R help - Oct 2009 - custom selfStart model works with getInitial but not nls

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.


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

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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