Extract quantities needed for plotting from model objects

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.

log_posterior(object, ...)

nuts_params(object, ...)

rhat(object, ...)

neff_ratio(object, ...)

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

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

# S3 method for CmdStanMCMC
log_posterior(object, inc_warmup = FALSE, ...)

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

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

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

# S3 method for CmdStanMCMC
nuts_params(object, pars = NULL, ...)

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

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

# S3 method for CmdStanMCMC
rhat(object, pars = NULL, ...)

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

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

# S3 method for CmdStanMCMC
neff_ratio(object, 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. When using pars for tidy parameter selection, the regex_pars argument is ignored since select helpers perform a similar function.

Value

log_posterior(): log_posterior() methods return a molten data frame (see reshape2::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 reshape2::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

# \dontrun{
library(rstanarm)
fit <- stan_glm(mpg ~ wt, data = mtcars, refresh = 0)

np <- nuts_params(fit)
head(np)
#>   Chain Iteration     Parameter     Value
#> 1     1         1 accept_stat__ 0.9959800
#> 2     1         2 accept_stat__ 0.9990818
#> 3     1         3 accept_stat__ 0.9922949
#> 4     1         4 accept_stat__ 0.9592249
#> 5     1         5 accept_stat__ 0.9959713
#> 6     1         6 accept_stat__ 0.9846108
tail(np)
#>       Chain Iteration Parameter    Value
#> 23995     4       995  energy__ 86.09516
#> 23996     4       996  energy__ 86.63987
#> 23997     4       997  energy__ 87.05197
#> 23998     4       998  energy__ 91.53823
#> 23999     4       999  energy__ 88.10087
#> 24000     4      1000  energy__ 89.14512

lp <- log_posterior(fit)
head(lp)
#>   Chain Iteration     Value
#> 1     1         1 -86.46143
#> 2     1         2 -86.45492
#> 3     1         3 -86.55465
#> 4     1         4 -87.06081
#> 5     1         5 -86.32876
#> 6     1         6 -86.77675
tail(lp)
#>      Chain Iteration     Value
#> 3995     4       995 -85.93512
#> 3996     4       996 -86.07147
#> 3997     4       997 -86.54743
#> 3998     4       998 -87.97370
#> 3999     4       999 -86.85226
#> 4000     4      1000 -88.45662
# }

Extract quantities needed for plotting from model objects

Arguments

Value

See also

Examples