lme: random effects of a quadratic term
I tried to replicate in R the example that Pinheiro and Bates present on section 1.5 of their mixed-effects book, the pixel intensity example.
fm1Pixel<-lme(pixel~day+day^2,data=Pixel,random=list(Dog=~day,Side=~1))
When I run it in R the second order term does not appear in the estimated model. But, when I write
fm1Pixel<-lme(pixel~day+I(day^2),data=Pixel,random=list(Dog=~day,Side=~1))
I get the same results as in the Pinheiro and Bates book, and the plot of the augPred values is a quadratic function as in Figure 1.18. The same happens with my data when I use the I(alcadakm^2) . Can it be that S accepts day^2 but R doesn't? Thanks again! Montse On Sat, 26 Mar 2005 17:39:43 +0000 (GMT), Prof Brian Ripley
<ripley at stats.ox.ac.uk> wrote:
On Sat, 26 Mar 2005, Montse Rue wrote:
Thanks! I already tried it, but then I have problems with the augPred values. I get straight lines instead of quadratic lines when plotting the augPred values. What can I do?
WHy are you expecting a non-linear plot from a linear fit?
Montse On Sat, 26 Mar 2005 09:39:07 +0000 (GMT), Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
On Sat, 26 Mar 2005, Montse Rue wrote:
I am estimating the following model: so2.lme<-lme(so2~1+I(alcadakm^2)+dia,data=subjectes2,na.action=na.omit) And when I try to plot the random effects of the quadratic term with respect to a covariate (mam) I get an error:
so2.lmeRE<-ranef(so2.lme,augFrame=T) plot(so2.lmeRE,form=I(alcadakm^2)~mam)
Error in plot.ranef.lme(so2.lmeRE, form = I(alcadakm^2) ~ mam ) :
Only single effects allowed in left side of form.
Any suggestion?
Try renaming the variable, e.g. alcadakm2 = alcadakm^2, and refit. NB: this is not `a quadratic term' but a transformed variable, since you used I(). -- Brian D. Ripley, ripley at stats.ox.ac.uk 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
-- Brian D. Ripley, ripley at stats.ox.ac.uk 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