[R] my error with augPred

[Petr Pikal]

Hallo

thank you for your response. I am not sure but maybe fixed effects 
cannot be set to be influenced by a factor to be able to use augPred.

lob<-Loblolly[Loblolly$Seed!=321,]
set.seed(1)
lob<-data.frame(lob, x1=sample(letters[1:3], replace=T)) # add a 
#factor
lob<-groupedData(height~age|Seed, data=lob)
fm1 <- nlme(height ~ SSasymp(age, Asym, R0, lrc),
            data = lob,
            fixed = Asym + R0 + lrc ~ 1,
            random = Asym ~ 1,
            start = c(Asym = 103, R0 = -8.5, lrc = -3.3))

fm2<-update(fm1, fixed=list(Asym~x1, R0+lrc~1), start=c(103,0,-8.5,-
3))
                                             ^^^^^^^
and

plot(augPred(fm2))

Throws an error.
So it is not possible to use augPred with such constructions.

Best regards.
Petr Pikal

On 2 Sep 2006 at 17:58, Spencer Graves wrote:

Date sent:      	Sat, 02 Sep 2006 17:58:05 -0700
From:           	Spencer Graves <spencer.graves at pdf.com>
To:             	Petr Pikal <petr.pikal at precheza.cz>
Copies to:      	r-help at stat.math.ethz.ch
Subject:        	Re: [R] my error with augPred

> <comments in line> 
> 
> Petr Pikal wrote:
> > Dear all
> >
> > I try to refine my nlme models and with partial success. The model
> > is refined and fitted (using Pinheiro/Bates book as a tutorial) but
> > when I try to plot
> >
> > plot(augPred(fit4))
> >
> > I obtain
> > Error in predict.nlme(object, value[1:(nrow(value)/nL), , drop =
> > FALSE],  : 
> >         Levels (0,3.5],(3.5,5],(5,7],(7,Inf] not allowed for 
> > vykon.fac
> >   
> >
> > Is it due to the fact that I have unbalanced design with not all
> > levels of vykon.fac present in all levels of other explanatory
> > factor variable?
> >   
> I don't know, but I'm skeptical. 
> > I try to repeat 8.19 fig which is OK until I try:
> >
> > fit4 <- update(fit2, fixed = list(A+B~1,xmid~vykon.fac, scal~1), 
> > start = c(57, 100, 700, rep(0,3), 13))
> >
> > I know I should provide an example but maybe somebody will be clever
> > enough to point me to an explanation without it.
> >   
> I'm not. 
> 
> To answer these questions without an example from you, I'd have to
> make up my own example and try to see if I could replicate the error
> messages you report, and I'm not sufficiently concerned about this
> right now to do that. 
> 
> Have you tried taking an example from the book and deleting certain
> rows from the data to see if you can force it to reproduce your error?
> 
> 
> Alternatively, have you tried using 'debug' to trace through the code
> line by line until you learn enough of what it's doing to answer your
> question? 
> 
> Spencer Graves
> > nlme version 3.1-75
> > SSfpl model
> > R 2.4.0dev (but is the same in 2.3.1), W2000.
> >
> > Thank you
> > Best regards.
> >
> > Petr PikalPetr Pikal
> > petr.pikal at precheza.cz
> >
> > ______________________________________________
> > R-help at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html and provide commented,
> > minimal, self-contained, reproducible code.
> >
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html and provide commented,
> minimal, self-contained, reproducible code.

Petr Pikal
petr.pikal at precheza.cz