random interactions in lme

On Apr 24, 2005, at 8:52 AM, Douglas Bates wrote:

Jacob Michaelson wrote:

Hi All,
I'm taking an Experimental Design course this semester, and have 
spent many long hours trying to coax the professor's SAS examples 
into something that will work in R (I'd prefer that the things I 
learn not be tied to a license).  It's been a long semester in that 
regard.
One thing that has really frustrated me is that lme has an extremely 
counterintuitive way for specifying random terms.  I can usually 
figure out how to express a single random term, but if there are 
multiple terms or random interactions, the documentation available 
just doesn't hold up.
Here's an example: a split block (strip plot) design evaluated in SAS 
with PROC MIXED (an excerpt of the model and random statements):
model DryMatter = Compacting|Variety / outp = residuals ddfm = 
satterthwaite;
random Rep Rep*Compacting Rep*Variety;
Now the fixed part of that model is easy enough in lme: 
"DryMatter~Compacting*Variety"
But I can't find anything that adequately explains how to simply add 
the random terms to the model, ie "rep + rep:compacting + 
rep:variety"; anything to do with random terms in lme seems to go off 
about grouping factors, which just isn't intuitive for me.

The grouping factor is rep because the random effects are associated 
with the levels of rep.

I don't always understand the SAS notation so you may need to help me 
out here.  Do you expect to get a single variance component estimate 
for Rep*Compacting and a single variance component for Rep*Variety?  
If so, you would specify the model in lmer by first creating factors 
for the interaction of Rep and Compacting and the interaction of Rep 
and Variety.

dat$RepC <- with(dat, Rep:Compacting)[drop=TRUE]
dat$RepV <- with(dat, Rep:Variety)[drop=TRUE]
fm <- lmer(DryMatter ~ Compacting*Variety+(1|Rep)+(1|RepC)+(1|RepV), dat)

Thanks for the prompt reply.  I tried what you suggested, here's what I 
got:

 > turf.lme=lmer(dry_matter~compacting*variety+(1|rep)+(1|rc)+(1|rv), 

turf.data)
Error in lmer(dry_matter ~ compacting * variety + (1 | rep) + (1 | rc) +  :
    entry 3 in matrix[9,2] has row 3 and column 2

Just to see what the problem was, I deleted the third random term, and 
it didn't complain:

 > turf.lme=lmer(dry_matter~compacting*variety+(1|rep)+(1|rv), turf.data)
 > anova(turf.lme)

Analysis of Variance Table
                   Df Sum Sq Mean Sq  Denom F value    Pr(>F)
compacting          5 10.925   2.185 36.000  18.166  5.68e-09 ***
variety             2  2.518   1.259 36.000  10.468 0.0002610 ***
compacting:variety 10  6.042   0.604 36.000   5.023 0.0001461 ***

Now obviously this isn't a valid result since I need that third term; 
but interestingly, it didn't matter which term I deleted, so long as 
there were only two random terms.  Any ideas as to what the error 
message is referring to?

Thanks for the help,

Jake Michaelson