nlme package

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nlme package

Vallejo, Roger
In using the NLME package (R 2.6.1 for Windows), I am having a problem in running an R script that used to run with no problems using a Linux OS in 2004. So I am wondering if during these last ~3 yrs we had major changes in the syntax of the NLME package that I am not aware.
 
This is the R script:
 
library(nlme)
 
treat=as.factor(c(1,2,1,2,1,2,1,2))
mouse=as.factor(c(1,1,2,2,3,3,4,4))
time=as.factor(c(1,1,1,1,2,2,2,2))

mouse.anova=function(vec){lme(vec~treat+time+treat*time,random=~1|mouse/time)}
 
lme.out=apply(exprmat,1,mouse.anova)
 
This is the ERROR message:
 
Error in lme.formula(vec ~ treat + time + treat * time, random = ~1 |  :
  nlminb problem, convergence error code = 1
  message = singular convergence (7)
 
I will appreciate your help in pointing mistakes in this R script.
Thank you very much.
Roger

Roger L. Vallejo, Ph.D.
Computational Biologist & Geneticist
U.S. Department of Agriculture, ARS
National Center for Cool & Cold Water Aquaculture
11861 Leetown Road
Kearneysville, WV 25430
Voice:  (304) 724-8340 Ext. 2141
Email:  [hidden email]
http://www.ars.usda.gov/pandp/people/people.htm?personid=37662


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Re: nlme package

Uwe Ligges

AGAIN, please do not crosspost!


Vallejo, Roger wrote:
> In using the NLME package (R 2.6.1 for Windows),

Which version of nlme? nlme is a contributed package that can be updated
independently of R releases.


> I am having a problem in running an R script that used to run with no problems using a Linux OS in 2004. So I am wondering if during these last ~3 yrs we had major changes in the syntax of the NLME package that I am not aware.

For sure you are not aware. And which version of nlme have you used in 2004?


> This is the R script:
>  
> library(nlme)
>  
> treat=as.factor(c(1,2,1,2,1,2,1,2))
> mouse=as.factor(c(1,1,2,2,3,3,4,4))
> time=as.factor(c(1,1,1,1,2,2,2,2))
>
> mouse.anova=function(vec){lme(vec~treat+time+treat*time,random=~1|mouse/time)}
>  
> lme.out=apply(exprmat,1,mouse.anova)


Well, out error message is:

Error in apply(exprmat, 1, mouse.anova) : object "exprmat" not found


Guess why ... and re-read the posting guide, please.


Uwe Ligges



> This is the ERROR message:
>  
> Error in lme.formula(vec ~ treat + time + treat * time, random = ~1 |  :
>   nlminb problem, convergence error code = 1
>   message = singular convergence (7)
>  
> I will appreciate your help in pointing mistakes in this R script.
> Thank you very much.
> Roger
>
> Roger L. Vallejo, Ph.D.
> Computational Biologist & Geneticist
> U.S. Department of Agriculture, ARS
> National Center for Cool & Cold Water Aquaculture
> 11861 Leetown Road
> Kearneysville, WV 25430
> Voice:  (304) 724-8340 Ext. 2141
> Email:  [hidden email]
> http://www.ars.usda.gov/pandp/people/people.htm?personid=37662
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] 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.

______________________________________________
[hidden email] 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.