# 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 if`FALSE`

, not if`TRUE`

). If specified in the`"mcmc"`

methods, - groups
- 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 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 for`scales`

(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`

and`thin`

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)
```

*Documentation reproduced from package coda, version 0.17-1, License: GPL (>= 2)*

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