gistfile1.txt

data {
  int<lower=1> K; // Number of classes

  int<lower=1> N; // Total number of data points
  int<lower=1> D; // Number of combinations
  int<lower=1> Di[N]; // Data point to combination index

  // Outcome
  int<lower=0> Count[N,K]; // Number of samples at data point N for class K

  // Covariates
  vector[N] Age; // Age at data point N 
}
parameters {
  matrix[D, K] beta_0;
  matrix[D, K] beta_A;
}
model {
  /* Prior specification */

  // Combination priors
  to_vector(beta_0) ~ normal(0, 1);
  to_vector(beta_A) ~ normal(0, 1);


  /* Calculate theta hat for each combination, and increment likelihood */
  {
    vector[K] theta;
    theta[1] = 0;
    for (n in 1:N) {
      // Increment likelihood

      for (k in 1:K) {
        theta[k] =  beta_0[Di[n], k] + beta_A[Di[n], k] * AgeZ[n];
      }
      Count[n] ~ multinomial(softmax(theta));
    }
  }
}