[R] Pr(>|z|) in lme4

[Uwe Ligges]

Martin Maechler wrote:

>>>>>>"Dieter" == Dieter Menne <dieter.menne at menne-biomed.de>
>>>>>>    on Fri, 28 May 2004 11:04:13 +0200 writes:
> 
> 
>     Dieter> Dear List, I am struggling understanding S4
>     Dieter> classes. For example, when GLMM
> 
>     Dieter>   summary(glmmML( whatever))
> 
>     Dieter> outputs the following line:
> 
>     Dieter>             Estimate Std. Error DF z value Pr(>|z|)
>     Dieter> (Intercept) 0.856 0.319 45 2.68 0.0073
> 
>     Dieter> How do I access the Pr column?
> 
> Did you try
> 
>     s <- summary(glmmML( whatever))
>     s ## to give the above
> 
>     str(s) ## to show the internal structure
> 
> If 's' itself is an object with a formal class (aka "S4 class"),
> str() will give sub-optimal (but still helpful) output in the
> current version of R [exposing the current implementation of S4
> slots, which you should never make use of].
> 
> Rather in "R Version 2.0.0 Under development (unstable)" 
> aka 'R-devel', it gives much nicer output
> 
> Martin
> 


Well, I wonder what Dieter Menne is looking for. GLMM() is in lme4 and 
uses S4 classes. glmmML() is in "glmmML" and uses S3 classes.

In the latter case, the p-values are calculated within print.glmmML() 
and the corresponding code is:

   1 - pchisq((coef(x)/x$sd)^2, 1)

where x is the glmmML object.

Uwe Ligges