Re: [R] Partially crossed and nested random factors in lme/lmer
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] __ R-help@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 __ R-help@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
Re: [R] Partially crossed and nested random factors in lme/lmer
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] __ R-help@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 [EMAIL PROTECTED]
[R] 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 peoples 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] __ R-help@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
