I’m wrapping up a case study, which uses cmdstanr. I’m trying to remove rstan depencies, by using bayesplots and posterior to do diagnostics. I have two outstanding problems with the trace plots.
- The chains are all a shade of blue, which makes it difficult to distinguish which trace corresponds to which chain.
- How can I added a shaded area to indicate which iterations are in the warmup phase and which ones are in the sampling phase?
Here’s the code for constructing the traceplots, using a cmdstanr fit object.
bayesplot::mcmc_trace(r_fit2$draws(), pars = pars)