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#undef TMB_OBJECTIVE_PTR
#define TMB_OBJECTIVE_PTR obj
// Adapted from Stan code by Maxwell B. Joseph,
// https://discourse.mc-stan.org/t/divergent-transition-every-iteration-multi-scale-occupancy-model/13739/5
// name of function below **MUST** match filename
template<class Type>
Type tmb_goccu(objective_function<Type>* obj) {
//Describe input data
DATA_MATRIX(y); //observations
DATA_INTEGER(T);
DATA_INTEGER(link);
DATA_MATRIX(Xpsi);
DATA_MATRIX(Xphi);
DATA_MATRIX(Xp);
DATA_INTEGER(n_possible);
DATA_MATRIX(alpha_potential);
DATA_VECTOR(known_present);
DATA_MATRIX(known_available);
DATA_MATRIX(missing_session);
PARAMETER_VECTOR(beta_psi);
PARAMETER_VECTOR(beta_phi);
PARAMETER_VECTOR(beta_p);
vector<Type> psi = Xpsi * beta_psi;
vector<Type> phi = Xphi * beta_phi;
vector<Type> p = Xp * beta_p;
if(link == 1){
//psi = cloglog(psi);
} else {
psi = invlogit(psi);
}
phi = invlogit(phi);
p = invlogit(p);
Type loglik = 0.0;
int M = y.rows();
int J = y.cols() / T;
Type obs_lp;
Type poss_lp;
Type exp_poss_lp;
int ystart;
vector<Type> ysite;
vector<Type> psite;
vector<Type> ysub;
vector<Type> psub;
int tstart;
int pstart;
for (int i=0; i<M; i++){
tstart = i*T;
pstart = i*(T*J);
ysite = y.row(i);
psite = p.segment(pstart, T*J);
if(known_present(i) == 1){
for (int t=0; t<T; t++){
if(missing_session(i, t) == 1) continue;
ystart = t*J;
psub = psite.segment(ystart, J);
ysub = ysite.segment(ystart, J);
obs_lp = log(phi(tstart+t));
for (int j=0; j<J; j++){
if(R_IsNA(asDouble(ysub(j)))) continue;
obs_lp += dbinom(ysub(j), Type(1), psub(j), true);
}
if(known_available(i, t) == 1){
loglik += obs_lp;
} else {
loglik += log(exp(obs_lp) + exp(log(1-phi(tstart+t))));
}
}
loglik += log(psi(i));
} else {
exp_poss_lp = 0.0;
for (int k=0; k<n_possible; k++){
poss_lp = log(psi(i));
for (int t=0; t<T; t++){
if(missing_session(i, t) == 1) continue;
ystart = t*J;
psub = psite.segment(ystart, J);
ysub = ysite.segment(ystart, J);
if(alpha_potential(k, t) == 0){
poss_lp += log(1 - phi(tstart+t));
} else {
poss_lp += log(phi(tstart+t));
for (int j=0; j<J; j++){
if(R_IsNA(asDouble(ysub(j)))) continue;
poss_lp += dbinom(ysub(j), Type(1), psub(j), true);
}
}
}
exp_poss_lp += exp(poss_lp);
}
exp_poss_lp += exp(log(1-psi(i)));
loglik += log(exp_poss_lp);
}
}
return -loglik;
}
#undef TMB_OBJECTIVE_PTR
#define TMB_OBJECTIVE_PTR this
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