = length(Rvec);
for (i = 0; i < n; i++) value += vec[i];
printf("The value is: %4.6f n", value);
return R_NilValue;
}
Rob Zinkov () Turbocharge your R July 12th, 2011 13 / 23](https://image.slidesharecdn.com/talk2-110714165345-phpapp02/85/Los-Angeles-R-users-group-July-12-2011-Part-2-13-320.jpg)
![.Call
SEXP ab(SEXP Ra, SEXP Rb){
int i, a, b;
SEXP Rval;
Ra = coerceVector(Ra, INTSXP);
Rb = coerceVector(Rb, INTSXP);
a = INTEGER(Ra)[0];
b = INTEGER(Rb)[0];
PROTECT(Rval = allocVector(INTSXP, b - a + 1));
for (i = a; i <= b; i++)
INTEGER(Rval)[i - a] = i;
UNPROTECT(1);
return Rval;
}
Rob Zinkov () Turbocharge your R July 12th, 2011 15 / 23](https://image.slidesharecdn.com/talk2-110714165345-phpapp02/85/Los-Angeles-R-users-group-July-12-2011-Part-2-15-320.jpg)
Los Angeles R users group - July 12 2011 - Part 2
- 1. Turbocharge your R Rob Zinkov July 12th, 2011 Rob Zinkov () Turbocharge your R July 12th, 2011 1 / 23
- 2. Outline 1 Introduction 2 .C 3 .Call 4 Rcpp Rob Zinkov () Turbocharge your R July 12th, 2011 2 / 23
- 3. Introduction What is the point of this talk? Show you how to speed up your R code Rob Zinkov () Turbocharge your R July 12th, 2011 3 / 23
- 4. Introduction Caveats • Please try to optimize your R code first • Some of these mechanisms will make coding harder Rob Zinkov () Turbocharge your R July 12th, 2011 4 / 23
- 5. .C • This is the basic mechanism • Explicitly copies the data into C • Only accepts integer vectors Rob Zinkov () Turbocharge your R July 12th, 2011 5 / 23
- 6. .C Step 1. Put function in file (foo.c) void foo(int *nin, double *x) { int n = nin[0]; int i; for (i=0; i<n; i++) x[i] = x[i] * x[i]; } Rob Zinkov () Turbocharge your R July 12th, 2011 6 / 23
- 7. .C • Note this is a void function • Note arguments are passed in as pointers • Try to limit one function per file Rob Zinkov () Turbocharge your R July 12th, 2011 7 / 23
- 8. .C Step 2. Compile file with R $ R CMD SHLIB foo.c Rob Zinkov () Turbocharge your R July 12th, 2011 8 / 23
- 9. .C Step 3. Load into R > dyn.load("foo.so") Rob Zinkov () Turbocharge your R July 12th, 2011 9 / 23
- 10. .C Step 4. Call your code .C("foo", n=as.integer(5), x=as.double(rnorm(5))) Rob Zinkov () Turbocharge your R July 12th, 2011 10 / 23
- 11. .C • Arguments to .C are name of function followed by arguments • Arguments must be the right type • Touching C code runs risks of segfaults Rob Zinkov () Turbocharge your R July 12th, 2011 11 / 23
- 12. .Call Why? • Less copying of data structures (lower memory) • Access more of R data structures • Access more kinds of R data • Do more in C Rob Zinkov () Turbocharge your R July 12th, 2011 12 / 23
- 13. .Call .Call code #include <R.h> #include <Rinternals.h> #include <Rmath.h> SEXP vecSum(SEXP Rvec){ int i, n; double *vec, value = 0; vec = REAL(Rvec); n = length(Rvec); for (i = 0; i < n; i++) value += vec[i]; printf("The value is: %4.6f n", value); return R_NilValue; } Rob Zinkov () Turbocharge your R July 12th, 2011 13 / 23
- 14. .Call R CMD SHLIB vecSum.c dyn.load("vecSum.so") .Call("vecSum", rnorm(10)) Rob Zinkov () Turbocharge your R July 12th, 2011 14 / 23
- 15. .Call SEXP ab(SEXP Ra, SEXP Rb){ int i, a, b; SEXP Rval; Ra = coerceVector(Ra, INTSXP); Rb = coerceVector(Rb, INTSXP); a = INTEGER(Ra)[0]; b = INTEGER(Rb)[0]; PROTECT(Rval = allocVector(INTSXP, b - a + 1)); for (i = a; i <= b; i++) INTEGER(Rval)[i - a] = i; UNPROTECT(1); return Rval; } Rob Zinkov () Turbocharge your R July 12th, 2011 15 / 23
- 16. .Call Since memory is shared explicit care must be taken not to collide with R Rob Zinkov () Turbocharge your R July 12th, 2011 16 / 23
- 17. Rcpp Why? • Use C++ instead of C • Ability to use objects to represent R more naturally • Easier to load code Rob Zinkov () Turbocharge your R July 12th, 2011 17 / 23
- 18. Rcpp src <- ’ IntegerVector tmp(clone(x)); double rate = as< double >(y); int tmpsize = tmp.size(); RNGScope scope; for (int ii =0; ii < tmpsize; ii++) { tmp(ii) = Rf_rbinom(tmp(ii), rate); }; return tmp; ’ require(inline) ## compile the function, inspect the process with verbose=T testfun2 = cxxfunction(signature(x=’integer’, y=’numeric’), src, plugin=’Rcpp’, verbose=T) Rob Zinkov () Turbocharge your R July 12th, 2011 18 / 23
- 19. Rcpp require(inline) testfun = cxxfunction( signature(x="numeric", i="integer"), body = ’ NumericVector xx(x); int ii = as<int>(i); xx = xx * ii; return( xx ); ’, plugin="Rcpp") testfun(1:5, 3) Rob Zinkov () Turbocharge your R July 12th, 2011 19 / 23
- 20. Rcpp Conclusions It is fairly easy to make R faster Rob Zinkov () Turbocharge your R July 12th, 2011 20 / 23
- 21. Rcpp Conclusions Now go make your R code faster Rob Zinkov () Turbocharge your R July 12th, 2011 21 / 23
- 22. Rcpp References • http://www.stat.umn.edu/ charlie/rc/ • http://helmingstay.blogspot.com/2011/06/efficient-loops-in-r- complexity-versus.html • http://www.sfu.ca/ sblay/R-C-interface.ppt • http://www.biostat.jhsph.edu/ bcaffo/statcomp/files/dotCall.pdf • http://cran.r-project.org/web/packages/Rcpp/vignettes/Rcpp- quickref.pdf • http://www.jstatsoft.org/v40/i08/paper Rob Zinkov () Turbocharge your R July 12th, 2011 22 / 23
- 23. Rcpp Questions? Rob Zinkov () Turbocharge your R July 12th, 2011 23 / 23