[R] lme, nlsList, nlsList.selfStart

[Spencer Graves]

	  Regarding the following:  	  	

 > mymod3<-nlsList(Conc~Dose * exp(lKe+lKa-lCl) *
 > (exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe)),
 >      data=mydata,
 >      start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
 > Error in model.frame(formula, rownames, variables, varnames, extras,
 > extranames,  :
 >         variable lengths differ

	  This example is NOT self contained and is entirely too complicated 
for me to try to replicate it myself in a reasonable period of time.  I 
will therefore ask one short question:  Are all the variable names in 
the "nlsList" call either columns of "mydata" or parameters to be 
estimated and therefore spelled out in "start"?  If I were you, I'd 
check this all very carefully, being especially careful about the 
distinction between "lCl" and "lC1", in particular.

	  If you'd like further help with this, I suggest you try to find the 
simplest possible example that generates problem you don't understand, 
then try to recast that example into one that is completely self 
contained, either a data set in the standard R or nlme distribution  or 
numbers that one can generate with a very few lines of code.  If you use 
random numbers, please "set.seed", to increase your confidence that 
someone else will see what you see.  (And please review the posting 
guide! "www.R-project.org/posting-guide.html".  Doing so may increase 
your chances of getting more useful information more quickly.)

	  spencer graves

Patrick Giraudoux wrote:

> Dear listers,
> 
> I am trying to fit a model using nlsList() using alternately a SSfol() 
> selfstart function or its developped equivalent formulae.
> 
> This preliminary trial works well
> 
> mydata<-groupedData(Conc~Tps|Organ,data=mydata)
> mymod1<-nls(Conc~SSfol(Dose,Tps,lKe,lKa,lCl),data=mydata)
> 
> as well as a developped form:
> 
> mymod2<-nls(Conc~Dose * exp(lKe+lKa-lCl) * 
> (exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe)),
>     data=mydata,
>     start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
>     )
> 
> However when trying to fit the model with nlsList, I get:
> 
> mymod3<-nlsList(Conc~Dose * exp(lKe+lKa-lCl) * 
> (exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe)),
>      data=mydata,
>      start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
>      )
> Error in model.frame(formula, rownames, variables, varnames, extras, 
> extranames,  :
>         variable lengths differ
> Error in model.frame(formula, rownames, variables, varnames, extras, 
> extranames,  :
>         variable lengths differ
> Error in model.frame(formula, rownames, variables, varnames, extras, 
> extranames,  :
>         variable lengths differ
> 
> Or specifying  the grouping factor explicitely:
> 
> mymod3<-nlsList(Conc~Dose * exp(lKe+lKa-lCl) * 
> (exp(-exp(lKe)*Tps)-exp(-exp(lKa)*Tps)) /(exp(lKa)-exp(lKe))|Organ,
>      data=mydata,
>      start= c(lKe=-2.77, lKa=-1.41, lCl=-1.13)
>      )
> 
> Error in model.frame(formula, rownames, variables, varnames, extras, 
> extranames,  :
>         variable lengths differ
> Error in model.frame(formula, rownames, variables, varnames, extras, 
> extranames,  :
>         variable lengths differ
> Error in model.frame(formula, rownames, variables, varnames, extras, 
> extranames,  :
>         variable lengths differ
> 
> 
> I cannot find out why the grouping factor cannot be used (it has the 
> same length as the other variables...)
> 
> Another strange thing occurs: in the example given in the help of 
> nlsList.selfstart, the following command works  well:
> 
>  fm1 <- nlsList(SSasympOff, CO2)
> 
> However its seemingly equivalent applied to the case above fails:
> 
> mymod4<-nlsList(SSfol,data=mydata)
> Error in eval(expr, envir, enclos) : object "input" not found
> Error in eval(expr, envir, enclos) : object "input" not found
> Error in eval(expr, envir, enclos) : object "input" not found
> 
> 
> Any hint/suggestion appreciated.
> 
> Kind regards,
> 
> Patrick Giraudoux
> 
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