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\name{trellisplots}
\title{Trellis plots for mcmc objects}
\alias{densityplot.mcmc}
\alias{levelplot.mcmc}
\alias{qqmath.mcmc}
\alias{xyplot.mcmc}
\alias{densityplot.mcmc.list}
\alias{levelplot.mcmc.list}
\alias{qqmath.mcmc.list}
\alias{xyplot.mcmc.list}
\alias{acfplot}
\alias{acfplot.mcmc}
\alias{acfplot.mcmc.list}
\usage{
\method{densityplot}{mcmc}(x, data,
outer, aspect = "xy",
default.scales = list(relation = "free"),
start = 1, thin = 1,
main = attr(x, "title"),
xlab = "",
plot.points = "rug",
\dots,
subset)
\method{densityplot}{mcmc.list}(x, data,
outer = FALSE, groups = !outer,
aspect = "xy",
default.scales = list(relation = "free"),
start = 1, thin = 1,
main = attr(x, "title"),
xlab = "",
plot.points = "rug",
\dots,
subset)
\method{levelplot}{mcmc}(x, data, main = attr(x, "title"),
start = 1, thin = 1,
\dots,
xlab = "", ylab = "",
cuts = 10, at,
col.regions = topo.colors(100),
subset)
\method{qqmath}{mcmc}(x, data,
outer, aspect = "xy",
default.scales = list(y = list(relation = "free")),
prepanel = prepanel.qqmathline,
start = 1, thin = 1,
main = attr(x, "title"),
ylab = "",
\dots,
subset)
\method{qqmath}{mcmc.list}(x, data,
outer = FALSE, groups = !outer,
aspect = "xy",
default.scales = list(y = list(relation = "free")),
prepanel = prepanel.qqmathline,
start = 1, thin = 1,
main = attr(x, "title"),
ylab = "",
\dots,
subset)
\method{xyplot}{mcmc}(x, data,
outer, layout = c(1, ncol(x)),
default.scales = list(y = list(relation = "free")),
type = 'l',
start = 1, thin = 1,
ylab = "",
xlab = "Iteration number",
main = attr(x, "title"),
\dots,
subset)
\method{xyplot}{mcmc.list}(x, data, outer = FALSE, groups = !outer,
aspect = "xy", layout = c(1, ncol(x[[1]])),
default.scales = list(y = list(relation = "free")),
type = 'l',
start = 1, thin = 1,
main = attr(x, "title"),
ylab = "",
\dots,
subset)
acfplot(x, data, \dots)
\method{acfplot}{mcmc}(x, data, outer,
prepanel, panel,
type = 'h',
aspect = "xy",
start = 1, thin = 1,
lag.max = NULL,
ylab = "Autocorrelation",
xlab = "Lag",
main = attr(x, "title"),
\dots,
subset)
\method{acfplot}{mcmc.list}(x, data, outer = FALSE, groups = !outer,
prepanel, panel,
type = if (groups) 'b' else 'h',
aspect = "xy",
start = 1, thin = 1,
lag.max = NULL,
ylab = "Autocorrelation",
xlab = "Lag",
main = attr(x, "title"),
\dots,
subset)
}
\description{
These methods use the Trellis framework as implemented in the
\code{lattice} package to produce space-conserving diagnostic plots
from \code{"mcmc"} and \code{"mcmc.list"} objects. The \code{xyplot}
methods produce trace plots. The \code{densityplot} methods and
\code{qqmath} methods produce empirical density and probability
plots. The \code{levelplot} method depicts the correlation of the
series. The \code{acfplot} methods plot the auto-correlation in the
series.
Not yet available in S-PLUS.
}
\arguments{
\item{x}{ an \code{"mcmc"} or \code{"mcmc.list"} object. }
\item{data}{ ignored, present for consistency with generic. }
\item{outer}{ for the \code{"mcmc.list"} methods, a logical flag to
control whether multiple runs of a series are displayed in the same
panel (they are if \code{FALSE}, not if \code{TRUE}). If specified
in the \code{"mcmc"} methods, this argument is ignored with a
warning. }
\item{groups}{ for the \code{"mcmc.list"} methods, a logical flag to
control whether the underlying \code{lattice} call will be supplied
a \code{groups} arguments indicating which run a data point
originated from. The panel function is responsible for handling
such an argument, and will usually differentiate runs within a panel
by using different graphical parameters. When \code{outer=FALSE},
the default of \code{groups} is \code{TRUE} if the corresponding
default panel function is able to make use of such information.
When \code{outer=FALSE}, \code{groups=TRUE} will be ignored with a
warning. }
\item{aspect}{ controls the physical aspect ratio of the panel. See
\code{\link[lattice:xyplot]{xyplot}} for details. The default for
these methods is chosen carefully - check what the default plot
looks like before changing this parameter.}
\item{default.scales}{ this parameter provides a reasonable default
value of the \code{scales} parameter for the method. It is unlikely
that a user will wish to change this parameter. Pass a value for
\code{scales} (see \code{\link[lattice:xyplot]{xyplot}}) instead,
which will override values specified here. }
\item{type}{ a character vector that determines if lines, points,
etc. are drawn on the panel. The default values for the methods are
carefully chosen. See
\code{\link[lattice:panel.xyplot]{panel.xyplot}} for possible
values. }
\item{thin}{ an optional thinning interval that is applied before the
plot is drawn.}
\item{start}{ an optional value for the starting point within the
series. Values before the starting point are considered part of the
"burn-in" of the series and dropped.}
\item{plot.points}{ character argument giving the style in which
points are added to the plot. See
\code{\link[lattice:panel.densityplot]{panel.densityplot}} for
details. }
\item{layout}{a method-specific default for the \code{layout} argument
to the lattice functions.}
\item{xlab,ylab,main}{Used to provide default axis annotations and
plot labels.}
\item{cuts, at}{ defines number and location of values where colors
change }
\item{col.regions}{ color palette used }
\item{lag.max}{ maximum lag for which autocorrelation is computed. By
default, the value chosen by \code{\link{acf}} is used }
\item{prepanel,panel}{ suitable prepanel and panel functions for
\code{acfplot}. The prepanel function omits the lag-0
auto-correlation (which is always 1) from the range calculations. }
\item{\dots}{other arguments, passed to the lattice function.
Documentation of the corresponding generics in the \code{lattice}
package should be consulted for possible arguments. }
\item{subset}{indices of the subset of the series to plot. The
default is constructed from the \code{start} and \code{thin}
arguments.}
}
\value{
An object of class \code{"trellis"}. The relevant
\code{\link[lattice:update.trellis]{update}} method can be used to
update components of the object and the
\code{\link[lattice:print.trellis]{print}} method (usually called by
default) will plot it on an appropriate plotting device.
}
\seealso{
\code{\link[lattice:Lattice]{Lattice}} for a brief introduction to
lattice displays and links to further documentation.
}
\author{ Deepayan Sarkar \email{Deepayan.Sarkar@R-project.org}}
\examples{
data(line)
\dontrun{
xyplot(line)
xyplot(line[[1]], start = 10)
densityplot(line, start = 10)
qqmath(line, start = 10)
levelplot(line[[2]])
acfplot(line, outer = TRUE)
}
}
\keyword{hplot}
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