diagnose_ess <- function(ess, ss) {
ess / ss < 0.1
}
diagnose_mcse <- function(mcse, psd) {
mcse / psd > 0.15
}
diagnose_rhat <- function(rhat) {
rhat > 1.1
}
diagnose_parameters <- function(stanfit, pars) {
pars <- match_parameter_names(stanfit, pars)
sim <- rstan::extract(stanfit, pars, permuted = FALSE, inc_warmup = FALSE)
mon <- rstan::monitor(sim, probs = 0.5, print = FALSE)
# mon <- monitor(stanfit, pars = c("mu11", "mu21"), 0.5)
sampleSize <- extract_sample_size(stanfit)
ind <-
diagnose_rhat(mon[, "Rhat"]) |
diagnose_ess(mon[, "n_eff"], sampleSize) |
diagnose_mcse(mon[, "se_mean"], mon[, "sd"])
ind
}
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