[R] Problem with 'nls' fitting logistic model (5PL)

[Michal Figurski]

Bert,

Thank you for your thoughts.

I can assure you I have plotted the data back and forth many times, and 
that overfitting has nothing to do with it. This is not a _statistical_ 
problem, but a _technical_ problem. Something that works well in ANY 
reliable statistical software doesn't work in R with 'nls'.

This just makes me think that 'nls' is a dysfunctional piece of junk 
that can't handle even a very simple problem. Not to mention that 
'predict()' for 'nls' doesn't give you any sort of confidence interval.

I wonder if there's another package in R that could be used to fit 
5P-logistic model. Any idea?

In the end I may attempt to write a fitting function myself, but that 
would be the last resort.

--
Michal J. Figurski, PhD
HUP, Pathology & Laboratory Medicine
Biomarker Research Laboratory
3400 Spruce St. 7 Maloney S
Philadelphia, PA 19104
tel. (215) 662-3413


On 5/2/2012 3:47 PM, Bert Gunter wrote:
> Plot the data. You're clearly overfitting.
>
> (If you don't know what this means or why it causes the problems you
> see, try a statistical help list or consult your local statistician).
>
> -- Bert
>
> On Wed, May 2, 2012 at 12:32 PM, Michal Figurski
> <figurski at mail.med.upenn.edu>  wrote:
>> Dear R-Helpers,
>>
>> I'm working with immunoassay data and 5PL logistic model. I wanted to
>> experiment with different forms of weighting and parameter selection, which
>> is not possible in instrument software, so I turned to R.
>>
>> I am using R 2.14.2 under Win7 64bit, and the 'nls' library to fit the model
>> - I started with the same model and weighting type (1/y) as in the
>> instrument to see if I'll get similar results. However, in some instances I
>> don't get any results - just errors.
>>
>> Here is an example calibration data, representative of my experiment.
>> Instrument soft had no problem fitting it:
>> x<- structure(list(SPL = structure(c(1L, 1L, 2L, 2L, 3L, 3L, 4L,
>> 4L, 5L, 5L, 6L, 6L, 7L, 7L), .Label = c("St1", "St2", "St3",
>> "St4", "St5", "St6", "St7"), class = "factor"), MFI = c(10755.5,
>> 9839, 5142.5, 4857, 1510.5, 1505, 502.5, 451, 215, 195.5, 58,
>> 57, 15, 15), nom = c(206, 206, 125, 125, 68, 68, 38, 38, 24,
>> 24, 13, 13, 6.5, 6.5), weights = c(0.0013946353028683, 0.00152454517735542,
>> 0.00291686922702965, 0.00308832612723904, 0.0099304865938431,
>> 0.00996677740863787, 0.0298507462686567, 0.0332594235033259,
>> 0.0697674418604651, 0.0767263427109974, 0.258620689655172,
>> 0.263157894736842,
>> 1, 1)), .Names = c("SPL", "MFI", "nom", "weights"), row.names = c(NA,
>> -14L), class = "data.frame")
>>
>> And here is the nls fit:
>> fit<- nls(MFI~a + b/((1+(nom/c)^d)^f), data=x, weights=x$weights,
>> start=c(a=100, b=10000, c=100, d=-1, f=1))
>>
>> I've tried every possible combination of starting values, including the
>> values fitted by the instrument soft - to no avail. I've probably seen all
>> possible error messages from 'nls' trying to fit this.
>>
>> If anyone has an idea why it's not working - let me know.
>>
>> Best regards,
>>
>> --
>> Michal J. Figurski, PhD
>> HUP, Pathology&  Laboratory Medicine
>> Biomarker Research Laboratory
>> 3400 Spruce St. 7 Maloney S
>> Philadelphia, PA 19104
>> tel. (215) 662-3413
>>
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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.
>
>
>