On Thu, 9 Feb 2006, Paul Cossens wrote: > 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.
That is an R/S difference (documented in the FAQ). In R day^2 is the same as day in a formula. The book is about S, not R (as its title tells you). > 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. You cannot deduce `always' from one example. It depends if (in your case) the Wafers are numbered uniquely or the same in each Lot. This comes up frequently with muiti-stratum aov and lme. Notice that Dr Bates carefully said `It happens in this case', so he did not generalize from a single example. [...] -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
