R help - Apr 2006 - Partially crossed and nested random factors in lme/lmer

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
Universit?t 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

1.  Are you familiar with Pinheiro and Bates (2000) Mixed-Effects 
Models in S and S-Plus (Springer)?  I've learned a lot from this book 
both about mixed models generally and about "lme" in particular -- and
even indirectly about "lmer".  Examples in this book would, I believe,
help you figure out how to get what you want from "lme".  Files 
containing virtually all the R commands in that book can be found in 
"~\library\nlme\scripts" in your R installation directory.  You can
make
a local copy and walk through the code line by line, trying various 
modifications as you go.

	  2.  Are you familiar both with Doug Bates' recent article on mixed 
models in R News and with his "mlmRev" package and
"MlmSoftRev"
vignette?  You can get an R script file of virtually all the R commands 
in the *.PDF file accompanying the vignette, which you can then modify 
as you wish to help you learn from the vignette.  Examples in the 
"vignette" help file tell you how to do this.  [If you use XEmacs, the
"edit(v1)" line there may not work.  Instead, try
"Stangle(v1$file)"
then look for a new *.R file in your working directory -- identified by 
getwd().]

	  If you've spent some time with both of these and still would like 
further help from this group, please submit another post -- after first 
reading the posting guide! "www.R-project.org/posting-guide.html", 
especially the bit about providing a self-contained example.  Many 
different things might contribute to the problem you describe that "the 
program terminates" with the second lmer example.  I tried copying your 
script into R and got, 'object "duration.root.transf" not
found' from
both "lmer" and "lme".  If your example had been
self-contained -- and
the simpler the better -- I might have been able to help more.

	  hope this helps,
	  spencer graves

Corsin M?ller, Zoologisches Inst. wrote:
> 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
> Universit?t 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
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
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> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html