lme convergence error

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.Onkelinx at 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-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
Namens Ben Grannan
Verzonden: maandag 25 juli 2011 23:00
Aan: r-help at 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

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