Summarize divergent transitions in glance

[nehill197]

Divergent transitions in Stan indicate that something is wrong with your model. Currently, it is only in debug mode that the Stan warning messages are printed, which include warnings of divergent transitions.

We should add a column (divergences/diverge/divergent) that summarizes whether or not there were any divergent transitions in the glance table for all models.

Since a single divergent transition is enough to warrant concern, this should be a binary column for Stan models. JAGS models should show NA.

Potentially helpful code:

# Returns parameter arrays separated into divergent and non-divergent transitions
partition_div <- function(fit) {
  nom_params <- rstan::extract(fit, permuted=FALSE)
  n_chains <- dim(nom_params)[2]
  params <- as.data.frame(do.call(rbind, lapply(1:n_chains, function(n) nom_params[,n,])))
  
  sampler_params <- rstan::get_sampler_params(fit, inc_warmup=FALSE)
  divergent <- do.call(rbind, sampler_params)[,'divergent__']
  params$divergent <- divergent
  
  div_params <- params[params$divergent == 1,]
  nondiv_params <- params[params$divergent == 0,]
  
  return(list(div_params, nondiv_params))
}
div <- partition_div(analysis$stanfit)
paste("There were", nrow(div[[1]]), "divergent transitions")