[R] lme convergence error

[ONKELINX, Thierry]

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