[Ifeffit] Reduced chi square values versus F-tests for second shell fits

[Matt Siebecker]

Thanks again Bruce.  Yes
that helps.  What I want to do is defend
the criticism of my fits by honestly assessing their quality, i.e., not over
stating the results based on fits that compromise accuracy for precision.  As you describe in the 2009 RP&C paper on
mercury binding to DNA, when dealing with a limited number of independent data
points yet several paths that contribute significantly to the EXAFS signal, logically
creative methods to constrain fitting parameters are necessary.
 
I have found the method that Matt Newville describes in that
thread to be a useful method during the data analysis process.  However, I have found it to be very important to
re-open the fit to both shells after fitting the second shell.  I use this method of fitting the second shell
while fixing the first shell to filter out models of similar first and second shell
structure yet different second shell composition, e.g., a mixed metal versus a
single metal in the second shell.  For both
fitting models, the first shell is very similar (e.g., circa 6 oxygens).  If both models have similar first shell
values and correlations, perhaps it is reasonable to ignore them during part of
the fitting routine to focus on the small details of the second shell that can
get lost in the more dominant features of the first shell.  Essentially, I compare the RCS values of the
second shell fits of two models that have the same first shell to choose which
model is better.  I will test varying
some of the procedural parameters in the fit (k-weighting, k and R ranges) as
you suggested.  I’ve seen some discussion
about this on the mail list, and it is also strongly recommended there.
 
For those interested in F-tests, I’ve found the following
resources helpful:
 
Title: F-test in EXAFS fitting of structural models. Author(s): Michalowicz, A; Provost, K; Laruelle, S; etal. Source: JOURNAL OF SYNCHROTRON
RADIATION  Volume: 6   Pages: 233-235   DOI: 10.1107/S0909049599000734 Part: Part
3   Published: MAY 1 1999
 
Title: Statistical evaluations in fitting problems. Author(s): Klementev, KV. Source: JOURNAL OF SYNCHROTRON RADIATION  Volume: 8   Pages: 270-272   DOI:
10.1107/S0909049500015351   Part: Part
2   Published: MAR 2001
 
Title: A Variation of the F-Test for Determining Statistical
Relevance of Particular Parameters in EXAFS Fits. Author: Downward, L. Booth,
C.H. Lukens, W.W. Bridges, F.
Publication Date: 07-25-2006 Publication Info: Lawrence Berkeley
National Laboratory Permalink: http://www.escholarship.org/uc/item/5p60c864
 
And also here on the mailing list:
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-August/008983.html
 
In the Michalowicz paper I’ve found values slightly different when
reproducing his numbers.  I use some okay
free web-based F-test calculators or excel – but if anyone has a preferred web-based
F-test calculator that information would also be appreciated.
 
Kind regards,
Matt S.
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