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 provided for stanfit (rstan), CmdStanMCMC (cmdstanr), 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 'CmdStanMCMC'
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 'CmdStanMCMC'
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 'CmdStanMCMC'
rhat(object, 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, ...)
## S3 method for class 'CmdStanMCMC'
neff_ratio(object, pars = NULL, ...)
Arguments
object |
The object to use. |
... |
Arguments passed to individual methods. |
inc_warmup |
A logical scalar (defaulting to |
pars |
An optional character vector of parameter names. For
|
regex_pars |
An optional regular expression to use for
parameter selection. Can be specified instead of |
Value
log_posterior()
-
log_posterior()
methods return a molten data frame (seereshape2::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 (seereshape2::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.
See Also
Examples
## Not run:
library(rstanarm)
fit <- stan_glm(mpg ~ wt, data = mtcars, refresh = 0)
np <- nuts_params(fit)
head(np)
tail(np)
lp <- log_posterior(fit)
head(lp)
tail(lp)
## End(Not run)