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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/retrieve.R
\name{retrieve}
\alias{retrieve}
\title{Get summary statistics from shinystan object}
\usage{
retrieve(sso, what, ...)
}
\arguments{
\item{sso}{A \code{\link[=as.shinystan]{shinystan object}}.}
\item{what}{What do you want to get? See Details, below.}
\item{...}{Optional arguments, in particular \code{pars} to specify parameter
names (by default all parameters will be used). For NUTS sampler parameters
only (e.g. stepsize, treedepth) \code{inc_warmup} can also be specified to
include/exclude warmup iterations (the default is \code{FALSE}). See
Details, below.}
}
\description{
From a shinystan object get rhat, effective sample size, posterior
quantiles, means, standard deviations, sampler diagnostics, etc.
}
\details{
The argument \code{what} can take on the values below. 'Args:
\code{arg}' means that \code{arg} can be specified in \code{...} for this
value of \code{what}.
\describe{
\item{\code{"rhat"}, \code{"Rhat"}, \code{"r_hat"}, or \code{"R_hat"}}{returns: Rhat statistics. Args: \code{pars}}
\item{\code{"N_eff"}, \code{"n_eff"}, \code{"neff"}, \code{"Neff"}, \code{"ess"}, or \code{"ESS"}}{returns: Effective sample sizes. Args: \code{pars}}
\item{\code{"mean"}}{returns: Posterior means. Args: \code{pars}}
\item{\code{"sd"}}{returns: Posterior standard deviations. Args: \code{pars}}
\item{\code{"se_mean"} or \code{"mcse"}}{returns: Monte Carlo standard error. Args: \code{pars}}
\item{\code{"median"}}{returns: Posterior medians. Args: \code{pars}.}
\item{\code{"quantiles"} or any string with \code{"quant"} in it (not case sensitive)}{returns: 2.5\%, 25\%, 50\%, 75\%, 97.5\% posterior quantiles. Args: \code{pars}.}
\item{\code{"avg_accept_stat"} or any string with \code{"accept"} in it (not case sensitive)}{returns: Average value of "accept_stat" (which itself is the average acceptance probability over the NUTS subtree). Args: \code{inc_warmup}}
\item{\code{"prop_divergent"} or any string with \code{"diverg"} in it (not case sensitive)}{returns: Proportion of divergent iterations for each chain. Args: \code{inc_warmup}}
\item{\code{"max_treedepth"} or any string with \code{"tree"} or \code{"depth"} in it (not case sensitive)}{returns: Maximum treedepth for each chain. Args: \code{inc_warmup}}
\item{\code{"avg_stepsize"} or any string with \code{"step"} in it (not case sensitive)}{returns: Average stepsize for each chain. Args: \code{inc_warmup}}
}
}
\note{
Sampler diagnostics (e.g. \code{"avg_accept_stat"}) only available for
models originally fit using Stan.
}
\examples{
# Using example shinystan object 'eight_schools'
sso <- eight_schools
retrieve(sso, "rhat")
retrieve(sso, "mean", pars = c('theta[1]', 'mu'))
retrieve(sso, "quantiles")
retrieve(sso, "max_treedepth") # equivalent to retrieve(sso, "depth"), retrieve(sso, "tree"), etc.
retrieve(sso, "prop_divergent")
retrieve(sso, "prop_divergent", inc_warmup = TRUE)
}
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