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#undef TMB_OBJECTIVE_PTR
#define TMB_OBJECTIVE_PTR obj
// name of function below **MUST** match filename
template <class Type>
Type tmb_occu(objective_function<Type>* obj) {
//Describe input data
DATA_MATRIX(y); //observations
DATA_VECTOR(no_detect); //Indicator for if site had no detections
DATA_INTEGER(link);
DATA_MATRIX(X_state); //psi fixed effect design mat (state=psi)
DATA_SPARSE_MATRIX(Z_state); //psi random effect design mat
DATA_VECTOR(offset_state);
DATA_INTEGER(n_group_vars_state); //# of grouping variables for psi
DATA_IVECTOR(n_grouplevels_state); //# of levels of each grouping variable
DATA_MATRIX(X_det); //same thing but for p
DATA_SPARSE_MATRIX(Z_det);
DATA_VECTOR(offset_det);
DATA_INTEGER(n_group_vars_det);
DATA_IVECTOR(n_grouplevels_det);
PARAMETER_VECTOR(beta_state); //Fixed effect params for psi
PARAMETER_VECTOR(b_state); //Random intercepts and/or slopes for psi
PARAMETER_VECTOR(lsigma_state); //Random effect variance(s) for psi
PARAMETER_VECTOR(beta_det); //Same thing but for det
PARAMETER_VECTOR(b_det);
PARAMETER_VECTOR(lsigma_det);
Type loglik = 0.0;
int M = y.rows(); //# of sites
int J = y.cols(); //# of observations per site
//Construct psi vector
vector<Type> psi = X_state * beta_state + offset_state;
psi = add_ranef(psi, loglik, b_state, Z_state, lsigma_state,
n_group_vars_state, n_grouplevels_state);
if(link == 1){
psi = cloglog(psi);
} else {
psi = invlogit(psi);
}
//Construct p vector
vector<Type> p = X_det * beta_det + offset_det;
p = add_ranef(p, loglik, b_det, Z_det, lsigma_det,
n_group_vars_det, n_grouplevels_det);
p = invlogit(p);
//Standard occupancy likelihood calculation
for (int i=0; i<M; i++){
int pind = i * J;
Type cp = 1.0;
for (int j=0; j<J; j++){
if(R_IsNA(asDouble(y(i,j)))) continue;
cp *= pow(p(pind), y(i,j)) * pow(1-p(pind), 1-y(i,j));
pind += 1;
}
loglik -= log(psi(i) * cp + (1-psi(i)) * no_detect(i));
}
return loglik;
}
#undef TMB_OBJECTIVE_PTR
#define TMB_OBJECTIVE_PTR this
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