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" <[EMAIL PROTECTED]> To: "Deepayan Sarkar" <[EMAIL PROTECTED]> 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:[EMAIL PROTECTED] > 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 <[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. Petr Pikal [EMAIL PROTECTED] ______________________________________________ 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.