data {
	int<lower=1> N; // number of observations
	vector[N]    y; // outcomes
	int<lower=1> K; // number of covariates+intercept for mu
	int<lower=1> K1; // number of covariates+intercept for q1
	int<lower=1> H; // number of covariates+intercept for phi
	matrix[N,K]    X; // covariate for mu
	matrix[N,K1]    X1; // covariate for q1
	matrix[N,H]    Z; // covariate for phi
	int<lower=1> link_code_mu;
	int<lower=1> link_prior_beta;
	int<lower=1> link_prior_omega1;
	real hyperprior_beta;  // Prior standard deviation
	real hyperprior_omega1;  // Prior standard deviation
	int<lower=2> link_code_phi;
	int<lower=1> link_prior_psi;
	real hyperprior_psi;  // Prior standard deviation
}

parameters {
	vector[K] beta;
	vector[K1] omega1;
	vector[H] psi;
}


transformed parameters {
	vector<lower=0,upper=1>[N]  mu;
	vector<lower=0>[N]  phi;
	vector<lower=0>[N] a;
	vector<lower=0>[N] b;
	vector<lower=0, upper=1>[N] q1;

	q1 = inv_logit(X1 *omega1);
	
	if(link_code_mu == 1)
		mu = inv_logit(X * beta);
	else if(link_code_mu == 2)
		mu = Phi(X * beta);
	else if(link_code_mu == 3)
		mu = inv_cloglog(X * beta);
	else if(link_code_mu == 4)
		mu = exp(-exp(X * beta));

	if(link_code_phi == 2)
		phi = exp(Z * psi);
	else if(link_code_phi == 3)
		phi = square(Z * psi);

for (i in 1:N){
	b[i] = (1-mu[i])*phi[i];
	a[i] = mu[i]*phi[i];
}
}

model {
	//priors

	for (l in 1:K) {
	if(link_prior_beta == 1)
		beta[l] ~ normal(0, hyperprior_beta);
	else if(link_prior_beta == 2)
		beta[l] ~ cauchy(0, hyperprior_beta);
	}
	for (l in 1:K1) {
	if(link_prior_omega1 == 1)
		omega1[l] ~ normal(0, hyperprior_omega1);
	else if(link_prior_omega1 == 2)
		omega1[l] ~ cauchy(0, hyperprior_omega1);
	}

	for (l in 1:H) {
	if(link_prior_psi == 1)
		psi[l] ~ normal(0, hyperprior_psi);
	else if(link_prior_psi == 2)
		psi[l] ~ cauchy(0, hyperprior_psi);
	}

	// likelihood of log(y)

	for(i in 1:N){
	if (y[i]==1)
 	target += log(q1[i]);
 	else
	target += log1m(q1[i])+beta_lpdf(y[i] | a[i],b[i]);
}
}


generated quantities{
	vector[N] log_lik;
	for(i in 1:N){
if (y[i]==1)
 	log_lik[i]= log(q1[i]);
else
		log_lik[i] = log1m(q1[i])+beta_lpdf(y[i] | a[i],b[i]);
	}
}   
