#Repeated measures Example 

library(nlme)

#help(ergoStool)
#Devore (2000) cites data from an article in _Ergometrics_ (1993,
#pp. 519-535) on ``The Effects of a Pneumatic Stool and a
#One-Legged Stool on Lower Limb Joint Load and Muscular Activity.''
#This data frame contains the following columns:
#
#     effort a numeric vector giving the effort (Borg scale) required to
#          arise from a stool.
#
#     Type a factor with levels 'T1',  'T2',  'T3', and  'T4' giving the
#          stool type.
#
#     Subject an ordered factor giving a unique identifier for the
#          subject in the experiment.

ergoStool

pdf("ergoplots.pdf")
par(pty="s")
plot(ergoStool)

#visually compare magnitude of the effects of Type and Subject factors
plot.design(ergoStool)

fm1 <- lme(effort~Type, data=ergoStool, random=~1 | Subject)
anova(fm1)
summary(fm1)

#examine the fit and residuals
intervals(fm1)
plot(fm1)
qqnorm(resid(fm1))

#for residuals vs fitted values by Subject, also see plot.lme
plot(fm1, resid(.)~fitted(.) | Subject, abline=0, lty=2)

#for standardized residuals versus fitted values by Subject
plot(fm1, resid(., type = "p") ~ fitted(.) | Subject, abline = 0)

dev.off()