Re: [R] glmmPQL in 2.3.1

From: Christian Gold <>
Date: Sun 29 Oct 2006 - 08:38:35 GMT

I have come across the previous communication on this list in September (copied below) because I had received the same error message.

I understand from Brian Ripley's reply that anova should not be used with glmmPQL because it is not an adequate method, and that this is now shown with an error message.
My question is, what method *should* be used? Using summary does not give me the result I want, because it shows the significance of each combination of factor *levels*, rather than factors, which can quickly become very hard to interpret.

Many thanks for your input!

Christian Gold

Re: [R] glmmPQL in 2.3.1
This message: [ Message body ] [ More options ] Related messages: [ Next message ] [ Previous message ] [ In reply to ] [ [R] glmmPQL in 2.3.1 ]
From: Prof Brian Ripley <> Date: Tue 26 Sep 2006 - 09:58:19 GMT

On Mon, 25 Sep 2006, Justin Rhodes wrote:

> Dear R-help,
> I recently tried implementing glmmPQL in 2.3.1,

I thought *I* had implemented it: are you talking about my function in package MASS or your own implementation?

> and I discovered a few differences as compared to 2.2.1.

You appear to be talking about contributed packages (MASS, and glmmPQL also depends on nlme) without giving their version numbers.

> I am fitting a regression with fixed and random effects with Gamma error
> structure. First, 2.3.1 gives different estimates than 2.2.1, and
> 2.3.1, takes more iterations to converge.

We have no idea, given the lack of reproducible example. glmmPQL does give the same answers as before for the book examples for which it is support software. This may well be due to an underlying change in nlme.

> Second, when I try using the anova function it says, "'anova' is not
> available for PQL fits", why? Any help would be greatly appreciated.

Because anova implies you are using an optimization criterion, such as least squares or maximum likelihood, and so there is something like a deviance to partition. It was not used in the book with glmmPQL supports, but it seems some people were using glmmPQL without reference to that book so I made a number of their misuses explicit errors. This *is* in the NEWS and WHATS.NEWS files for MASS and VR: There are anova() and logLik() methods for class "glmmPQL" to stop misuse.


______________________________________________ mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
Received on Sun Oct 29 19:45:42 2006

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.1.8, at Sun 29 Oct 2006 - 21:30:14 GMT.

Mailing list information is available at Please read the posting guide before posting to the list.