From: Douglas Bates <bates_at_stat.wisc.edu>

Date: Tue 26 Apr 2005 - 09:40:21 EST

*>
*

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

*> got:
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*>
*

*> > 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)
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*> > anova(turf.lme)
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*> Analysis of Variance Table
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*> Df Sum Sq Mean Sq Denom F value Pr(>F)
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*> 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 ***
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*>
*

*> 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
*

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Tue Apr 26 09:44:01 2005

Date: Tue 26 Apr 2005 - 09:40:21 EST

Jacob Michaelson wrote:

*>
*

> 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

Unfortunately, yes I do know what the error message is referring to - a condition that should not happen. This is what Bill Venables would call an "infelicity" in the code and others with less tact than Bill might call a bug.

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Tue Apr 26 09:44:01 2005

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