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\docType{methods}
\name{traceplot}
\alias{traceplot}
\alias{traceplot,stanfit-method}
\title{Markov chain traceplots}
\description{Draw the traceplot corresponding to one or more
Markov chains, providing a visual way to inspect sampling behavior
and assess mixing across chains and convergence.}
\usage{
%% traceplot(object, \dots)
\S4method{traceplot}{stanfit}(object, pars, include = TRUE, unconstrain = FALSE,
inc_warmup = FALSE, window = NULL, nrow = NULL, ncol = NULL, ...)
}
\section{Methods}{
\describe{
\item{traceplot}{\code{signature(object = "stanfit")} Plot the sampling paths for all chains.}
}
}
\arguments{
\item{object}{An instance of class \code{\linkS4class{stanfit}}.}
\item{pars}{A character vector of parameter names. Defaults to all parameters
or the first 10 parameters (if there are more than 10).}
\item{include}{Should the parameters given by the \code{pars} argument be
included (the default) or excluded from the plot? Only relevant if
\code{pars} is not missing.}
\item{inc_warmup}{\code{TRUE} or \code{FALSE}, indicating whether
the warmup sample are included in the trace plot; defaults to \code{FALSE}.}
\item{window}{A vector of length 2. Iterations between \code{window[1]}
and \code{window[2]} will be shown in the plot. The default is to
show all iterations if \code{inc_warmup} is \code{TRUE} and all iterations
from the sampling period only if \code{inc_warmup} is \code{FALSE}. If
\code{inc_warmup} is \code{FALSE} the iterations specified in \code{window}
should not include iterations from the warmup period.}
\item{unconstrain}{Should parameters be plotted on the unconstrained space?
Defaults to \code{FALSE}.}
\item{nrow,ncol}{Passed to \code{\link[ggplot2]{facet_wrap}}.}
\item{\dots}{Optional arguments to pass to \code{\link[ggplot2]{geom_path}}
(e.g. \code{size}, \code{linetype}, \code{alpha}, etc.).}
}
\value{A \code{\link[ggplot2]{ggplot}} object that can be further customized
using the \pkg{ggplot2} package.}
\seealso{
\code{\link[=rstan-plotting-functions]{List of RStan plotting functions}},
\code{\link[=rstan_gg_options]{Plot options}}
}
\examples{\dontrun{
# Create a stanfit object from reading CSV files of samples (saved in rstan
# package) generated by funtion stan for demonstration purpose from model as follows.
#
excode <- '
transformed data {
array[20] real y;
y[1] <- 0.5796; y[2] <- 0.2276; y[3] <- -0.2959;
y[4] <- -0.3742; y[5] <- 0.3885; y[6] <- -2.1585;
y[7] <- 0.7111; y[8] <- 1.4424; y[9] <- 2.5430;
y[10] <- 0.3746; y[11] <- 0.4773; y[12] <- 0.1803;
y[13] <- 0.5215; y[14] <- -1.6044; y[15] <- -0.6703;
y[16] <- 0.9459; y[17] <- -0.382; y[18] <- 0.7619;
y[19] <- 0.1006; y[20] <- -1.7461;
}
parameters {
real mu;
real<lower=0, upper=10> sigma;
vector[2] z[3];
real<lower=0> alpha;
}
model {
y ~ normal(mu, sigma);
for (i in 1:3)
z[i] ~ normal(0, 1);
alpha ~ exponential(2);
}
'
# exfit <- stan(model_code = excode, save_dso = FALSE, iter = 200,
# sample_file = "rstan_doc_ex.csv")
#
exfit <- read_stan_csv(dir(system.file('misc', package = 'rstan'),
pattern='rstan_doc_ex_[[:digit:]].csv',
full.names = TRUE))
print(exfit)
traceplot(exfit)
traceplot(exfit, size = 0.25)
traceplot(exfit, pars = "sigma", inc_warmup = TRUE)
trace <- traceplot(exfit, pars = c("z[1,1]", "z[3,1]"))
trace + scale_color_discrete() + theme(legend.position = "top")
}
}
\keyword{methods}
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