From: Mark Difford <mark_difford_at_yahoo.co.uk>

Date: Fri, 14 Dec 2007 19:26:21 -0800 (PST)

*> "leaffra" "leafvim"
*

> test<-groupedData(heightfra~week|rep,outer=~treat,test)

> Error in lme.formula(heightfra ~ treat, random = ~week

*> | rep) :
*

*> nlminb problem, convergence error code = 1;
*

*> message = iteration limit reached without convergence
*

*> (9)
*

*>
*

> test<-groupedData(leaffra~week|rep,outer=~treat,test)

> Error in lme.formula(leaffra ~ treat, random = ~week |

*> rep) :
*

*> nlminb problem, convergence error code = 1;
*

*> message = iteration limit reached without convergence
*

*> (9)
*

*>
*

> test<-groupedData(leafvim~week|rep,outer=~treat,test)

> Error in summary(model) : object "model" not found

> Linear mixed-effects model fit by REML

*> Data: NULL
*

*> AIC BIC logLik
*

*> 129.6743 139.4999 -58.83717
*

*>
*

*> Random effects:
*

*> Formula: ~week | rep
*

*> Structure: General positive-definite, Log-Cholesky
*

*> parametrization
*

*> StdDev Corr
*

*> (Intercept) 4.4110478 (Intr)
*

*> week 0.7057311 -0.999
*

*> Residual 0.5976143
*

*>
*

*> Fixed effects: leafvim ~ treat
*

*> Value Std.Error DF t-value p-value
*

*> (Intercept) 5.924659 0.1653596 30 35.82893 0.0000
*

*> treatpHs 0.063704 0.2338538 8 0.27241 0.7922
*

*> Correlation:
*

*> (Intr)
*

*> treatpHs -0.707
*

*>
*

*> Standardized Within-Group Residuals:
*

*> Min Q1 Med Q3
*

*> Max
*

*> -1.34714254 -0.53042878 -0.01769195 0.40644540
*

*> 2.29301560
*

*>
*

*> Number of Observations: 40
*

*> Number of Groups: 10
*

*>
*

*> Is there a solution for this problem?
*

*>
*

*> Thanks!!!
*

*>
*

*> Ilona
*

*>
*

*> --- Douglas Bates <bates_at_stat.wisc.edu> schrieb:
*

*>
*

*>
*

> ______________________________________________

*> R-help_at_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.
*

*>
*

*>
*

Date: Fri, 14 Dec 2007 19:26:21 -0800 (PST)

Hi Ilona,

>> Is there a solution for this problem?

Mixed-Effects Models in S and S-PLUS, by: Pinheiro, José, Bates, Douglas http://www.springer.com/west/home/statistics/computational?SGWID=4-10130-22-2102822-0

Hope this speeds you on your way...

Regards, Mark.

Ilona Leyer wrote:

*>
**>
*

> Here an simple example:

*>
**> rep treat heightfra leaffra leafvim week
**> ID1 pHf 1.54 4 4 4
**> ID2 pHf 1.49 4 4 4
**> ID3 pHf 1.57 4 5 4
**> ID4 pHf 1.48 4 4 4
**> ID5 pHf 1.57 4 4 4
**> ID6 pHs 1.29 4 5 4
**> ID7 pHs 0.97 4 5 4
**> ID8 pHs 2.06 4 4 4
**> ID9 pHs 0.88 4 4 4
**> ID10 pHs 1.47 4 4 4
**> ID1 pHf 3.53 5 6 6
**> ID2 pHf 4.08 6 6 6
**> ID3 pHf 3.89 6 6 6
**> ID4 pHf 3.78 5 6 6
**> ID5 pHf 3.92 6 6 6
**> ID6 pHs 2.76 5 5 6
**> ID7 pHs 3.31 6 7 6
**> ID8 pHs 4.46 6 7 6
**> ID9 pHs 2.19 5 5 6
**> ID10 pHs 3.83 5 5 6
**> ID1 pHf 5.07 7 7 9
**> ID2 pHf 6.42 7 8 9
**> ID3 pHf 5.43 6 8 9
**> ID4 pHf 6.83 6 8 9
**> ID5 pHf 6.26 6 8 9
**> ID6 pHs 4.57 6 9 9
**> ID7 pHs 5.05 6 7 9
**> ID8 pHs 6.27 6 8 9
**> ID9 pHs 3.37 5 7 9
**> ID10 pHs 5.38 6 8 9
**> ID1 pHf 5.58 7 9 12
**> ID2 pHf 7.43 8 9 12
**> ID3 pHf 6.18 8 10 12
**> ID4 pHf 6.91 7 10 12
**> ID5 pHf 6.78 7 10 12
**> ID6 pHs 4.99 6 13 12
**> ID7 pHs 5.50 7 8 12
**> ID8 pHs 6.56 7 10 12
**> ID9 pHs 3.72 6 10 12
**> ID10 pHs 5.94 6 10 12
**>
**>
**> I used the procedure described in Crawley´s new R
**> Book.
**> For two of the tree response variables
**> (heightfra,leaffra) it doesn´t work, while it worked
**> with leafvim (but in another R session, yesterday,
**> leaffra worked as well...).
**>
**> Here the commands:
**>
*

>> attach(test) >> names(test)

> [1] "week" "rep" "treat" "heightfra"

>> library(nlme) >>

> test<-groupedData(heightfra~week|rep,outer=~treat,test)

>> model1<-lme(heightfra~treat,random=~week|rep)

> Error in lme.formula(heightfra ~ treat, random = ~week

>>

> test<-groupedData(leaffra~week|rep,outer=~treat,test)

>> model2<-lme(leaffra~treat,random=~week|rep)

> Error in lme.formula(leaffra ~ treat, random = ~week |

>>

> test<-groupedData(leafvim~week|rep,outer=~treat,test)

>> model3<-lme(leafvim~treat,random=~week|rep) >> summary(model)

> Error in summary(model) : object "model" not found

>> summary(model3)

> Linear mixed-effects model fit by REML

>> On Dec 13, 2007 4:15 PM, Ilona Leyer >> <ileyer_at_yahoo.de> wrote: >> > Dear All, >> > I want to analyse treatment effects with time >> series >> > data: I measured e.g. leaf number (five replicate >> > plants) in relation to two soil pH - after 2,4,6,8 >> > weeks. I used mixed effects models, but some >> analyses >> > didn´t work. It seems for me as if this is a >> randomly >> > occurring problem since sometimes the same model >> works >> > sometimes not. >> > >> > An example: >> > > names(test) >> > [1] "rep" "treat" "leaf" "week" >> > > library (lattice) >> > > library (nlme) >> > > >> test<-groupedData(leaf~week|rep,outer=~treat,test) >> > > model<-lme(leaf~treat,random=~leaf|rep) >> > Error in lme.formula(leaf~ treat, random = >> ~week|rep) >> >> Really!? You gave lme a model with random = ~ leaf | >> rep (and no data >> specification) and it tried to fit a model with >> random = ~ week | rep? >> Are you sure that is an exact transcript? >> >> > : >> > nlminb problem, convergence error code = >> 1; >> > message = iteration limit reached without >> convergence >> > (9) >> >> > Has anybody an idea to solve this problem? >> >> Oh, I have lots of ideas but without a reproducible >> example I can't >> hope to decide what might be the problem. >> >> It appears that the model may be over-parameterized. >> Assuming that >> there are 4 different values of week then ~ week | >> rep requires >> fitting 10 variance-covariance parameters. That's a >> lot. >> The error code indicates that the optimizer is >> taking >>

> ______________________________________________

-- View this message in context: http://www.nabble.com/convergence-error-code-in-mixed-effects-models-tp14325990p14340592.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help_at_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.Received on Sat 15 Dec 2007 - 03:29:57 GMT

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