Imputation of a 3 category covariate to model a binary outcome


#1

Hi everyone:

It seems this question is starting to become a classic. It is related to log_mix, log_exp_sum and the imputation of a 3 categorical covariate to model a binary outcome. I have checked several similar questions and references:





But it is still not enough clear for me. I have done the exploration of what works hierarchically. I am comparing step bu step output from JAGS and STAN. I get to the point to impute the categorical covariate using only complete data and it works like a charm (same coefficients and posterior predictive of the categories). So I know the problem comes when moving to use the data that includes the unobserved categories.

In the following code
y is the binary outcome
cov_cat_1 and cov_cat_3 are dummy variables for the categories 1 and 3 (-1 when NA)
day and lat are predictors of the log odds to be in category 1-3

So as you can see theta is a vector of length 3 containing the log odds to be in category 1-3
and once this category is imputed the idea is to use this imputation to estimate a0, beta_bp, and beta_m.

My questions are: what is wrong? What do you suggest? I would really appreciate suggestions to be as clear as possible, please.

model{
  a0 ~ normal(0,30); 
  beta_bp ~ normal(0,30); 
  beta_m ~ normal(0,30); 
  a_imp ~ normal(0,30); // explained above
  b1_imp ~ normal(0,30); // explained above
  b2_imp ~ normal(0,30); // explained above
  

  for (i in 1:n_obs) {
    
    if (cov_cat_miss[i] == 0) {
      y[i] ~ bernoulli_logit(a0+
                               beta_bp*cov_cat_1[i]+
                               beta_m*cov_cat_3[i]);}
    
    else {
      vector[n_cat] theta;
      vector[n_cat] log_prob_theta;
      matrix[n_cat, n_cat] lp;  
      
      real p2 = a_imp[2] + b1_imp[2]*day[i] + b2_imp[2]*lat[i]; 
      real p3 = a_imp[3] + b1_imp[3]*day[i] + b2_imp[3]*lat[i]; 
      
      theta[1] = 0;
      theta[2] = p2;
      theta[3] = p3; 
      log_prob_theta=log_softmax(theta);
      
      lp[1,1] = log_prob_theta[1] + bernoulli_logit_lpmf( y[i] | a0  + beta_bp); //cat 1
      lp[2,1] = log_prob_theta[1] + bernoulli_logit_lpmf( y[i] | a0); //cat 2 (baseline)
      lp[3,1] = log_prob_theta[1] + bernoulli_logit_lpmf( y[i] | a0  + beta_m); //cat 3
      lp[1,2] = log_prob_theta[2] + bernoulli_logit_lpmf( y[i] | a0  + beta_bp);
      lp[2,2] = log_prob_theta[2] + bernoulli_logit_lpmf( y[i] | a0);
      lp[3,2] = log_prob_theta[2] + bernoulli_logit_lpmf( y[i] | a0  + beta_m);
      lp[1,3] = log_prob_theta[3] + bernoulli_logit_lpmf( y[i] | a0  + beta_bp);
      lp[2,3] = log_prob_theta[3] + bernoulli_logit_lpmf( y[i] | a0);
      lp[3,3] = log_prob_theta[3] + bernoulli_logit_lpmf( y[i] | a0  + beta_m);
      
      target += log_sum_exp(lp); 
      
    }
  }
}

#2

Diego,

At first glance, it looks like you haven’t specified how day and late are predictors of the categorical covariate in cases where the categorical covariate are actually observed. For cases where cov_cat is observed you need a line like:

if (cov_cat_miss[i] == 0) {
  y[i] ~ bernoulli_logit(a0+
                           beta_bp*cov_cat_1[i]+
                           beta_m*cov_cat_3[i]);
cov_cat[i] ~ categorical_logit( p );
}

As is, it looks like there’s no data informing linear models p2 and p3. I accidentally omitted this step from my example in Log_mix for missing categorical data. See my edit to that post for an updated example script. I didn’t catch the error before because I assigned uniform probabilities to each category, so it didn’t matter that they weren’t being informed by data so long as they had reasonable priors.


#3

AWESOME!!

This is the complete solution for the introducing example:

model{
a0 ~ normal(0,30);
beta_bp ~ normal(0,30);
beta_m ~ normal(0,30);
a_imp ~ normal(0,30); // explained above
b1_imp ~ normal(0,30); // explained above
b2_imp ~ normal(0,30); // explained above

for (i in 1:n_obs) {

vector[n_cat] p;
vector[n_cat] theta;

p[2] = a_imp[2] + b1_imp[2]*day[i] + b2_imp[2]*lat[i]; 
p[3] = a_imp[3] + b1_imp[3]*day[i] + b2_imp[3]*lat[i]; 

if (cov_cat_miss[i] == 0) {
  y[i] ~ bernoulli_logit(a0+
                           beta_bp*cov_cat_1[i]+
                           beta_m*cov_cat_3[i]);}

theta[1] = 0;
theta[2] = p[2];
theta[3] = p[3]; 
repro_cat_obs[i] ~ categorical( softmax(theta));

else {
  vector[n_cat] log_prob_theta;
  matrix[n_cat, n_cat] lp;  
  
  theta[1] = 0;
  theta[2] = p[2];
  theta[3] = p[3]; 
  log_prob_theta=log_softmax(theta);
  
  lp[1,1] = log_prob_theta[1] + bernoulli_logit_lpmf( y[i] | a0  + beta_bp); //cat 1
  lp[2,1] = log_prob_theta[1] + bernoulli_logit_lpmf( y[i] | a0); //cat 2 (baseline)
  lp[3,1] = log_prob_theta[1] + bernoulli_logit_lpmf( y[i] | a0  + beta_m); //cat 3
  lp[1,2] = log_prob_theta[2] + bernoulli_logit_lpmf( y[i] | a0  + beta_bp);
  lp[2,2] = log_prob_theta[2] + bernoulli_logit_lpmf( y[i] | a0);
  lp[3,2] = log_prob_theta[2] + bernoulli_logit_lpmf( y[i] | a0  + beta_m);
  lp[1,3] = log_prob_theta[3] + bernoulli_logit_lpmf( y[i] | a0  + beta_bp);
  lp[2,3] = log_prob_theta[3] + bernoulli_logit_lpmf( y[i] | a0);
  lp[3,3] = log_prob_theta[3] + bernoulli_logit_lpmf( y[i] | a0  + beta_m);
  
  target += log_sum_exp(lp); 
  
}

}
}