Re: [R] custom selfStart model works with getInitial but not nls
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?
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 PB
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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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 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 PB
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 PB
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.
