R: Trellis plots for mcmc objects

trellisplots {coda} | 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

### See Also

`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)

[Package coda version 0.19-1 Index]