[R] custom selfStart model works with getInitial but not nls

[Douglas Bates]

On Fri, Oct 16, 2009 at 7:09 PM, Michael A. Gilchrist <mikeg at utk.edu> wrote:
> Hello,
>
> I'm having problems creating and using a selfStart model with nlme.
>  Briefly, I've defined the model, a selfStart object, and then combined them
> to make a selfStart.default model.
>
> If I apply getInitial to the selfStart model, I get results.  However, if I
> try usint it with nls or nlsList, these routines complain about a lack of
> initial conditions.
>
> If someone could point out what I'm doing wrong, I'd greatly appreciate it.

Thanks for providing the code.  Could you also provide some data as a test case?

>
> Details:
> ## Nonlinear model I want to fit to the data
> const.PBMC.tcell.model <- function(B0, t, aL, aN, T0){
>
>  Tb0 = B0;
>
>  x = exp(-log(aL) + log(T0*aL+(-1+exp(t * aL))*Tb0 * aN) - t * aL);
>
>  return(x);
> }
>
>
> ##Define selfStart routine
> const.PBMC.tcell.selfStart<- function(mCall, LHS, data){
>
>  t0 = 0;
>  t1 = 24;
>  t2 = 48;
>
>  ##Get B0 Value
>  B0 =  data[1, "B0"];
>
>  T0 = mean(data[data$Time==t0, "Count"]);
>  T1 = mean(data[data$Time==t1, "Count"]);
>  T2 = mean(data[data$Time==t2, "Count"]);
>
>  if(T0 < T2){ ##increase -- doesn't work
>    stop(paste("Error in const.PBMC.tcell.start: T0 < T2 for data: ", data[1,
> ]));
>
>  }
>  ##Estimate aL based on exponential decline from t=0 to t=24
>  aLVal = -(log(T1) - log(T0))/(t1-t0);
>
>  ##Estimate aNVal based on final value
>  aNVal = aLVal*T2/B0;
>
>  values = list(aLVal, aNVal, T0);
>  names(values) <- mCall[c("aL", "aN", "T0")]; #mimic syntax used by P&B
>  return(values)
> }
>
>
>
> ##Now create new model with selfStart attributes
> const.PBMC.tcell.modelSS<-  selfStart(model = const.PBMC.tcell.model,
> initial=const.PBMC.tcell.selfStart)
>
>
> ##Test routines using getInitial -- This works
>>
>> getInitial(Count ~ const.PBMC.tcell.modelSS(B0, Time,aL, aN, T0), data =
>> tissueData)
>
> [1] 0.05720924
> $aL
> [1] 0.05720924
>
> $aN
> [1] 0.1981895
>
> $T0
> [1] 1360.292
>
> ##Now try to use the SS model -- this doesn't work
>>
>> nls(Count ~ const.PBMC.tcell.modelSS(B0, Time,aL, aN, T0), data =
>> tissueData)
>
> Error in numericDeriv(form[[3L]], names(ind), env) :
>  Missing value or an infinity produced when evaluating the model
> In addition: Warning message:
> In nls(Count ~ const.PBMC.tcell.modelSS(B0, Time, aL, aN, T0), data =
> tissueData) :
>  No starting values specified for some parameters.
> Intializing 'aL', 'aN', 'T0' to '1.'.
> Consider specifying 'start' or using a selfStart model
>
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