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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