[R] lme syntax for P&B examples

From: Paul Cossens <paul.cossens_at_thewarehouse.co.nz>
Date: Wed 08 Feb 2006 - 16:08:21 EST


Hi helpeRs,  

I've been working through some examples in Pinhiero & Bates( 2000) trying to understand how to translate to the new Lme4 syntax but without much luck.
Below is what I think I should do, but either the answers don't come out the same or I get errors.
In the Oxide problems I'm particularly interested in obtaining the levels coeficients but this options no longer seems to be available in lme4. How can levels infor be obtained in lme4?  

If someone can recreate the examples below in lme4 syntax so I can follow what is happening in the text I'd be grateful.  

Cheers  

Paul Cossens    

#Pixel
# P&B(2000) p40-45  

Pixel<-read.csv("Pixel.csv",header=TRUE); Pixel$Side<-as.factor(Pixel$Side)
Pixel$Dog<-as.factor(Pixel$Dog)  

(fm1Pixel <- lmer(pixel ~ day + I(day^2) +(day|Dog)+(1|Side), data =
Pixel))
(fm2Pixel <- lmer(pixel ~ day + I(day^2) +(day|Dog), data = Pixel))
(fm3Pixel <- lmer(pixel ~ day + I(day^2) +(1|Dog:Side), data = Pixel))
or should I do it this way?
Pixel$DS<-with(Pixel,Dog:Side)[drop=TRUE]
(fm3Pixel <- lmer(pixel ~ day + I(day^2) +(1|DS), data = Pixel))
 

(fm4Pixel <- lmer(pixel ~ day + I(day^2) +Side , data = Pixel))
 

#Oxide
# P&B(2000) p167-170  

Oxide<-read.csv("Oxide.csv",header=TRUE);

Oxide$Source<-as.factor(Oxide$Source)
Oxide$Lot<-as.factor(Oxide$Lot)
Oxide$Wafer<-as.factor(Oxide$Wafer)
Oxide$Site<-as.factor(Oxide$Site)

fm1Oxide<-lmer(Thickness~ (1|Lot)+(1|Lot:Wafer),data=Oxide) )
(fm2Oxide<-lmer(Thickness~ (1|Lot),data=Oxide) )
coef(fm1Oxide)

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