[SciPy-user] scipy.optimize.leastsq and covariance matrix meaning
Wed Nov 12 09:36:31 CST 2008
Bruce Southey wrote:
> You also have a very bad fit as the standard errors are huge relative to
> the estimate meaning your parameters are not statistically different
> from zero.
Parameters: 4.90666526e+06 4.78090340e+09
Scaled error bars: 6.99319913e+04 6.68959208e+08
It seems values are estimated with roughly 1% and 10% confidence,
respectively. Am I wrong?
> Physics is one thing but the data tell a very different story
> perhaps due to measurement errors.
The data are right.
> The linear regression of x on y gives
> a residual variance of 2.86121E-22 and R-squared is 73% (approx 73% for
> the model above). I don't see any evidence for a nonlinear fit
> especially if you bother to plot the data. As I previously said, you
> probably would get a better fit using splines or similar because of the
> variability present.
I am probably bad at communicating, so I repeat.
This is a SECTION of the data. A tiny SECTION of a 2048-point force
curve. Being a small section, it is not surprising it is almost linear.
I just posted that bunch of points because they fitted correctly with
the equation and it was totally pointless to copy and paste hundreds of
numbers just to make people sleep happily about my own data.
Each peak in the force curve is clearly non linear, and I posted
examples of what I mean. If you want, you can download the software from
http://code.google.com/p/hooke and I can send you examples of whole
relevant data, fresh from the instrument.
I am not trying to fit the data with whatever model works best. I *want
to pick up well defined parameters* from a physical model.
If you have doubts on the physical consistency of the model or on its
application to my data, you're welcome to come here and discuss with me
and my coworkers (among them physicists).
Thanks for your interest, but really, you are misunderstanding the
issue. If you want information on single molecule force spectroscopy of
polymers, I can give you some reference.
Thanks for the bibliography too!
Massimo Sandal , Ph.D.
University of Bologna
Department of Biochemistry "G.Moruzzi"
Via Irnerio 48, 40126 Bologna, Italy
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