R: Plot Diagnostics for an BAS Object

plot.bas {BAS} | R Documentation

## Plot Diagnostics for an BAS Object

### Description

Four plots (selectable by 'which') are currently available: a plot of residuals against fitted values, Cumulative Model Probabilities, log marginal likelihoods versus model dimension, and marginal inclusion probabilities.

### Usage

    ## S3 method for class 'bas'
    plot(
      x,
      which = c(1:4),
      caption = c("Residuals vs Fitted", "Model Probabilities", "Model Complexity",
        "Inclusion Probabilities"),
      panel = if (add.smooth) panel.smooth else points,
      sub.caption = NULL,
      main = "",
      ask = prod(par("mfcol")) < length(which) && dev.interactive(),
      col.in = 2,
      col.ex = 1,
      col.pch = 1,
      cex.lab = 1,
      ...,
      id.n = 3,
      labels.id = NULL,
      cex.id = 0.75,
      add.smooth = getOption("add.smooth"),
      label.pos = c(4, 2),
      subset = NULL,
      drop.always.included = FALSE
    )

### Arguments

`x` | `bas` BMA object result of 'bas'
`which` | if a subset of the plots is required, specify a subset of the numbers '1:4'
`caption` | captions to appear above the plots
`panel` | panel function. The useful alternative to 'points', 'panel.smooth' can be chosen by 'add.smooth = TRUE'
`sub.caption` | common title-above figures if there are multiple; used as 'sub' (s.'title') otherwise. If 'NULL', as by default, a possible shortened version of `deparse(x$call)` is used
`main` | title to each plot-in addition to the above 'caption'
`ask` | logical; if 'TRUE', the user is asked before each plot, see 'par(ask=.)'
`col.in` | color for the included variables
`col.ex` | color for the excluded variables
`col.pch` | color for points in panels 1-3
`cex.lab` | graphics parameter to control size of variable names
`...` | other parameters to be passed through to plotting functions
`id.n` | number of points to be labeled in each plot, starting with the most extreme
`labels.id` | vector of labels, from which the labels for extreme points will be chosen. 'NULL' uses observation numbers
`cex.id` | magnification of point labels.
`add.smooth` | logical indicating if a smoother should be added to most plots; see also 'panel' above
`label.pos` | positioning of labels, for the left half and right half of the graph respectively, for plots 1-4
`subset` | indices of variables to include/exclude in plot of marginal posterior inclusion probabilities (NULL).
`drop.always.included` | logical variable to drop marginal posterior inclusion probabilities for variables that are always forced into the model. FALSE by default.

### Details

This provides a panel of 4 plots: the first is a plot of the residuals versus fitted values under BMA. The second is a plot of the cumulative marginal likelihoods of models; if the model space cannot be enumerated then this provides some indication of whether the probabilities are leveling off. The third is a plot of log marginal likelihood versus model dimension and the fourth plot show the posterior marginal inclusion probabilities.

### Author(s)

Merlise Clyde, based on plot.lm by John Maindonald and Martin Maechler

### See Also

`plot.coef.bas` and `image.bas`.

Other bas plots: `image.bas()`, `plot.coef.bas()`

### Examples

    data(Hald)
    hald.gprior =  bas.lm(Y~ ., data=Hald, prior="g-prior", alpha=13,
                          modelprior=beta.binomial(1,1),
                          initprobs="eplogp")

    plot(hald.gprior)

[Package BAS version 1.5.5 Index]