From: Ilona Leyer <ileyer_at_yahoo.de>

Date: Fri, 14 Dec 2007 11:40:55 +0100 (CET)

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 Fri 14 Dec 2007 - 10:51:45 GMT

Date: Fri, 14 Dec 2007 11:40:55 +0100 (CET)

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

Here the commands:

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

[1] "week" "rep" "treat" "heightfra"
"leaffra" "leafvim"

*> 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
| rep) :

*>
*

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

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

Error in lme.formula(leaffra ~ treat, random = ~week |
rep) :

*>
*

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

Data: NULL

AIC BIC logLik

129.6743 139.4999 -58.83717

(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:

> 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
**>
*

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