Calling compiled C from R with .C()
- by Sarah
I'm trying to call a program (function getNBDensities in the C executable measurementDensities_out) from R. The function is passed several arrays and the variable double runsum. Right now, the getNBDensities function basically does nothing: it prints to screen the values of passed parameters. My problem is the syntax of calling the function:
array(.C("getNBDensities",
hr = as.double(hosp.rate), # a vector (s x 1)
sp = as.double(samplingProbabilities), # another vector (s x 1)
odh = as.double(odh), # another vector (s x 1)
simCases = as.integer(x[c("xC1","xC2","xC3")]), # another vector (s x 1)
obsCases = as.integer(y[c("yC1","yC2","yC3")]), # another vector (s x 1)
runsum = as.double(runsum), # double
DUP = TRUE, NAOK = TRUE, PACKAGE = "measurementDensities_out")$f,
dim = length(y[c("yC1","yC2","yC3")]),
dimnames = c("yC1","yC2","yC3"))
The error I get, after proper execution of the function (i.e., the right output is printed to screen), is
Error in dim(data) <- dim : attempt to set an attribute on NULL
I'm unclear what the dimensions are that I should be passing the function: should it be s x 5 + 1 (five vectors of length s and one double)? I've tried all sorts of combinations (including sx5+1) and have found only seemingly conflicting descriptions/examples online of what's supposed to happen here.
For those who are interested, the C code is below:
#include <R.h>
#include <Rmath.h>
#include <math.h>
#include <Rdefines.h>
#include <R_ext/PrtUtil.h>
#define NUM_STRAINS 3
#define DEBUG
void getNBDensities( double *hr, double *sp, double *odh, int *simCases, int *obsCases, double *runsum );
void getNBDensities( double *hr, double *sp, double *odh, int *simCases, int *obsCases, double *runsum ) {
#ifdef DEBUG
for ( int s = 0; s < NUM_STRAINS; s++ ) {
Rprintf("\nFor strain %d",s);
Rprintf("\n\tHospitalization rate = %lg", hr[s]);
Rprintf("\n\tSimulation probability = %lg",sp[s]);
Rprintf("\n\tSimulated cases = %d",simCases[s]);
Rprintf("\n\tObserved cases = %d",obsCases[s]);
Rprintf("\n\tOverdispersion parameter = %lg",odh[s]);
}
Rprintf("\nRunning sum = %lg",runsum[0]);
#endif
}
naive solution
While better (i.e., potentially faster or syntactically clearer) solutions may exist (see Dirk's answer below), the following simplification of the code works:
out<-.C("getNBDensities",
hr = as.double(hosp.rate),
sp = as.double(samplingProbabilities),
odh = as.double(odh),
simCases = as.integer(x[c("xC1","xC2","xC3")]),
obsCases = as.integer(y[c("yC1","yC2","yC3")]),
runsum = as.double(runsum))
The variables can be accessed in >out.
