internal.h

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#ifndef _PHYLOPOMP_INTERNAL_H_
#define _PHYLOPOMP_INTERNAL_H_
 
#define R_NO_REMAP
 
#include <R.h>
#include <Rmath.h>
#include <Rdefines.h>
 
#ifdef __cplusplus
#include <cassert>
#else
#include <assert.h>
#endif
 
#ifndef STANDALONE
 
#define err(...) Rf_errorcall(R_NilValue,__VA_ARGS__)
#define warn(...) Rf_warningcall(R_NilValue,__VA_ARGS__)
#define rprint(S) Rprintf("%s\n",(S).c_str())
 
#else
 
#include <iostream>
#include <cstdio>
#define err(...) {printf(__VA_ARGS__); printf("\n"); exit(-1);}
#define warn(...) {printf(__VA_ARGS__); printf("\n");}
#define rprint(S) printf("%s\n",(S).c_str())
 
#endif
 
#ifdef __cplusplus
 
#include <string>
#include <cstring>
 
typedef std::string string_t;
 
#endif
 
#ifdef __cplusplus
 
#define mkChar Rf_mkChar
#define mkString Rf_mkString
#define ScalarInteger Rf_ScalarInteger
#define ScalarReal Rf_ScalarReal
#define install Rf_install
#define isNull Rf_isNull
 
#endif
 
typedef Rbyte raw_t;
typedef double slate_t;
typedef size_t name_t;
 
// interface with R's integer RNG
static inline int random_integer (int n) {
  return (int) floor(R_unif_index((double) n));
}
 
// select n of the first N integers at random
static inline void random_sample_wo_repl (int *samples, int N, int n) {
  int k = 0; // total input records dealt with
  int m = 0; // number of items selected so far
  while (m < n && k < N) {
    int u = random_integer(N-k);
    if (u < n-m) {
      samples[m++] = k;
    }
    k++;
  }
}
 
// helper function for filling a return list
static inline int set_list_elem
(
 SEXP list, SEXP names, SEXP element,
 const char *name, int pos
 ) {
  SET_ELEMENT(list,pos,element);
  SET_STRING_ELT(names,pos,Rf_mkChar(name));
  return ++pos;
}
 
static inline int rcateg (double erate, double *rate, int nrate) {
  double u = erate*unif_rand();
  int e = 0;
  while (u > rate[e] && e < nrate) {
    if (rate[e] < 0)
      err("in '%s': invalid rate rate[%d]=%lg",__func__,e,rate[e]); // #nocov
    u -= rate[e++];
  }
  assert(e!=nrate);             // #nocov
  return e;
}
 
#endif