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 

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 titleabove figures if there are multiple; used as
'sub' (s.'title') otherwise. If 'NULL', as by default, a possible shortened
version of 
main 
title to each plotin 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 13 
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 14 
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="gprior", alpha=13,
modelprior=beta.binomial(1,1),
initprobs="eplogp")
plot(hald.gprior)