plot.bma {BAS}R Documentation

Plot Diagnostics for an blm 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 'bma':
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(), ..., id.n = 3, labels.id =
                 names(residuals(x)), cex.id = 0.75, add.smooth =
                 getOption("add.smooth"), label.pos = c(4, 2))

Arguments

x 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=.)'
... other parameters to be passed through to plotting functions
id.n number of points to be labelled 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 1-3

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.bma and image.bma.

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 0.45 Index]