extract_sampler_params: Extract sampler parameters from a fit.

In colemonnahan/adnuts: No-U-Turn MCMC Sampling for 'ADMB' Models

Extract sampler parameters from a fit.

Description

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.

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.

Value

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

See Also

launch_shinyadmb.

Examples

fit <- readRDS(system.file('examples', 'fit.RDS', package='adnuts'))
sp <- extract_sampler_params(fit, inc_warmup=TRUE)
str(sp)

colemonnahan/adnuts documentation built on Feb. 10, 2024, 3:30 a.m.