R: Extract quantities needed for plotting from model objects

bayesplot-extractors {bayesplot}

R Documentation

Extract quantities needed for plotting from model objects

Description

Generics and methods for extracting quantities needed for plotting from various types of model objects. Currently methods are only provided for stanfit (rstan) and stanreg (rstanarm) objects, but adding new methods should be relatively straightforward.

Usage

log_posterior(object, ...)

nuts_params(object, ...)

rhat(object, ...)

neff_ratio(object, ...)

## S3 method for class 'stanfit'
log_posterior(object, inc_warmup = FALSE, ...)

## S3 method for class 'stanreg'
log_posterior(object, inc_warmup = FALSE, ...)

## S3 method for class 'stanfit'
nuts_params(object, pars = NULL, inc_warmup = FALSE, ...)

## S3 method for class 'stanreg'
nuts_params(object, pars = NULL, inc_warmup = FALSE, ...)

## S3 method for class 'list'
nuts_params(object, pars = NULL, ...)

## S3 method for class 'stanfit'
rhat(object, pars = NULL, ...)

## S3 method for class 'stanreg'
rhat(object, pars = NULL, regex_pars = NULL, ...)

## S3 method for class 'stanfit'
neff_ratio(object, pars = NULL, ...)

## S3 method for class 'stanreg'
neff_ratio(object, pars = NULL, regex_pars = NULL, ...)

Arguments

`object`	The object to use.
`...`	Arguments passed to individual methods.
`inc_warmup`	A logical scalar (defaulting to `FALSE`) indicating whether to include warmup draws, if applicable.
`pars`	An optional character vector of parameter names. For `nuts_params` these will be NUTS sampler parameter names rather than model parameters. If `pars` is omitted all parameters are included.
`regex_pars`	An optional regular expression to use for parameter selection. Can be specified instead of `pars` or in addition to `pars`.

Value

log_posterior: log_posterior methods return a molten data frame (see melt). The data frame should have columns "Iteration" (integer), "Chain" (integer), and "Value" (numeric). See Examples, below.
nuts_params: nuts_params methods return a molten data frame (see melt). The data frame should have columns "Parameter" (factor), "Iteration" (integer), "Chain" (integer), and "Value" (numeric). See Examples, below.
rhat, neff_ratio: Methods return (named) vectors.

Examples

## Not run: 
library(rstanarm)
fit <- stan_glm(mpg ~ wt, data = mtcars)

np <- nuts_params(fit)
head(np)
tail(np)

lp <- log_posterior(fit)
head(lp)
tail(lp)

## End(Not run)