[R] augPred plot in nlme library
afshart at exchange.sba.miami.edu
Sat Sep 9 19:39:04 CEST 2006
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,
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)
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?
> 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.
> 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)
> # Quadratic!
> I hope that this helps you resolve the problem.
> 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 |
> > 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 &
> > >
> > > 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
More information about the R-help