Extract the values of sampler diagnostics for each iteration and
chain of MCMC. To instead get summaries of these diagnostics and associated
warning messages use the
$diagnostic_summary()
method.
sampler_diagnostics( inc_warmup = FALSE, format = getOption("cmdstanr_draws_format", "draws_array") )
inc_warmup | (logical) Should warmup draws be included? Defaults to |
---|---|
format | (string) The draws format to return. See draws for details. |
Depends on format
, but the default is a 3-D
draws_array
object (iteration x chain x
variable). The variables for Stan's default MCMC algorithm are
"accept_stat__"
, "stepsize__"
, "treedepth__"
, "n_leapfrog__"
,
"divergent__"
, "energy__"
.
# \dontrun{ fit <- cmdstanr_example("logistic") sampler_diagnostics <- fit$sampler_diagnostics() str(sampler_diagnostics)#> 'draws_array' num [1:1000, 1:4, 1:6] 3 2 2 2 3 1 1 2 2 2 ... #> - attr(*, "dimnames")=List of 3 #> ..$ iteration: chr [1:1000] "1" "2" "3" "4" ... #> ..$ chain : chr [1:4] "1" "2" "3" "4" #> ..$ variable : chr [1:6] "treedepth__" "divergent__" "energy__" "accept_stat__" ...#> # A draws_df: 1000 iterations, 4 chains, and 6 variables #> treedepth__ divergent__ energy__ accept_stat__ stepsize__ n_leapfrog__ #> 1 3 0 68 1.00 0.87 7 #> 2 2 0 73 0.60 0.87 7 #> 3 2 0 72 1.00 0.87 3 #> 4 2 0 67 0.97 0.87 3 #> 5 3 0 68 1.00 0.87 7 #> 6 1 0 68 0.82 0.87 3 #> 7 1 0 70 0.57 0.87 3 #> 8 2 0 67 1.00 0.87 3 #> 9 2 0 67 0.82 0.87 3 #> 10 2 0 67 0.98 0.87 3 #> # ... with 3990 more draws #> # ... hidden reserved variables {'.chain', '.iteration', '.draw'}# or specify format to get a data frame instead of calling as_draws_df fit$sampler_diagnostics(format = "df")#> # A draws_df: 1000 iterations, 4 chains, and 6 variables #> treedepth__ divergent__ energy__ accept_stat__ stepsize__ n_leapfrog__ #> 1 3 0 68 1.00 0.87 7 #> 2 2 0 73 0.60 0.87 7 #> 3 2 0 72 1.00 0.87 3 #> 4 2 0 67 0.97 0.87 3 #> 5 3 0 68 1.00 0.87 7 #> 6 1 0 68 0.82 0.87 3 #> 7 1 0 70 0.57 0.87 3 #> 8 2 0 67 1.00 0.87 3 #> 9 2 0 67 0.82 0.87 3 #> 10 2 0 67 0.98 0.87 3 #> # ... with 3990 more draws #> # ... hidden reserved variables {'.chain', '.iteration', '.draw'}# }