## ----echo=FALSE,eval=FALSE----------------------------------------------------
# options(width=80)

## ----results='hide',eval=FALSE------------------------------------------------
# library(catdata)
# data(knee)

## ----eval=FALSE---------------------------------------------------------------
# knee <- reshape(knee, direction="long", varying=list(5:8), v.names="R",timevar="Time")
# 
# knee$RD <- rep(0, length(knee$R))
# knee$RD[knee$R>2] <- 1

## ----eval=FALSE---------------------------------------------------------------
# knee$Age <- knee$Age - 30
# knee$Age2 <- knee$Age^2

## ----eval=FALSE---------------------------------------------------------------
# knee <- knee[knee$Time!=1,]

## ----eval=FALSE---------------------------------------------------------------
# library(glmmML)

## ----eval=FALSE---------------------------------------------------------------
# kneeGHQ <- glmmML(RD ~ as.factor(Th) + as.factor(Sex) + Age + Age2, data=knee,
# family=binomial(), method="ghq", n.points=20, cluster=id)
# summary(kneeGHQ)

## ----eval=FALSE---------------------------------------------------------------
# kneePQL <- glmmPQL(RD ~ as.factor(Th) + as.factor(Sex) + Age + Age2, data=knee,
# random = ~ 1|id, family=binomial())
# summary(kneePQL)

## ----eval=FALSE---------------------------------------------------------------
# library(gee)

## ----eval=FALSE---------------------------------------------------------------
# knee <- knee[order(knee$id),]
# kneeGEE <- gee(RD ~ as.factor(Th) + as.factor(Sex) + Age + Age2, data=knee,
# family=binomial(), id=id, corstr="exchangeable")
# summary(kneeGEE)

## ----echo=FALSE,eval=FALSE----------------------------------------------------
# detach(package:gee)