Fail to complete an IRT model with missing data

Modeling
1

Hello,

the following model is related to a previous post: Fail to run due to relatively high number of missing observations.

The model is the following:

functions {
  real rsm(int y, real theta, real beta, vector kappa) {
    vector[rows(kappa) + 1] unsummed;
    vector[rows(kappa) + 1] probs;
    unsummed = append_row(rep_vector(0, 1), theta - beta - kappa);
    probs = softmax(cumulative_sum(unsummed));
    return categorical_lpmf(y + 1 | probs);
  }
  real rsm_rng(real theta, real beta, vector kappa) {
    vector[rows(kappa) + 1] unsummed;
    vector[rows(kappa) + 1] probs;
    unsummed = append_row(rep_vector(0, 1), theta - beta - kappa);
    probs = softmax(cumulative_sum(unsummed));
    return categorical_rng(probs);
  }
}

data {
  int<lower=1> I;               // # items
  int<lower=1> J;               // # persons
  int<lower=1> N;               // # observations
  int<lower=0> N_mis;           // # missing observations
  int<lower=0,upper=1> R[N];    // whether observation j is missing
  int<lower=1, upper=I> ii[N];  // item for n
  int<lower=1, upper=J> jj[N];  // person for n
  int<lower=0> y[N];            // response for n
}

transformed data {
  int m;                        // # steps
  m = max(y);
}

parameters {
  vector[I] beta;
  vector[m-1] kappa_free;
  vector[J] theta;
  real<lower=0> sigma;
}

transformed parameters {
  vector[m] kappa;
  kappa[1:(m-1)] = kappa_free;
  kappa[m] = -1*sum(kappa_free);
}
  
model {
  beta ~ normal(0, 3);
  target += normal_lpdf(kappa | 0, 3);
  theta ~ normal(0, sigma);
  sigma ~ exponential(.1);
  for (n in 1:N) {
    if (R[n] == 1) {
      target += rsm(y[n], theta[jj[n]], beta[ii[n]], kappa);
    }
  } 
}

generated quantities {  
vector[N] y_mis;
for (n in 1:N) {
if (R[n] == 0){
  y_mis[n] = rsm_rng(theta[jj[n]], beta[ii[n]], kappa);
    }
  }  
}

The model runs but it fails to complete generating the following message:

Error in validObject(.Object) :
invalid class “stanfit” object: The following variables have undefined values: y_mis[5],The following variables have undefined values: y_mis[8],…

The latter part of the message is repeated numerous times for different observations. We are not sure how deal with this issue. Any directions?

2

Glancing at the generated quantities block, it looks like you’re only filling in some of the values in y_mis so the rest don’t exist. You can either give the other values some placeholder value so they get initialized and then ignore them or you can define y_mis to only have size equal to the number of elements you want to fill in.

3

Thank you!