library(reshape)

ffm <- melt(french_fries, id.var=1:4)

ffrep <- cast (ffm, time+treatment+subject+variable ~ rep)

# just for convenience:
names(ffrep)[c(5,6)] <- c("X1","X2")

qplot(X1,X2, data=ffrep)
qplot(X1,X2, data=ffrep, facets=.~variable)

# reps by week
qplot(X1,X2, data=ffrep, facets=time~variable)

qplot(X1,X2, data=ffrep, facets=time~variable, geom=c("point","abline"))

qplot(X1,X2, data=ffrep, facets=time~variable, geom=c("point","abline", "smooth"), method=lm)

#############
# reps by subject
qplot(X1,X2, data=ffrep, facets=subject~variable, colour=as.numeric(time))

##########################
# separate subjects

pers <- cast(ffm, time+treatment+rep ~variable|subject)
summary(pers)
p1 <- pers[[1]]
qplot(X1,X2, data=pers[[2]], facets=.~variable, colour=as.numeric(time))

# tweak french_fries

french_fries$rep <- factor(french_fries$rep)
ffm <- melt(french_fries, id.var=1:4)
pers <- cast(ffm, time+treatment+rep ~variable|subject)
lapply(pers, rescaler)

# remove subject effects:
all <- melt(lapply(pers, rescaler))
all <- rename(all, c(L1="subject"))

all$subject <- factor(all$subject)
# treatment effect over time?
qplot(time, value, data=all, facets=variable~treatment, geom="line", group=treatment:subject:rep, colour=treatment)