lme nesting/interaction advice

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.

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".

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.

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

Once I have sorted how to specify such trivial model I'll face the
horror of the nesting, in any case I attach a toy dataset I created
especially to test how to specify the correct model (silly me).

Well, these data seem to differ.  Is replica block?  If not, then how
can we reproduce your results?  And, if I assume that it is, then the
output df differ from what you sent in your original mail.  So, I find
this confusing.

Then, from your original mail,

The easiest model ignores the nested random effects and uses just
selection, males and replica and the relative interactions. The
model

lme(y ~ selection * males, random = ~1|replica/selection/males,  
mydata)

forgive me, but I seem to see nesting in the random statement.  That  
is
what happens when we separate factors with a '/'; they are nested.  We
would expect that statement to not provide the correct df for the
bog-standard fully crossed design.

Perhaps if you were to comply with the request at the bottom of each