Re: [R] custom selfStart model works with getInitial but not nls
On Sat, 17 Oct 2009, Douglas Bates wrote:
On Fri, Oct 16, 2009 at 7:09 PM, Michael A. Gilchrist 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
$T0
[1] 1360.292
##Now try to use the SS model -- this doesn't work
nls(Count ~ const.PBMC.tcell.modelSS(B0, Time,aL, aN, T0), data =
tissueData)
Error in numericDeriv(form[[3L]], names(ind), env) :
Missing value or an infinity produced when evaluating the model
In addition: Warning message:
In nls(Count ~ const.PBMC.tcell.modelSS(B0, Time, aL, aN, T0), data =
tissueData) :
No starting values specified for some parameters.
Intializing 'aL', 'aN', 'T0' to '1.'.
Consider specifying 'start' or using a selfStart model
__
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and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] custom selfStart model works with getInitial but not nls
On Fri, Oct 16, 2009 at 7:09 PM, Michael A. Gilchrist wrote:
> Hello,
>
> I'm having problems creating and using a selfStart model with nlme.
> Briefly, I've defined the model, a selfStart object, and then combined them
> to make a selfStart.default model.
>
> If I apply getInitial to the selfStart model, I get results. However, if I
> try usint it with nls or nlsList, these routines complain about a lack of
> initial conditions.
>
> If someone could point out what I'm doing wrong, I'd greatly appreciate it.
Thanks for providing the code. Could you also provide some data as a test case?
>
> Details:
> ## Nonlinear model I want to fit to the data
> const.PBMC.tcell.model <- function(B0, t, aL, aN, T0){
>
> Tb0 = B0;
>
> x = exp(-log(aL) + log(T0*aL+(-1+exp(t * aL))*Tb0 * aN) - t * aL);
>
> return(x);
> }
>
>
> ##Define selfStart routine
> const.PBMC.tcell.selfStart<- function(mCall, LHS, data){
>
> t0 = 0;
> t1 = 24;
> t2 = 48;
>
> ##Get B0 Value
> B0 = data[1, "B0"];
>
> T0 = mean(data[data$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
>
> $T0
> [1] 1360.292
>
> ##Now try to use the SS model -- this doesn't work
>>
>> nls(Count ~ const.PBMC.tcell.modelSS(B0, Time,aL, aN, T0), data =
>> tissueData)
>
> Error in numericDeriv(form[[3L]], names(ind), env) :
> Missing value or an infinity produced when evaluating the model
> In addition: Warning message:
> In nls(Count ~ const.PBMC.tcell.modelSS(B0, Time, aL, aN, T0), data =
> tissueData) :
> No starting values specified for some parameters.
> Intializing 'aL', 'aN', 'T0' to '1.'.
> Consider specifying 'start' or using a selfStart model
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] custom selfStart model works with getInitial but not nls
Hello,
I'm having problems creating and using a selfStart model with nlme. Briefly,
I've defined the model, a selfStart object, and then combined them to make a
selfStart.default model.
If I apply getInitial to the selfStart model, I get results. However, if I try
usint it with nls or nlsList, these routines complain about a lack of initial
conditions.
If someone could point out what I'm doing wrong, I'd greatly appreciate it.
Details:
## Nonlinear model I want to fit to the data
const.PBMC.tcell.model <- function(B0, t, aL, aN, T0){
Tb0 = B0;
x = exp(-log(aL) + log(T0*aL+(-1+exp(t * aL))*Tb0 * aN) - t * aL);
return(x);
}
##Define selfStart routine
const.PBMC.tcell.selfStart<- function(mCall, LHS, data){
t0 = 0;
t1 = 24;
t2 = 48;
##Get B0 Value
B0 = data[1, "B0"];
T0 = mean(data[data$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
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
