These methods use the Trellis framework as implemented in the
lattice package to produce space-conserving diagnostic plots
from "mcmc" and "mcmc.list" objects. The xyplot
methods produce trace plots. The densityplot methods and
qqmath methods produce empirical density and probability
plots. The levelplot method depicts the correlation of the
series. The acfplot methods plot the auto-correlation in the
series.
Not yet available in S-PLUS.
# S3 method for mcmc
densityplot(x, data,
outer, aspect = "xy",
default.scales = list(relation = "free"),
start = 1, thin = 1,
main = attr(x, "title"),
xlab = "",
plot.points = "rug",
…,
subset)
# S3 method for mcmc.list
densityplot(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",
…,
subset)
# S3 method for mcmc
levelplot(x, data, main = attr(x, "title"),
start = 1, thin = 1,
…,
xlab = "", ylab = "",
cuts = 10, at,
col.regions = topo.colors(100),
subset)
# S3 method for mcmc
qqmath(x, data,
outer, aspect = "xy",
default.scales = list(y = list(relation = "free")),
prepanel = prepanel.qqmathline,
start = 1, thin = 1,
main = attr(x, "title"),
ylab = "",
…,
subset)
# S3 method for mcmc.list
qqmath(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 = "",
…,
subset)
# S3 method for mcmc
xyplot(x, data,
outer, layout = c(1, nvar(x)),
default.scales = list(y = list(relation = "free")),
type = 'l',
start = 1, thin = 1,
xlab = "Iteration number",
ylab = "",
main = attr(x, "title"),
…,
subset)
# S3 method for mcmc.list
xyplot(x, data, outer = FALSE, groups = !outer,
aspect = "xy", layout = c(1, nvar(x)),
default.scales = list(y = list(relation = "free")),
type = 'l',
start = 1, thin = 1,
xlab = "Iteration number",
ylab = "",
main = attr(x, "title"),
…,
subset)
acfplot(x, data, …)
# S3 method for mcmc
acfplot(x, data, outer,
prepanel, panel,
type = 'h',
aspect = "xy",
start = 1, thin = 1,
lag.max = NULL,
ylab = "Autocorrelation",
xlab = "Lag",
main = attr(x, "title"),
…,
subset)
# S3 method for mcmc.list
acfplot(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"),
…,
subset)an "mcmc" or "mcmc.list" object.
ignored, present for consistency with generic.
for the "mcmc.list" methods, a logical flag to
control whether multiple runs of a series are displayed in the same
panel (they are if FALSE, not if TRUE). If specified
in the "mcmc" methods, this argument is ignored with a
warning.
for the "mcmc.list" methods, a logical flag to
control whether the underlying lattice call will be supplied
a 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 outer=FALSE,
the default of groups is TRUE if the corresponding
default panel function is able to make use of such information.
When outer=FALSE, groups=TRUE will be ignored with a
warning.
controls the physical aspect ratio of the panel. See
xyplot for details. The default for
these methods is chosen carefully - check what the default plot
looks like before changing this parameter.
this parameter provides a reasonable default
value of the scales parameter for the method. It is unlikely
that a user will wish to change this parameter. Pass a value for
scales (see xyplot) instead,
which will override values specified here.
a character vector that determines if lines, points,
etc. are drawn on the panel. The default values for the methods are
carefully chosen. See
panel.xyplot for possible
values.
an optional thinning interval that is applied before the plot is drawn.
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.
character argument giving the style in which
points are added to the plot. See
panel.densityplot for
details.
a method-specific default for the layout argument
to the lattice functions.
Used to provide default axis annotations and plot labels.
defines number and location of values where colors change
color palette used
maximum lag for which autocorrelation is computed. By
default, the value chosen by acf is used
suitable prepanel and panel functions for
acfplot. The prepanel function omits the lag-0
auto-correlation (which is always 1) from the range calculations.
other arguments, passed to the lattice function.
Documentation of the corresponding generics in the lattice
package should be consulted for possible arguments.
indices of the subset of the series to plot. The
default is constructed from the start and thin
arguments.
An object of class "trellis". The relevant
update method can be used to
update components of the object and the
print method (usually called by
default) will plot it on an appropriate plotting device.
Lattice for a brief introduction to
lattice displays and links to further documentation.
# NOT RUN {
data(line)
# }
# NOT RUN {
xyplot(line)
xyplot(line[[1]], start = 10)
densityplot(line, start = 10)
qqmath(line, start = 10)
levelplot(line[[2]])
acfplot(line, outer = TRUE)
# }
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