[R] mgcv::gam.check qq plot residuals are not standardized?

[Simon Wood]

Hi Michael,

You seem to have a quite recent mgcv if you are using qq.gam, so a help 
file for version 1.3 is probably not going to be much help (gam.fit2 no 
longer exists, for example).

By default qq.gam plots deviance residuals (see ?qq.gam). So the default 
is standardization. When possible it then computes correct reference 
quantiles for these, assuming that the model is correct.

See...
http://www.sciencedirect.com/science/article/pii/S0167947312000692
for details (or http://opus.bath.ac.uk/27091/1/qq_gam_resub.pdf)

best,
Simon

On 25/04/14 20:49, Folkes, Michael wrote:
> Hello all,
>
> I looking for confirmation of what I'm seeing. The qq plot in gam.check
> and qq.gam is not standardizing the residuals.
>
> The current help doesn't suggest they're standardized.
>
> Somehow I found, online, a help for gam.check from  version [Package
> mgcv version 1.3-23 Index]:
>
> "If the fit method is based on magic or gam.fit2 then there is no global
> search and the problems with phantom local minima are much reduced. The
> first plot in this case will simply be a normal QQ plot of the
> standardized residuals."
>
>
>
> This text is absent from the current help file.
>
> If I'm correct, why is it that they aren't being standardized?
>
> Much appreciated.
>
> Michael
>
> _______________________________________________________
>
> Michael Folkes
>
> Salmon Stock Assessment
>
> Canadian Dept. of Fisheries & Oceans
>
> Pacific Biological Station
>
> 3190 Hammond Bay Rd.
>
> Nanaimo, B.C., Canada
>
> V9T-6N7
>
> Ph (250) 756-7264 Fax (250) 756-7053  Michael.Folkes at dfo-mpo.gc.ca
> <mailto:Michael.Folkes at dfo-mpo.gc.ca>
>
>
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-- 
Simon Wood, Mathematical Science, University of Bath BA2 7AY UK
+44 (0)1225 386603               http://people.bath.ac.uk/sw283