[R] Partially crossed and nested random factors in lme/lmer

Corsin Müller , Zoologisches Inst. corsin.mueller at zool.unizh.ch
Wed Apr 26 13:32:52 CEST 2006

I do have Pinheiro and Bates 2000 and went through it several times – 
unfortunately without success for my particular issue. I was not aware of 
the article in R news or the mlmRev package you referred to, though. I will 
try with that.

The example I gave was not self-contained. Sorry, my fault.


On Wed, 26 Apr 2006 03:11:52 -0700
  Spencer Graves <spencer.graves at pdf.com> wrote:
> 	  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 Müller, 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, 
>> 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, 
>> should be nested within acceptor.grp. When trying the to me intuitively 
>> sensible
>>>lmer.inspection <- lmer(duration.root.transf~ … + (1|acceptor.grp/id) + 
>> 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
>> ______________________________________________
>> R-help at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide! 


Corsin Müller
Universität Zürich
Zoologisches Institut
Winterthurerstr. 190
8057 Zürich

Tel +41-(0)44-63 55277
Fax +41-(0)44-63 55490
Email corsin at zool.unizh.ch

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