[Ifeffit] Question about transform windows and statistical parameters

Scott Calvin dr.scott.calvin at gmail.com
Thu May 12 10:51:01 CDT 2011

Hi Brandon,

Matt and Bruce both gave good, thorough answers to your questions this  
morning. Nevertheless, I'm going to chime in too, because there are  
some aspects of this issue I'd like to put emphasis on.

On May 11, 2011, at 8:46 PM, Brandon Reese wrote:

>  I tried your suggestion with epsilon and the chi-square values came  
> out to be very similar values with the different windows.  Does this  
> mean that reporting reduced chi-square values in a paper that  
> compared several data sets would not be necessary and/or appropriate?

Bruce said "no" emphatically, and I say "yes," but I think we've  
understood the question differently. As Bruce says:

> Of course, reduced chi-square can only be compared for fitting  
> models which compute epsilon the same way or use the same value for  
> epsilon.

That's the key point. I've gotten away from reporting values for  
reduced chi-square (RCS). That's a personal choice, and is not in  
accord with the International X-Ray Absorption Society's Error  
Reporting Recommendation, available here:


I think the difficulty in choosing epsilon is more likely to make a  
reduced chi-square number confusing than enlightening. But I am moving  
increasingly toward reporting changes in reduced chi-square between  
fits on the same data, and applying Hamilton's test to determine if  
improvements are statistically significant.

>  Would setting a value for epsilon allow comparisons across  
> different k-ranges, different (but similar) data sets, or a  
> combination of the two using the chi-square parameter?

Maybe not. After all, the epsilon should be different for different k- 
ranges, as your signal to noise ratio probably changes as a function  
of k. Using the same epsilon doesn't reflect that.

> In playing around with different windows and dk values my fit  
> variables generally stayed within the error bars, but the size of  
> the error bars could change more than a factor 2.  Does this mean  
> that it would make sense to find a window/dk that seems to "work"  
> for a given group of data and stay consistent when analyzing that  
> data group?

The fact that your variables stay within the error bars is good news.  
The change in the size of the error bars may be related to a less-than- 
ideal value for dk you may have used for the Kaiser-Bessel window.

But yes, find a window and dk combination that seems to work well and  
then stay consistent for that analysis. Unless the data is  
particularly problematic, I'd prefer making a reasoned choice before  
beginning to fit and then sticking with it; a posteriori choices for  
that kind of thing make me a little nervous.

* * *

At the risk of being redundant, four quick examples.

Example 1: You change the range of R values in the Fourier transform  
over which you are fitting a data set.
For this example, RCS is a valuable statistic for letting you know  
whether the fit supports the change in R-range.

Example 2: You change the range of k values over which you are fitting  
your data.
For this example, comparing RCS is unlikely to be useful. You are  
likely trying different k-ranges because you are suspicious about some  
of the data at the extremes of your range. Including or excluding that  
data likely implies epsilon should be changed, but by how much? Thus  
the unreliability of comparing RCS in this case.

Example 3: You change constraints on a fit on the same data range.
For this example, comparing RCS is very useful.

Example 4: You compare fits on the same data range, with the same  
model, on two different data sets which were collected during the same  
synchrotron run under similar conditions.
For this example, proceed with caution. You may decide to trust  
Ifeffit's method for estimating epsilon, or you may be able to come up  
with your own (perhaps basing it on the size of the edge jumps).  
Hopefully issues like glitches and high-frequency jitter are nearly  
the same for both samples, which gives you a fighting chance of making  
reasonable estimates of epsilon. Done with a little care, there may be  
value in comparing RCS for this kind of case.

--Scott Calvin
Sarah Lawrence College

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