[R] augPred plot in nlme library

[Afshartous, David]

Hi Andrew,

Thanks for your email.  I assume you mean age^2 instead of age.2 for
fm2a,
and for fm2b, I get the following error:

> fm2b <- lme(distance ~ age + I(age^2), data = Orthodont)
Error in lme.formula(distance ~ age + I(age^2), data = Orthodont) : 
        iteration limit reached without convergence (9)

do you get his error as well?  

Finally, the Pixel example on p.42 of Pinheiro & Bates gets the 
quadratic plot w/o using I() as you do below; is this due to 
a difference between S and R?

thanks!
dave

ps - sorry for not making the data available; if anyone is interested
please
let me know and I'll send it directly.  




-----Original Message-----
From: Andrew Robinson [mailto:A.Robinson at ms.unimelb.edu.au] 
Sent: Friday, September 08, 2006 5:46 PM
To: Afshartous, David
Cc: Deepayan Sarkar; r-help at stat.math.ethz.ch
Subject: Re: [R] augPred plot in nlme library

Hi David,

this is the sort of thing that Deepayan meant.  Make a dataset available
to us, or use one that will be installed by default on R.

eg

require(nlme)
fm1 <- lme(distance ~ age, data = Orthodont)
plot(augPred(fm1))

#  All linear

fm2a <- lme(distance ~ age + age.2, data = Orthodont)
plot(augPred(fm2a))

# Still linear

fm2b <- lme(distance ~ age + I(age^2), data = Orthodont)
plot(augPred(fm2b))

# Quadratic!

I hope that this helps you resolve the problem.

Andrew



On Fri, Sep 08, 2006 at 05:18:13PM -0400, Afshartous, David wrote:
>  
> Deepayan,
> 
> Thanks for your suggestion.  Here are more details:
> 
> I have a grouped data object for repeated measures data just like the 
> Pixel grouped data object on p.42 of Pinheiro and Bates (2000).
> 
> comp.adj.UKV.3 <- groupedData(adj.UKV ~ Time | Patient_no/Lisinopril, 
> 	data = comp.adj.UKV.frm, order.groups = F
> 	#labels = list(x = "Hour", y = "adj.UKV")
> )
> 
> i.e., the response is continuous, Time is not treated as a factor, and

> there exists two factors, one nested within the other (Lisinopril 
> nested
> 
> witin patient, similar to Side within Dog on p.42).
> 
> I also fit a model very similar to their model:
> 
> fm1comp = lme(adj.UKV ~ Time + Time.sq, data = comp.adj.UKV.3, random 
> = list(Patient_no = ~ 1 , Lisinopril = ~ 1) )
> 
> 
> However, the command below does not produce the fitted curves from 
> this model, but rather it seems to be the fitted curves from a linear 
> model.
> 
> plot(augPred(fm3comp))
> 
> Possibly augPred behaves differently in R than in S, but reading the R

> help and trying various other approaches has not solved this.
> 
> Thanks!
> Dave
> 
> 
> 
> 
> -----Original Message-----
> From: Deepayan Sarkar [mailto:deepayan.sarkar at gmail.com]
> Sent: Friday, September 08, 2006 4:37 PM
> To: Afshartous, David
> Cc: r-help at stat.math.ethz.ch
> Subject: Re: [R] augPred plot in nlme library
> 
> On 9/8/06, Afshartous, David <afshart at exchange.sba.miami.edu> wrote:
> > All,
> >
> > I've solved part of the problem below by making sure that the 
> > formula in the grouped data object is the same as the formula 
> > specified within
> 
> > lme (this isn't the case in the cited example from Pinheiro &
Bates).
> >
> > However, augPred seems to plot only a linear model instead of the 
> > polynomial model.  Does anyone know how to make sure that augPred 
> > plots the same model as that specified in the model (as below)?
> 
> You are unlikely to get any helpful answers unless you give us more 
> information, as every r-help message asks you to do:
> 
> > 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.
> 
> -Deepayan
> 
> ______________________________________________
> 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.

--
Andrew Robinson  
Department of Mathematics and Statistics            Tel: +61-3-8344-9763
University of Melbourne, VIC 3010 Australia         Fax: +61-3-8344-4599
Email: a.robinson at ms.unimelb.edu.au         http://www.ms.unimelb.edu.au