[R] augPred plot in nlme library

Afshartous, David afshart at exchange.sba.miami.edu
Mon Sep 11 15:09:36 CEST 2006 

Hi Peter,

Thanks for the email.  No, plot(augPred(fm2c)) still
graphs the original points but doesn't graph the 
prediction curve.  However, this is solved by hardcording
the dependent variable as below.  yes, I attached Orthodont.


cheers,
dave


-----Original Message-----
From: Petr Pikal [mailto:petr.pikal at precheza.cz] 
Sent: Monday, September 11, 2006 2:52 AM
To: Afshartous, David; r-help at stat.math.ethz.ch
Subject: Re: [R] augPred plot in nlme library

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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