[Rd] FW: Passing lists from R to C, extracting elements, and sending lists back again
Michael Braun
braunm at MIT.EDU
Mon Dec 25 00:58:50 CET 2006
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);
}
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