[R] Partially crossed and nested random factors in lme/lmer
Corsin Müller , Zoologisches Inst.
corsin.mueller at zool.unizh.ch
Sat Apr 22 16:22:48 CEST 2006
Hi all,
I am not a very proficient R-user yet, so I hope I am not wasting people’s
time. I want to run a linear mixed model with 3 random factors (A, B, C)
where A and B are partially crossed and C is nested within B. I understand
that this is not easily possible using lme but it might be using lmer. I
encountered two problems when trying:
Firstly, I can enter two random factors in lmer but I do not get complete
outputs using both anova () and summary (). For instance, I only get df, SS,
and MS using anova(). Even so the model runs without giving an error
message.
> lmer.inspection <- lmer(duration.root.transf~sex*sample.sex+age+sample.age+sample.type+first.bout+location+sample.source + (1|acceptor.grp) + (1|donor.grp))
> anova (lmer.inspection)
Analysis of Variance Table
Df Sum Sq Mean Sq
sex 1 0.06653 0.06653
sample.sex 1 0.60389 0.60389
Running the same model in lme using only one random factor works fine.
> lme.inspection <- lme(duration.root.transf~sex*sample.sex+age+sample.age+sample.type+first.bout+location+sample.source, random=~1|acceptor.grp)
> anova (lme.inspection)
numDF denDF F-value p-value
(Intercept) 1 4427 47690.12 <.0001
sex 1 4427 7.93 0.0049
sample.sex 1 4427 65.71 <.0001
Running the example given in “?lmer” also does not give a complete anova
table. However, the example discussed in the email by Jacob Michaelson on
the 24th of April 2005 “[R] random interactions in lme” gives a complete
output. So I seem to miss out on something.
Secondly, I am at a loss with how I can enter the third random factor, which
should be nested within acceptor.grp. When trying the to me intuitively
sensible
> lmer.inspection <- lmer(duration.root.transf~
+ (1|acceptor.grp/id) + (1|donor.grp))
the program terminates
I am grateful for any suggestions.
Version used: R 2.2.1 for Windows
Thanks,
Corsin Mueller
________________________________________
Corsin Mueller
Universität of Zuerich
Zoological Institute
Winterthurerstr. 190
8057 Zuerich
Switzerland
fon +41-(0)44-63 55277
fax +41-(0)44-63 55490
email corsin at zool.unizh.ch
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