*10. Multi-level Models, Repeated Measures and Time Series
## 10.1 Multi-Level Models, Including Repeated Measures Models
## 10.1.1 The Kiwifruit Shading Data, Again
library(nlme)
kiwishade$plot<-factor(paste(kiwishade$block, kiwishade$shade, 
  sep="."))
kiwishade.lme<-lme(yield~shade,random=~1|block/plot, data=kiwishade)
summary(kiwishade.lme)
anova(kiwishade.lme)
intervals(kiwishade.lme)
kiwishade.aov<-aov(yield~block+shade+Error(block:shade),data=kiwishade)
summary(kiwishade.aov)

## 10.1.2 The Tinting of Car Windows
itstar.lme<-lme(log(it)~tint*target*agegp*sex,
random=~1|id, data=tinting,method="ML")
it2.lme<-lme(log(it)~(tint+target+agegp+sex)^2,
random=~1|id, data=tinting,method="ML")
it1.lme<-lme(log(it)~(tint+target+agegp+sex),
random=~1|id, data=tinting,method="ML")
anova(itstar.lme,it2.lme,it1.lme)
it2.reml<-update(it2.lme,method="REML")
options(digits=3)
summary(it2.reml)$tTable
## 10.1.3  The Michelson Speed of Light Data 
library(MASS)  # if needed
michelson$Run <- as.numeric(michelson$Run) # Ensure Run is a variable
mich.lme1 <- lme(fixed = Speed ~ Run, data = michelson, 
	  random =  ~ Run| Expt, correlation = corAR1(form =  ~ 1 | Expt), 
    weights = varIdent(form =  ~ 1 | Expt))
summary(mich.lme1)

## 10.2 Time Series Models
## 10.3 Exercises
## 10.4 References