I have an ANOVA model with 2 factors "Environment" and "Site", "Diameter" is the response variable. Site should be nested within Environment. Site is also a random factor while Environment is fixed. I can do this analysis using the "aov" function by using these commands: >model<-aov(Diam~Env+Error(Env%in%Site),data=environ) >summary(model) >summary(aov(Diam~Env/Site,data=environ)) But the model is unbalanced and I want to calculate estimates of the variance components. In this case the REML approach should give more reliable estimates than the method I have used. But I am unable to work out how to specify a nested factor using the "lme" function. I have tried: >firstgo<-lme(Diam~Env+Env:Site,data=environ) >secondgo<-lme(Diam~Env+Env%in%Site,data=environ) >thirdgo<-lme(Diam~Env+Env/Site,data=environ) But I keep getting this error: Error in getGroups.data.frame(dataMix, groups) : Invalid formula for groups If anyone could help me with code for specifying a random nested factor using lme that would be great. Thanks, David Semmens.
nested ANOVA using lme
2 messages · David Semmens, Dimitris Rizopoulos
in lme() you need to specify the random-effects with a formula passed to the 'random' argument, e.g., something like fit <- lme(Diam ~ Env + Site, random = ~ 1 | Env / Site, data = environ) summary(fit) I hope it helps. Best, Dimitris ---- Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm ----- Original Message ----- From: "David Semmens" <d.semmens at pgrad.unimelb.edu.au> To: <r-help at stat.math.ethz.ch> Sent: Wednesday, August 09, 2006 11:03 AM Subject: [R] nested ANOVA using lme
I have an ANOVA model with 2 factors "Environment" and "Site", "Diameter" is the response variable. Site should be nested within Environment. Site is also a random factor while Environment is fixed. I can do this analysis using the "aov" function by using these commands:
model<-aov(Diam~Env+Error(Env%in%Site),data=environ) summary(model) summary(aov(Diam~Env/Site,data=environ))
But the model is unbalanced and I want to calculate estimates of the variance components. In this case the REML approach should give more reliable estimates than the method I have used. But I am unable to work out how to specify a nested factor using the "lme" function. I have tried:
firstgo<-lme(Diam~Env+Env:Site,data=environ) secondgo<-lme(Diam~Env+Env%in%Site,data=environ) thirdgo<-lme(Diam~Env+Env/Site,data=environ)
But I keep getting this error: Error in getGroups.data.frame(dataMix, groups) : Invalid formula for groups If anyone could help me with code for specifying a random nested factor using lme that would be great. Thanks, David Semmens.
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