# trellisplots: Trellis plots for mcmc objects In coda: Output Analysis and Diagnostics for MCMC

 trellisplots R Documentation

## Trellis plots for mcmc objects

### Description

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.

### 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, this argument is ignored with a warning. `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 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. `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 this parameter. `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 `xyplot`) instead, which will override values specified here. `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 possible values. `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

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.

### Author(s)

Deepayan Sarkar Deepayan.Sarkar@R-project.org

`Lattice` for a brief introduction to lattice displays and links to further documentation.

### Examples

``````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)

## End(Not run)
``````

coda documentation built on May 29, 2024, 11:23 a.m.