From braunm at MIT.EDU  Mon Dec 25 00:58:50 2006
From: braunm at MIT.EDU (Michael Braun)
Date: Sun, 24 Dec 2006 18:58:50 -0500
Subject: [Rd] FW: Passing lists from R to C, extracting elements,
 and sending lists back again
Message-ID: <20061224185851125.00000000424@MBRAUN>

 

Thank you to everyone who responded to my previous post regarding the integration into R of C programs that use external libraries.  I have another issue that I simply have not been able to figure out using documentation, list archives, and so forth.

I have data that is stored in R lists.  I would like to pass the list to C code using the .Call function, perform mathematical operations on the elements of the lists (which might be other lists), and return results in a new list.

As a simple example, suppose I have a list of n matrices (dimension k-by-k) that I want to invert, and return the result in another list.  I wrote the C code below that reads the list as a SEXP.  Then, for each of the i=1..n matrices, I convert the R vector to a gsl matrix, perform the linear algebra operations and populate the new list with the inverted matrix.

The problem is that I can't figure out the best way to get the real elements into the list SEXP to return it to R.  When I run the code below, the compiler (R CMD SHLIB sexp1.c) gives me:

-bash-3.00$ R CMD SHLIB sexp1.c
gcc -I/usr/lib64/R/include -I/usr/lib64/R/include -I/usr/include -I/usr/local/include   -fpic  -O2 -g -c sexp1.c -o sexp1.o
sexp1.c: In function `invMatList':
sexp1.c:37: warning: passing arg 3 of `SET_VECTOR_ELT' from incompatible pointer type gcc -shared -L/usr/local/lib64 -o sexp1.so sexp1.o -L/usr/lib64 -lgsl -lgslcblas -L/usr/lib  -L/usr/lib64/R/lib -lR

So, not only would it be helpful to understand how to solve this specific problem, but I would greatly appreciate some general guidance on how to best more data from lists or C datatypes and back again (especially arrays).  Also, are the functions and macros described in the Rinternals header documented anywhere?  I can't seem to find the source code, or a description of what these functions actually do.

Thanks again for any help you can provide.

Best wishes,

Michael Braun
MIT Sloan School of Management
braunm at mit.edu

	SEXP r = PROTECT(allocVector(VECSXP,n));
	double rm[k][k];

	for (i=0; i<n; i=i+1) {

		for (a=0; a<k; ++a){ // convert to gsl matrix
			for (b=0; b<k; ++b){
				ind = b*k + a;
				m = REAL(VECTOR_ELT(list,i))[ind];
				gsl_matrix_set(mat, b, a, m);
			}
		} // end conversion loops

 		gsl_linalg_LU_decomp(mat, p, &s);
		gsl_linalg_LU_invert(mat, p, inv);


		for (a=0; a<k; ++a){ // convert from gsl matrix
			for (b=0; b<k; ++b){
				rm[b][a] = gsl_matrix_get(inv,b,a);
			}
		}
		SET_VECTOR_ELT(r, i, rm);
	}
	UNPROTECT(1);
	return (r);
}



[Rd] FW: Passing lists from R to C, extracting elements, and sending lists back again
Michael Braun