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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_multinomPois(objective_function<Type>* obj) {
//Describe input data
DATA_MATRIX(y); //observations
DATA_MATRIX(X_state); //lambda fixed effect design mat
DATA_SPARSE_MATRIX(Z_state); //psi random effect design mat
DATA_VECTOR(offset_state);
DATA_INTEGER(n_group_vars_state); //# of grouping variables for lambda
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);
DATA_INTEGER(pifun_type);
PARAMETER_VECTOR(beta_state); //Fixed effect params for lamda
PARAMETER_VECTOR(b_state); //Random intercepts and/or slopes for lambda
PARAMETER_VECTOR(lsigma_state); //Random effect variance(s) for lambda
PARAMETER_VECTOR(beta_det); //Same thing but for det
PARAMETER_VECTOR(b_det);
PARAMETER_VECTOR(lsigma_det);
//Define the log likelihood so that it can be calculated in parallel over sites
Type loglik = 0.0;
int M = y.rows(); // # of sites
int J = y.cols(); // # of obs per site
int R = X_det.rows() / M; // # of detection probs per site
//Construct lambda vector
vector<Type> lam = X_state * beta_state + offset_state;
lam = add_ranef(lam, loglik, b_state, Z_state, lsigma_state,
n_group_vars_state, n_grouplevels_state);
lam = exp(lam);
//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);
//Likelihood
for (int i=0; i<M; i++){
//Not sure if defining these inside loop is necessary for parallel
int pstart = i * R;
vector<Type> ysub = y.row(i);
vector<Type> psub = p.segment(pstart, R);
vector<Type> pi_lam = pifun(psub, pifun_type) * lam(i);
for (int j=0; j<J; j++){
if(R_IsNA(asDouble(ysub(j)))) continue;
loglik -= dpois(ysub(j), pi_lam(j), true);
}
}
return loglik;
}
#undef TMB_OBJECTIVE_PTR
#define TMB_OBJECTIVE_PTR this
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