trellisplots
From coda v0.17-1
by Martyn Plummer
Trellis plots for mcmc objects
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.
- Keywords
- hplot
Usage
## S3 method for class '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 class '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 class '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 class '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 class '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 class '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 class '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 class '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 class '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)
Arguments
- x
- an
"mcmc"
or"mcmc.list"
object. - data
- ignored, present for consistency with generic.
- outer
- for the
"mcmc.list"
methods, a logical flag to control whether multiple runs of a series are displayed in the same panel (they are ifFALSE
, not ifTRUE
). If specified in the"mcmc"
methods, - groups
- for the
"mcmc.list"
methods, a logical flag to control whether the underlyinglattice
call will be supplied agroups
arguments indicating which run a data point originated from. The panel function is res - aspect
- 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 - default.scales
- 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 forscales
(see - 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
panel.xyplot
for possibl - thin
- an optional thinning interval that is applied before the plot is drawn.
- 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.
- plot.points
- character argument giving the style in which
points are added to the plot. See
panel.densityplot
for details. - layout
- a method-specific default for the
layout
argument to the lattice functions. - xlab,ylab,main
- Used to provide default axis annotations and plot labels.
- cuts, at
- defines number and location of values where colors change
- col.regions
- color palette used
- lag.max
- maximum lag for which autocorrelation is computed. By
default, the value chosen by
acf
is used - prepanel,panel
- 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. - subset
- indices of the subset of the series to plot. The
default is constructed from the
start
andthin
arguments.
Value
See Also
Lattice
for a brief introduction to
lattice displays and links to further documentation.
Examples
data(line)
xyplot(line)
xyplot(line[[1]], start = 10)
densityplot(line, start = 10)
qqmath(line, start = 10)
levelplot(line[[2]])
acfplot(line, outer = TRUE)
Community examples
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