On 9/9/06, Afshartous, David <[EMAIL PROTECTED]> 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:[EMAIL PROTECTED] > 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:[EMAIL PROTECTED] > > 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 <[EMAIL PROTECTED]> 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.