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 >> 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 [EMAIL PROTECTED] >> >> ______________________________________________ >> [email protected] 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 [EMAIL PROTECTED] ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
