Re: [R] lme nesting/interaction advice

From: Rolf Turner <r.turner_at_auckland.ac.nz>
Date: Mon, 12 May 2008 10:34:40 +1200

On 12/05/2008, at 9:45 AM, Andrew Robinson wrote:

> On Sun, May 11, 2008 at 07:52:50PM +0100, Federico Calboli wrote:
>>
>> The main point of my question is, having a 3 way anova (or ancova, if
>> you prefer), with *no* nesting, 2 fixed effects and 1 random effect,
>> why is it so boneheaded difficult to specify a bog standard fully
>> crossed model? I'm not talking about some rarified esoteric model
>> here, we're talking about stuff tought in a first year Biology Stats
>> course here[1].
>
> That may be so, but I've never needed to use one.

	So what?  This is still a standard, common, garden-variety
	model that you will encounter in exercises in many (if not
	all!) textbooks on experimental design and anova.

>
> If it's bog-standard and yet boneheaded difficult, then presumably
> someone else would have had this problem before you. Perhaps a search
> of the archives will help? If you try, you will find many qualifiers
> to the effect that "lme isn't very well set up for crossed random
> effects".
	But that avoids the question as to *why* it isn't very well
	set up for crossed random effects?  What's the problem?
	What are the issues?  The model is indeed bog-standard.
	It would seem not unreasonable to expect that it could be
	fitted in a straightforward manner, and it is irritating to
	find that it cannot be.  If SAS and Minitab can do it at
	the touch of a button, why can't R do it?

>
>> Now, to avoid any chances of being misunderstood in my use of the
>> words 'fully crossed model', what I mean is a simple
>>
>> y ~ effect1 * effect2 * effect3
>>
>> with effect3 being random (all all the jazz that comes from this
>> fact). I fully apprecciate that the only reasonable F-tests would be
>> for effect1, effect2 and effect1:effect2, but there is no way I can
>> use lme to specify such simple thing without getting the *wrong*
>> denDF. I need light on this topic and I'd say it's a general enough
>> question not to need much more handholding than this.
>
> Perhaps there are some circumstances unique to your situation.

        Huh?
>
>> I fully apprecciate that R is developed for love, not money,
>
> ... as is the R-help community ...
>
>> and if I
>> knew how to write an user friendly frontend for nlme and lme4 (and I
>> knew how to actually get the model I want) I'd be pretty happy to do
>> so and submit it as a library. In any case, I feel my complaint is
>> pefectly valid, because specifying such basic model should ideally
>> not such a chore, and I think the powers that be might actually find
>> some use from user feedback.
>
> This is not feedback. It is a compliant. But, the complaint boils
> down to the fact that you don't know what you're doing

	That's rubbish. I think it's fairly clear that Federico does
	have a pretty good idea of what he's doing, but is flummoxed
	by the arcana of lme().  As am I.

> and you show
> no evidence of having searched the R-help archives. How is that
> helpful?

	It doesn't seem to me to be a complaint as such.  It is a
	request for insight.  I too would like some insight as to
	what on earth is going on.  And why do you say Federico
	shows no evidence of having searched the archives?  One can
	search till one is blue in the face and come away no wiser
	on this issue.

		cheers,

			Rolf Turner

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