Using C, C++, and Fortran within R and Splus

Note that when working with C (also GSL functions), matrices are row-major - namely they are stored by row in a vector. So the second element of the vector is the second element of the first row. In contrast Fortran and Matlab are column major so the second element would be the second element of the first column.

• R
  • create your C or C++ or Fortran code; you may need to include the header #include R.h; if using C++, enclose all your functions with
    extern C{
    ... your function code ... 
    }
  • to use Fortran code, I usually call the Fortran function from C or C++; remember to declare the Fortran function, e.g.:
    extern C void rkbesld_(double* x,double* alpha,int* nb,int* ize,double* bk, in t* ncalc); // the function would be named rkbesld in the fortran file 
    extern C void myfun(int *n,double *x,double* out){ 
    ... function code ... 
    }
  • from the UNIX/Linux command prompt
    >R COMPILE rkbesld.f; R CMD SHLIB file.C rkbesld.o
  • Or, if you're not calling a fortran function, just
    >R CMD SHLIB file.C
  • start R and load the .so file created by the previous step
    >dyn.load(file.so)
  • write and use a wrapper function to access the C/C++ function (see below)
• Splus
  • old UNIX 3.X version:
    from UNIX: >Splus COMPILE file.c
    in S: >dyn.load2(file.o)
  • Linux version:
    >Splus CHAPTER file.{c,f}   # this creates a Makefile; it's ok if you already have chapter created (I think)
    >Splus make  # You may need to change the libraries and linking that are specified in the Makefile created in CHAPTER command
  • write and use a wrapper function to access the C/C++ function (see below)
• wrapper functions
  • the R/S wrapper function deals with the overhead of communicating with C and lets you call your function as if it is in native R/S code, for example, if the function name in file.{c,f} is myfun, create the following wrapper:
    >myfun=function(n, x){ 
       out <- NULL 
       .C(myfun,as.integer(n),as.double(x),as.double(out))[[3]] # returns out (the third element of the list returned by .C) 
    }
    make sure the C/C++/Fortran function has all args passed by reference (i.e., as pointers) and returns void (or else just write a C/C++/Fortran wrapper to do this)