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nll_occu.cpp
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nll_occu.cpp
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#include <RcppArmadillo.h>
#include <float.h>
using namespace Rcpp ;
// [[Rcpp::export]]
double nll_occu(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, std::string link_psi) {
int R = X.n_rows;
int J = y.n_elem / R;
//Calculate psi
arma::colvec psi_lp = X*beta_psi + X_offset;
arma::colvec psi(R);
if(link_psi == "cloglog"){
psi = 1 - exp(-exp(psi_lp));
} else {
psi = 1.0/(1.0+exp(-psi_lp));
}
//Calculate p
arma::colvec logit_p = V*beta_p + V_offset;
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);
}
return -ll;
}