[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.
Cheers,
Corsin
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,
>>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
>>
>> ______________________________________________
>> R-help at 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
________________________________________
Corsin Müller
Universität Zürich
Zoologisches Institut
Winterthurerstr. 190
8057 Zürich
Switzerland
Tel +41-(0)44-63 55277
Fax +41-(0)44-63 55490
Email corsin at zool.unizh.ch
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