[R] augPred plot in nlme library
afshart at exchange.sba.miami.edu
Sat Sep 9 17:13:28 CEST 2006
Thanks for your email. I assume you mean age^2 instead of age.2 for
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?
ps - sorry for not making the data available; if anyone is interested
let me know and I'll send it directly.
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
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.
fm1 <- lme(distance ~ age, data = Orthodont)
# All linear
fm2a <- lme(distance ~ age + age.2, data = Orthodont)
# Still linear
fm2b <- lme(distance ~ age + I(age^2), data = Orthodont)
I hope that this helps you resolve the problem.
On Fri, Sep 08, 2006 at 05:18:13PM -0400, Afshartous, David wrote:
> 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
> 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
> Possibly augPred behaves differently in R than in S, but reading the R
> help and trying various other approaches has not solved this.
> -----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 &
> > 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.
> R-help at stat.math.ethz.ch mailing list
> PLEASE do read the posting guide
> and provide commented, minimal, self-contained, reproducible code.
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