src/nll_occuPEN.cpp


1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37

#include <RcppArmadillo.h>
#include <float.h>

using namespace Rcpp ;

// [[Rcpp::export]]
double nll_occuPEN(arma::icolvec y, arma::mat X, arma::mat V,
    arma::colvec beta_psi, arma::colvec beta_p, Rcpp::IntegerVector nd,
    Rcpp::LogicalVector knownOcc, Rcpp::LogicalVector navec,
    arma::colvec X_offset, arma::colvec V_offset, double penalty) {

  int R = X.n_rows;
  int J = y.n_elem / R;
  arma::colvec logit_psi = X*beta_psi + X_offset;
  arma::colvec logit_p = V*beta_p + V_offset;
  arma::colvec psi = 1.0/(1.0+exp(-logit_psi));
  arma::colvec p = 1.0/(1.0+exp(-logit_p));
  double ll=0.0;
  int k=0; // counter
  for(int i=0; i<R; i++) {
    double cp=1.0;
    for(int j=0; j<J; j++) {
      if(!navec(k))
	cp *= pow(p(k),y(k)) * pow(1-p(k), 1-y(k));
      k++;
    }
    if(knownOcc(i))
      psi(i) = 1.0;
    if(nd(i)==0)
      ll += log(cp * psi(i) + DBL_MIN);
    else if(nd(i)==1)
      ll += log(cp * psi(i) + (1-psi(i)) + DBL_MIN);
  }
  ll = ll - penalty;
  return -ll;
}