From: Petr Pikal <petr.pikal_at_precheza.cz>

Date: Mon 11 Sep 2006 - 06:51:31 GMT

R-help@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. Received on Mon Sep 11 17:57:24 2006

Date: Mon 11 Sep 2006 - 06:51:31 GMT

Hi

please try not to hide an information

> plot(augPred(fm2c))

Error in log(distance) : object "distance" not found

Is it what you have got and what you mean by "does not graph any prediction at all"?

If not did you attached Orthodont before?

I suppose plot.augPred probably expects the same name for original and and fitted data. You can go through source code to see what happens by

nlme:::plot.augPred

**HTH
**

Petr

On 9 Sep 2006 at 13:39, Afshartous, David wrote:

Date sent: Sat, 9 Sep 2006 13:39:04 -0400 From: "Afshartous, David" <afshart@exchange.sba.miami.edu> To: "Deepayan Sarkar" <deepayan.sarkar@gmail.com> Copies to: r-help@stat.math.ethz.ch Subject: Re: [R] augPred plot in nlme library

*>
*

> 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@gmail.com]
**> Sent: Saturday, September 09, 2006 11:46 AM
**> To: Afshartous, David
**> Cc: Andrew Robinson; r-help@stat.math.ethz.ch
**> Subject: Re: [R] augPred plot in nlme library
**>
**> On 9/9/06, Afshartous, David <afshart@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@ms.unimelb.edu.au]
**> > Sent: Friday, September 08, 2006 5:46 PM
**> > To: Afshartous, David
**> > Cc: Deepayan Sarkar; r-help@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@gmail.com]
**> > > Sent: Friday, September 08, 2006 4:37 PM
**> > > To: Afshartous, David
**> > > Cc: r-help@stat.math.ethz.ch
**> > > Subject: Re: [R] augPred plot in nlme library
**> > >
**> > > On 9/8/06, Afshartous, David <afshart@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@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@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@precheza.cz

R-help@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. Received on Mon Sep 11 17:57:24 2006

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