[R] augPred plot in nlme library

[Afshartous, David]

Thanks Deepayan and Andrew.

msMaxIter solved the convergence problem and plot(augPred) works 
with my data when I employ I() in the function call.

One other strange thing I noticed is that when I take logs of
dependent variable in the function call, the plot of augPred 
doesn't graph any prediction line at all.  

contr=nlmeControl(msMaxIter = 500)
fm2c <- lme(log(distance) ~ age + I(age^2), data = Orthodont,
control=contr)
plot(augPred(fm2c)) 

However, this is fixed by hard coding the dependent variable:

log.dist = log(distance)
fm2c <- lme(log.dist ~ age + I(age^2), data = Orthodont, control=contr)
plot(augPred(fm2c))



-----Original Message-----
From: Deepayan Sarkar [mailto:deepayan.sarkar at gmail.com] 
Sent: Saturday, September 09, 2006 11:46 AM
To: Afshartous, David
Cc: Andrew Robinson; r-help at stat.math.ethz.ch
Subject: Re: [R] augPred plot in nlme library

On 9/9/06, Afshartous, David <afshart at exchange.sba.miami.edu> wrote:
> 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?

For me, adding 'control = list(msMaxIter = 500)' worked. I'm writing
from memory, so the name may not be exactly right, see ?nlmeControl.

> 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?

Yes.

>
> 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