lme syntax for P&B examples

Hi Harold,


Thanks for your reply. I had already looked at all the reading material
you suggested but updated to the latest Matrix
as recommneded then spent all day trying to figure out what is
happening.

I worked through the problems and give my workings below that others may
find useful.
(My notation is to use lme> to show lme commands and lmer> to show lmer
commands.
I worked on two sessions in parallel. My comments are preceded by double
hashes '##' and
questions '##??'. I haven't included the datasets.)

I have a couple of comments and outstanding issues:

1. In the Pixel data set and formulas I think the formulas are printed
incorrectly in the
book as some use 'I(day^2)' while others use just 'day^2'. I have used
'I(day^2)'. I'm not sure why the I() function is used. In the fm4Pixel
example below the answers don't match up exactly but are close.

The lme example is
fm1Pixel<-lme(pixel~day+I(day^2),data=Pixel,random = list(Dog=~day
,Side=~1))
fm5Pixel <- update(fm1Pixel,pixel ~ day + I(day^2) + Side)
which I have converted to lmer:
fm4Pixel <- lmer(pixel ~ day + I(day^2) +Side +(day|Dog), data = Pixel)

The t-values for Side are close (sse below) but different enough to
wonder if I am still doing something wrong?

2. To me the specification description in the R-News article is
confusing as it seems
to suggest that nesting does not need to be completely specified if the
groupings and nestings are clear in data set.

Prof Bates article in R news vol 5/1 P 30  states "It happens in this
case that the grouping factors 'id' and 'sch' are not nested but if they
were nested there would be no change in the model specification"

If the lme formula is
fm1Oxide<-lme(Thickness~1,Oxide)

I have found the formula lmer parlance should be:
'fm1Oxide<-lmer(Thickness~ (1|Lot)+(1|Lot:Wafer),data=Oxide)'
not 'fm1Oxide<-lmer(Thickness~ (1|Lot)+(1|Wafer),data=Oxide)'
as the article reads to me.

In other words you always need to explicitly specify nesting levels.