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 [EMAIL PROTECTED] 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
sex1 4427 7.93 0.0049
sample.sex 1 442765.71 .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 [EMAIL PROTECTED]
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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 [EMAIL PROTECTED