[R] augPred plot in nlme library
Petr Pikal
petr.pikal at precheza.cz
Mon Sep 11 08:51:31 CEST 2006
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 at exchange.sba.miami.edu>
To: "Deepayan Sarkar" <deepayan.sarkar at gmail.com>
Copies to: r-help at 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 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
>
> ______________________________________________
> 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
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