Dear Ben, Maybe the model converges more slowy than other models. Running more iterations might solve the problem. Have a look at ?lme and ?lmeControl.
Best regards, Thierry PS R-sig-mixedmodels is a better list for questions on lme(). ---------------------------------------------------------------------------- ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek team Biometrie & Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium Research Institute for Nature and Forest team Biometrics & Quality Assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey > -----Oorspronkelijk bericht----- > Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > Namens Ben Grannan > Verzonden: maandag 25 juli 2011 23:00 > Aan: r-help@r-project.org > Onderwerp: [R] lme convergence error > > Hello, I am working from a linux 64 machine on a server with R-2.12 (I can't > update to 2.13). I am iterating through many linear mixed models for > longitudinal data and I occasionally receive the following convergence > error: > > > BI.lme <- lme(cd4 ~ time + genBI + genBI:time + C1 + C2 + C11 + C12, > random =~ 1 + time | IID, data = d) > > Error in lme.formula(cd4 ~ time + genBI + genBI:time + PC1 + : > nlminb problem, convergence error code = 1 > message = false convergence (8) > > >From iteration to iteration, genBI is the only variable which changes > >and it > is a numerical variable equal to 1, 2, or 3 for a given IID. When I remove > the > interaction term genBI:cd4years there is no problem with convergence. > Also, I have played around with scaling time (days to years, eg) which can > solve > the problem but then leads to convergence issues in other iterations. > When I shift the time (say in units of years by +2) the model also converges. > So > it seems like the genBI:time is the issue. Do you have any suggestions for > exploring why I get these convergence errors only on certain iterations? I > really > appreciate any suggestions! > > Ben > > Here is a summary of the included variables just in case it is helpful: > > IID (808 groups) cd4 time ( in years) > C1 > ACTG_617 : 26 Min. : 0.0 Min. :0.0000 Min. :-0.032700 > ACTG_1055: 25 1st Qu.: 288.0 1st Qu.:0.4603 1st Qu.: 0.001600 > ACTG_1590: 25 Median : 434.0 Median :1.1534 Median : 0.004300 > ACTG_200 : 23 Mean : 461.3 Mean :1.2107 Mean : 0.002139 > ACTG_420 : 23 3rd Qu.: 599.0 3rd Qu.:1.8630 3rd Qu.: 0.006100 > ACTG_454 : 23 Max. :2022.0 Max. :2.7808 Max. : 0.011300 > (Other) :11992 > > C2 C11 C12 > Sex > Min. :-0.105800 Min. :0.000 Min. :0.0000 Min. :1.000 > 1st Qu.: 0.002100 1st Qu.:0.000 1st Qu.:0.0000 1st Qu.:1.000 > Median : 0.007900 Median :0.000 Median :0.0000 Median :1.000 > Mean : 0.001803 Mean :0.367 Mean :0.3020 Mean :1.095 > 3rd Qu.: 0.011700 3rd Qu.:1.000 3rd Qu.:1.0000 3rd Qu.:1.000 > Max. : 0.030800 Max. :1.000 Max. :1.0000 Max. :2.000 > > genBI > Min. :1.000 > 1st Qu.:1.000 > Median :1.000 > Mean :1.369 > 3rd Qu.:2.000 > Max. :3.000 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org 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. ______________________________________________ R-help@r-project.org 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.
