Extract sampler parameters from a fit.

Extract information about NUTS trajectories, such as acceptance ratio and treedepth, from a fitted object.

Usage

extract_sampler_params(fit, inc_warmup = FALSE)

Arguments

fit

A list returned by sample_admb.

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.

Value

An invisible data.frame containing samples (rows) of each parameter (columns). If multiple chains exist they will be rbinded together.

Details

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.

See also

launch_shinyadmb.

Examples

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 ...