[R] different results with plot.lm vs. plot.lm(which=c(2))

[Prof Brian Ripley]

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On Wed, 12 Nov 2008, Effie Greathouse wrote:

> I am running GLM models using the gamma family.  For example:
> model <-glm(y ~ x, family=Gamma(link="identity"))
>
> I am getting different results for the normal Q-Q plot and the
> Scale-Location plot if I run the diagnostic plots without specifying the
> plot vs. if I specify the plot ... e.g., "plot(model)" gives me a different
> Normal Q-Q graph than "plot(model, which=c(2))".  The former gives data
> points distributed in a quadratic pattern, while the latter gives data
> points more or less along the 1:1 line.  Shouldn't these two commands be
> giving me the same exact graphs?  I have read the documentation on plot.lm
> and searched the help archives, but I am still learning GLM's and I'm not
> very familiar with understanding diagnostic plots for GLM's, so any help
> would be much appreciated!
>
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-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
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