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
$diagnostic_summary() method.
sampler_diagnostics(
inc_warmup = FALSE,
format = getOption("cmdstanr_draws_format", "draws_array")
)(logical) Should warmup draws be included? Defaults to FALSE.
(string) The draws format to return. See draws for details.
Depends on format, but the default is a 3-D
draws_array object (iteration x chain x
variable). The variables for Stan's default MCMC algorithm are
"accept_stat__", "stepsize__", "treedepth__", "n_leapfrog__",
"divergent__", "energy__".
# \dontrun{
fit <- cmdstanr_example("logistic")
sampler_diagnostics <- fit$sampler_diagnostics()
str(sampler_diagnostics)
#> 'draws_array' num [1:1000, 1:4, 1:6] 3 3 2 3 2 3 2 2 3 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__" ...
library(posterior)
as_draws_df(sampler_diagnostics)
#> # A draws_df: 1000 iterations, 4 chains, and 6 variables
#> treedepth__ divergent__ energy__ accept_stat__ stepsize__ n_leapfrog__
#> 1 3 0 68 0.91 0.83 7
#> 2 3 0 66 1.00 0.83 7
#> 3 2 0 66 0.89 0.83 3
#> 4 3 0 66 1.00 0.83 7
#> 5 2 0 67 0.95 0.83 3
#> 6 3 0 69 0.85 0.83 7
#> 7 2 0 66 1.00 0.83 3
#> 8 2 0 66 0.83 0.83 3
#> 9 3 0 65 0.94 0.83 7
#> 10 2 0 66 0.93 0.83 7
#> # ... 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 0.91 0.83 7
#> 2 3 0 66 1.00 0.83 7
#> 3 2 0 66 0.89 0.83 3
#> 4 3 0 66 1.00 0.83 7
#> 5 2 0 67 0.95 0.83 3
#> 6 3 0 69 0.85 0.83 7
#> 7 2 0 66 1.00 0.83 3
#> 8 2 0 66 0.83 0.83 3
#> 9 3 0 65 0.94 0.83 7
#> 10 2 0 66 0.93 0.83 7
#> # ... with 3990 more draws
#> # ... hidden reserved variables {'.chain', '.iteration', '.draw'}
# }