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

[Spencer Graves]

	  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 at 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
> 
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