Extract information about NUTS trajectories, such as acceptance ratio and treedepth, from a fitted object.
extract_sampler_params(fit, inc_warmup = FALSE)
| fit | A list returned by |
|---|---|
| inc_warmup | Whether to extract the warmup samples or not (default). Warmup samples should never be used for inference, but may be useful for diagnostics. |
An invisible data.frame containing samples (rows) of each parameter (columns). If multiple chains exist they will be rbinded together.
Each trajectory (iteration) in NUTS has associated information
about the trajectory: stepsize, acceptance ratio, treedepth, and number of
leapfrog steps. This function extracts these into a data.frame, which
may be useful for diagnosing issues in certain cases. In general, the
user should not need to examine them, or preferably should via
plot_sampler_params or launch_shinyadmb.
fit <- readRDS(system.file('examples', 'fit.RDS', package='adnuts')) sp <- extract_sampler_params(fit, inc_warmup=TRUE) str(sp)#> 'data.frame': 3000 obs. of 8 variables: #> $ chain : num 1 1 1 1 1 1 1 1 1 1 ... #> $ iteration : num 1 2 3 4 5 6 7 8 9 10 ... #> $ accept_stat__: num 1.33e-06 9.97e-01 9.62e-01 9.79e-01 7.32e-01 ... #> $ stepsize__ : num 0.0292 0.0288 0.0322 0.0404 0.0347 ... #> $ treedepth__ : num 4 4 2 4 1 3 1 3 4 2 ... #> $ n_leapfrog__ : num 15 15 3 11 1 7 1 7 11 3 ... #> $ divergent__ : num 0 0 0 0 0 0 0 0 0 0 ... #> $ energy__ : num 28.3 17.5 12 12.6 12.6 ...