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

[Michael A. Gilchrist]

On Sat, 17 Oct 2009, Douglas Bates wrote:
On Fri, Oct 16, 2009 at 7:09 PM, Michael A. Gilchrist <mi...@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?


Thanks for looking into this.  I've learned a lot from reading your book 
on nlme (and still have a lot to learn).  I've posted the data I've been 
working with at:
        www.tiem.utk.edu/~mikeg/software/R/selfStart/tissue.rda

Mike


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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and provide commented, minimal, self-contained, reproducible code.