Re: [R] 'nlme' crashes R (was: Using corStruct in nlme)

From: <grieve_at_u.washington.edu>
Date: Fri 21 Jul 2006 - 04:07:42 EST


Thanks Spencer. Here is my sessionInfo():

Version 2.3.1 (2006-06-01)
i386-pc-mingw32

attached base packages:

[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets" 
[7] "base"     

other attached packages:

    nlme
"3.1-75"

On Thu, 20 Jul 2006, Spencer Graves wrote:

> 	  Thanks for providing such a self-contained example by which 'nlme' 
> crashes R.  Could you please also give us 'sessionInfo()'?  I don't have 
> time to test it myself now, but perhaps if you identify your platform, you 
> might interest someone else in checking it.
> 
> 	  I'm sorry I couldn't be more helpful.
> 	  Spencer Graves
> 
> grieve@u.washington.edu wrote:

>> I am having trouble fitting correlation structures within nlme. I would
>> like to fit corCAR1, corGaus and corExp correlation structures to my data.
>> I either get the error "step halving reduced below minimum in pnls step"
>> or alternatively R crashes.
>>
>> My dataset is similar to the CO2 example in the nlme package. The one
>> major difference is that in my case the 'conc' steps are not the same for
>> each 'Plant'.
> I have replicated the problem using the CO2 data in nlme (based off of the 
> Ch08.R
> script).

>>
>> This works (when 'conc' is the same for each 'Plant':
>>
>> (fm1CO2.lis <- nlsList(SSasympOff, CO2))
>> (fm1CO2.nlme <- nlme(fm1CO2.lis, control = list(tolerance = 1e-2)))
>> (fm2CO2.nlme <- update(fm1CO2.nlme, random = Asym + lrc ~ 1))
>> CO2.nlme.var <- update(fm2CO2.nlme,
>> fixed = list(Asym ~ Type * Treatment, lrc + c0 ~ 1),
>> start = c(32.412, 0, 0, 0, -4.5603, 49.344),
>> weights=varConstPower(fixed=list(const=0.1, power=1)), verbose=T)
>>
>> CO2.nlme.CAR<-update(CO2.nlme.var, corr=corCAR1())
>>
>> CO2.nlme.gauss<-update(CO2.nlme.var,
>> correlation=corGaus(form=~as.numeric(conc)|Plant,nugget=F), data=CO2)
>>
>> CO2.nlme.exp<-update(CO2.nlme.var,
>> correlation=corExp(form=~as.numeric(conc)|Plant,nugget=F), data=CO2) But,
>> if i change each of the 'conc' numbers slightly so that they are no longer
> identical between subjects i can only get the corCAR1 correlation to work 
> while R
> crashes for both corExp and corGaus:

>>
>> for(i in 1:length(CO2$conc)){
>> CO2$conc[i]<-(CO2$conc[i]+rnorm(1))
>> }
>>
>> (fm1CO2.lis <- nlsList(SSasympOff, CO2))
>> (fm1CO2.nlme <- nlme(fm1CO2.lis, control = list(tolerance = 1e-2)))
>> (fm2CO2.nlme <- update(fm1CO2.nlme, random = Asym + lrc ~ 1))
>> CO2.nlme.var <- update(fm2CO2.nlme,
>> fixed = list(Asym ~ Type * Treatment, lrc + c0 ~ 1),
>> start = c(32.412, 0, 0, 0, -4.5603, 49.344),
>> weights=varConstPower(fixed=list(const=0.1, power=1)), verbose=T)
>>
>> CO2.nlme.CAR<-update(CO2.nlme.var, corr=corCAR1())
>>
>> CO2.nlme.gauss<-update(CO2.nlme.var,
>> correlation=corGaus(form=~as.numeric(conc)|Plant,nugget=F), data=CO2)
>>
>> CO2.nlme.exp<-update(CO2.nlme.var,
>> correlation=corExp(form=~as.numeric(conc)|Plant,nugget=F), data=CO2) I
>> have read Pinheiro & Bates (2000) and i think that it should be possible
>> to fit these correlation structures to my data, but maybe i am mistaken.
>>
>> I am running R 2.3.1 and have recently updated all packages.
>>
>> Thanks,
>> Katie Grieve
>>
>> Quantitative Ecology & Resource Management
>> University of Washington
>>
>> ______________________________________________
>> R-help@stat.math.ethz.ch mailing list
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>> PLEASE do read the posting guide!
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>

R-help@stat.math.ethz.ch 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 Jul 21 04:13:40 2006

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