I’m working with the posterior samples from a model fit using RStan. I started my normal routine of using
tidybayes to extract posterior samples from the
stanfit object and start plotting. However, I ran into an issue with the variable names that come out of
tidy_draws() where instead of the expected bracket notation e.g. x, I get the results in an unexpected dot notation form e.g. x.1. This mangling of the names does happen when i use
dimnames() on the
I hunted for a long time to find the source of the problem, reading the github repo for
rstan and I think I found the source of the problem.
rstan::As.mcmc.list appears to be the source of the unexpected renaming.
You can compare the outputs from the following
library(rstan) library(tidybayes) csvfiles <- dir(system.file('misc', package = 'rstan'), pattern = 'rstan_doc_ex_[0-9].csv', full.names = TRUE) fit <- read_stan_csv(csvfiles) dimnames(fit) As.mcmc.list(fit) tidy_draws(fit)
I’m not sure how to resolve this issue, because it appears to break a lot functionality with
tidybayes. For example, this now longer works because the intermediate
mcmc.list created by
rstan::As.mcmc.list doesn’t have the expected variable names.
gather_draws(fit, z[i, j])
Is this the correct venue to report this or should I take this to the