Re: [Ifeffit] Breaking down correlationships between parameters
Hi Bruce,
Thanks for your comments and links of your lectures. I forgot to mention that I use Artemis for fitting my data.
Best regards,
Jatin
-----Original Message-----
From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov
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Subject: Ifeffit Digest, Vol 145, Issue 45
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Today's Topics:
1. Re: Breaking down correlationships between parameters
(Bruce Ravel)
2. Re: Breaking down correlationships between parameters
(Rana, Jatinkumar Kantilal)
----------------------------------------------------------------------
Message: 1
Date: Mon, 23 Mar 2015 09:27:05 -0400
From: Bruce Ravel
The term N*S02 is fitted for each path of the FEFF calculation. So my question is, even if we know N with a great certainty for some path, how can we vary both N and S02 for other paths ? or Did I understand it wrong ?
At no point in your emails did you say that you are using Artemis to do your fitting. The comment I am about to make may not, therefore, be relevant to you.
In Ifeffit and Larch -- and therefore in Artemis -- we DO NOT fit N*SO2.
Fits in Ifeffit, Larch, and Artemis use a set of user-defined parameters as the variables of the fit. As part of the fitting model, the user relates the variables of the fit to the parameters of the EXAFS equation using math expression.
This benefit of the generality of the fitting model allows the user to easily encode prior knowledge into a fit. The cost is that the parameters have to be interpreted in some kind of physical context.
To answer you question specifically, Artemis allows you to set or float parameters for N and S02 and to define the amplitude term of the EXAFS equation for each path in any way that you see fit. In that way, you can implement all the suggestions that Matt, Scott, and Chris have made.
I discuss this in some detail starting at page 35 of this presentation.
https://speakerdeck.com/bruceravel/advanced-topics-in-exafs-analysis
Among the lectures at
http://www.diamond.ac.uk/Beamlines/Spectroscopy/Techniques/XAS.html,
this is the one called "Fit Evaluation and Fitting multiple structures".
HTH,
B
--
Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973
Homepage: http://bruceravel.github.io/home/
Software: https://github.com/bruceravel
Demeter: http://bruceravel.github.io/demeter/
------------------------------
Message: 2
Date: Mon, 23 Mar 2015 14:36:31 +0000
From: "Rana, Jatinkumar Kantilal"
On Mar 23, 2015, at 8:54 AM, Rana, Jatinkumar Kantilal
wrote: Hi Chris,
The term N*S02 is fitted for each path of the FEFF calculation. So my question is, even if we know N with a great certainty for some path, how can we vary both N and S02 for other paths ? or Did I understand it wrong ?
Best regards, Jatin
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov Sent: 23 March, 2015 12:16 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 42
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Today's Topics:
1. Re: Breaking down correlationships between parameters (Rana, Jatinkumar Kantilal) 2. Re: Breaking down correlationships between parameters (Chris Patridge)
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Message: 1 Date: Mon, 23 Mar 2015 11:00:19 +0000 From: "Rana, Jatinkumar Kantilal"
To: "ifeffit@millenia.cars.aps.anl.gov" Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: Content-Type: text/plain; charset="utf-8" Hi Scott,
Thank you for your comments. Can you please elaborate a little bit more on this "In cases like that, both N for all paths but one and S02 can be fit without 100% correlation."
Best regards, Jatin
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov Sent: 23 March, 2015 10:16 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 41
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Today's Topics:
1. Re: Breaking down correlationships between parameters (Scott Calvin) 2. Re: Breaking down correlationships between parameters (Matt Newville) 3. Re: Breaking down correlationships between parameters (Rana, Jatinkumar Kantilal)
----------------------------------------------------------------------
Message: 1 Date: Sun, 22 Mar 2015 13:44:28 -0400 From: Scott Calvin
To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: Content-Type: text/plain; charset="utf-8" One side-comment from me:
On Mar 22, 2015, at 12:52 PM, Matt Newville
mailto:newville@cars.uchicago.edu> wrote: N and S02 are always 100% correlated (mathematically, not merely by the finite k range).
Matt is saying that N and S02 are always 100% correlated for a single path. But in some situations you might know N for one path but not others. For example, you might know that the absorbing atom is octahedrally coordinated to oxygen but not be as certain as to next-nearest neighbors, or that there are copper atoms on the corners of a simple cubic lattice with a mixture of atoms at other positions. In cases like that, both N for all paths but one and S02 can be fit without 100% correlation.
The degeneracy of multiple-scattering paths can often be constrained in terms of the coordination numbers for direct-scattering paths, which can further reduce (not ?break?) the correlation.
In terms of the main question, I agree with Matt: I don?t think there?s much point in using the line-crossing technique nowadays; fitting using multiple k-weights simultaneously accomplishes the same thing but is a bit easier to interpret statistically.
?Scott Calvin Sarah Lawrence College -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/201503 22/f4e7b7e4/attachment-0001.htm>
------------------------------
Message: 2 Date: Sun, 22 Mar 2015 15:56:20 -0500 From: Matt Newville
To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID:
Content-Type: text/plain; charset="utf-8" On Sun, Mar 22, 2015 at 12:44 PM, Scott Calvin
wrote: One side-comment from me:
On Mar 22, 2015, at 12:52 PM, Matt Newville
wrote: N and S02 are always 100% correlated (mathematically, not merely by the finite k range).
Matt is saying that N and S02 are always 100% correlated *for a single path*. But in some situations you might know N for one path but not others. For example, you might know that the absorbing atom is octahedrally coordinated to oxygen but not be as certain as to next-nearest neighbors, or that there are copper atoms on the corners of a simple cubic lattice with a mixture of atoms at other positions. In cases like that, both N for all paths but one and S02 can be fit without 100% correlation.
Yes, I completely agree with Scott -- this is a good point that I neglected. In addition to looking at multiple shells, one might also consider using temperature or pressure dependence to separate N*S02 and sigma2. Those aren't without assumptions, and still don't remove the inherent correlation, but are useful approaches.
The degeneracy of multiple-scattering paths can often be constrained in
terms of the coordination numbers for direct-scattering paths, which can further reduce (not ?break?) the correlation.
In terms of the main question, I agree with Matt: I don?t think there?s much point in using the line-crossing technique nowadays; fitting using multiple k-weights simultaneously accomplishes the same thing but is a bit easier to interpret statistically.
?Scott Calvin Sarah Lawrence College
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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------------------------------
Message: 3 Date: Mon, 23 Mar 2015 09:16:02 +0000 From: "Rana, Jatinkumar Kantilal"
To: "ifeffit@millenia.cars.aps.anl.gov" Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: Content-Type: text/plain; charset="utf-8" Hi Matt,
Thank you very much for your detailed explanation. As you pointed out that this approach ignores the statistical significance of fits and assumes that all fits are "good" fits. Also, the point that this approach yields a value of the parameter which is only slightly less correlated with the other one, but not completely removes the correlation. It makes it really clear to me that how this approach works and what are the pros and cons.
Well, I myself has never tried this approach of minimizing the correlation between N*S02 and sigma2, but I read a lot about it in the literature. With my limited knowledge about the method, I could not judge this approach, although I had my own doubts.
I truly appreciate your efforts in providing me a deeper insight into this approach.
Best regards, Jatin
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov Sent: 22 March, 2015 18:00 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 40
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1. Re: Breaking down correlationships between parameters (Matt Newville)
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Message: 1 Date: Sun, 22 Mar 2015 11:52:30 -0500 From: Matt Newville
To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID:
Content-Type: text/plain; charset="utf-8" Hi Jatin,
On Sat, Mar 21, 2015 at 10:41 AM, Rana, Jatinkumar Kantilal < jatinkumar.rana@helmholtz-berlin.de> wrote:
Hi Matt,
Thanks a lot for your prompt reply. The method I am referring to is not the multiple k-weight fits by constraining N*S02. My apologies for not being clear enough. Let's do it again. I am actually referring to an approach where we take an advantage of a different k-dependence of various parameters to breakdown correlations between them. For example, S02 and sigma2. S02 is k-independent and Sigma2 has k^2 dependence.
Yes, I am familiar with this approach, and I understand that this is what you are using. What I am saying is that this does not work nearly as well as (sometimes) claimed, and is sort of cheating. It ignores the measures of statistical significance.
In this case, to breakdown correlation between S02 and sigma2,
The correlation between N*S02 and sigma2 is inherent to the finite k-range of the EXAFS signal. It cannot be "broken", though it might be reduced.
one can assume a series of S02 values and perform fits using a single k-weight each time (say k-weight 1,2 and 3) and record corresponding sigma2 values.
Let us say for k-weight =1, a series of preset S02 values will result in a
series of corresponding sigma2 values refined in fits, which can be plotted as a straight line in sigma2 vs. S02 plot.
OK, one can fit sigma2 with a series of preset values on N*S02. That's fine. But it does NOT lead to an infinitely thin line of sigma2 vs. N*S02. Each sigma2 value on that line has a width, corresponding to its uncertainty. In fact, the line you produce nicely demonstrates and measures the correlation of N*S02 and sigma2 as the slope of this line.
Similar straight lines can be obtained for fits using k-weight = 2 and then 3.
Now, these three lines may intersect at or near some point, which will
determine the "true" value of parameters independent of k-weight.
The different lines (each with finite thickness) will give a *range of values* for N*S02 and sigma2, not a single value.
The biggest problem with this approach is that it ignores the relative goodness-of-fits (let's just assume that is 'chi-square' for the purpose of this discussion) for the fits along these lines. Some fits are better than others, and this approach completely ignores that fact, and equally importantly ignores the fact that there is a range of values for chi-square that are consistent with "good". If you include these values, your linear plot will become contours of chi-square as a function of N*S02 and sigma2. And, yes, by using different k-weights and k-ranges and so on you can get overlapping contour plots which may reduce the correlation a small amount when looked at as an ensemble. And you can find a best set of values for N*S02 and sigma2, but *each* of these will have an uncertainty.
So, you can use this approach to find a good value for N*S02, but it is not breaking the correlation. You can do this by hand. Or you can just do a fit with datasets with different k-weights and k-ranges. When you do this as a fit, you will see that the correlation is still fairly large.
Also, just to be clear, this is absolutely not a "true" value. It is a measured value. Not at all the same thing.
One can then constrain S02 to a value obtained from the point of
intersection of three lines and vary sigma2 in a fit.
Well, one can certainly set N*S02 to some value and fit sigma2. As I said earlier, this ignores the correlation of N*S02 and sigma2, but does not remove that correlation.
In this particular case, however, the advantage is, S02 does not depend on changes inside sample and we have very good estimate of its range (say 0.7 - 1.0).
Now suppose instead of S02 (which i now set to a reasonable value), I am interested in determining N, but it is highly correlated with sigma2. Each time when disorder in the sample increases, the sigma2 increases and due to its high correlation, N is also overestimated. On the other hand, when the disorder in the sample decreases, the sigma2 decreases and I can have a "true" estimation of N in the sample. Can I still apply the above mentioned approach to break the correlationship between N and sigma2 and get a "true" estimation of N, even if disorder is high in my samples ? or it is simply not possible due to the fact that both N and sigma2 varies with changes inside the sample.
N and S02 are always 100% correlated (mathematically, not merely by the finite k range). So, to the extent that the approach works at all, you can use it for "N" or "S02". Really, the approach is comparing N*S02 and sigma2, in one case you asserted a value of "N" and projected all changes to "S02" -- you can equally assert "S02" and project all changes to "N".
To be clear, this is not going to find the "true" value of anything, because no analysis is ever going to find the "true" value -- it's going to find a measured value.
Finally, the correlation of N*S02 and sigma2 does not imply a bias in the values for N*S02. N*S02 is NOT overestimated because it is highly correlated with sigma2.
Hope that helps,
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Message: 2 Date: Mon, 23 Mar 2015 07:15:05 -0400 From: Chris Patridge
To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: <29942DF9-8043-424E-BDCC-9CA19EB4AC9B@buffalo.edu> Content-Type: text/plain; charset=utf-8 I think Scott was pointing out that first neighbors may be known with high certainty and therefore you can set this value thereby removing it and slightly reducing the correlations.
Chris
Sent from my iPhone
On Mar 23, 2015, at 7:00 AM, Rana, Jatinkumar Kantilal
wrote: Hi Scott,
Thank you for your comments. Can you please elaborate a little bit more on this "In cases like that, both N for all paths but one and S02 can be fit without 100% correlation."
Best regards, Jatin
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov Sent: 23 March, 2015 10:16 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 41
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1. Re: Breaking down correlationships between parameters (Scott Calvin) 2. Re: Breaking down correlationships between parameters (Matt Newville) 3. Re: Breaking down correlationships between parameters (Rana, Jatinkumar Kantilal)
--------------------------------------------------------------------- -
Message: 1 Date: Sun, 22 Mar 2015 13:44:28 -0400 From: Scott Calvin
To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: Content-Type: text/plain; charset="utf-8" One side-comment from me:
On Mar 22, 2015, at 12:52 PM, Matt Newville
mailto:newville@cars.uchicago.edu> wrote: N and S02 are always 100% correlated (mathematically, not merely by the finite k range).
Matt is saying that N and S02 are always 100% correlated for a single path. But in some situations you might know N for one path but not others. For example, you might know that the absorbing atom is octahedrally coordinated to oxygen but not be as certain as to next-nearest neighbors, or that there are copper atoms on the corners of a simple cubic lattice with a mixture of atoms at other positions. In cases like that, both N for all paths but one and S02 can be fit without 100% correlation.
The degeneracy of multiple-scattering paths can often be constrained in terms of the coordination numbers for direct-scattering paths, which can further reduce (not ?break?) the correlation.
In terms of the main question, I agree with Matt: I don?t think there?s much point in using the line-crossing technique nowadays; fitting using multiple k-weights simultaneously accomplishes the same thing but is a bit easier to interpret statistically.
?Scott Calvin Sarah Lawrence College -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150 3 22/f4e7b7e4/attachment-0001.htm>
------------------------------
Message: 2 Date: Sun, 22 Mar 2015 15:56:20 -0500 From: Matt Newville
To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID:
Content-Type: text/plain; charset="utf-8" On Sun, Mar 22, 2015 at 12:44 PM, Scott Calvin
wrote: One side-comment from me:
On Mar 22, 2015, at 12:52 PM, Matt Newville
wrote: N and S02 are always 100% correlated (mathematically, not merely by the finite k range).
Matt is saying that N and S02 are always 100% correlated *for a single path*. But in some situations you might know N for one path but not others. For example, you might know that the absorbing atom is octahedrally coordinated to oxygen but not be as certain as to next-nearest neighbors, or that there are copper atoms on the corners of a simple cubic lattice with a mixture of atoms at other positions. In cases like that, both N for all paths but one and S02 can be fit without 100% correlation. Yes, I completely agree with Scott -- this is a good point that I neglected. In addition to looking at multiple shells, one might also consider using temperature or pressure dependence to separate N*S02 and sigma2. Those aren't without assumptions, and still don't remove the inherent correlation, but are useful approaches.
The degeneracy of multiple-scattering paths can often be constrained in
terms of the coordination numbers for direct-scattering paths, which can further reduce (not ?break?) the correlation.
In terms of the main question, I agree with Matt: I don?t think there?s much point in using the line-crossing technique nowadays; fitting using multiple k-weights simultaneously accomplishes the same thing but is a bit easier to interpret statistically.
?Scott Calvin Sarah Lawrence College
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit --Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150 3 22/3dd3f763/attachment-0001.htm>
------------------------------
Message: 3 Date: Mon, 23 Mar 2015 09:16:02 +0000 From: "Rana, Jatinkumar Kantilal"
To: "ifeffit@millenia.cars.aps.anl.gov" Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID: Content-Type: text/plain; charset="utf-8" Hi Matt,
Thank you very much for your detailed explanation. As you pointed out that this approach ignores the statistical significance of fits and assumes that all fits are "good" fits. Also, the point that this approach yields a value of the parameter which is only slightly less correlated with the other one, but not completely removes the correlation. It makes it really clear to me that how this approach works and what are the pros and cons.
Well, I myself has never tried this approach of minimizing the correlation between N*S02 and sigma2, but I read a lot about it in the literature. With my limited knowledge about the method, I could not judge this approach, although I had my own doubts.
I truly appreciate your efforts in providing me a deeper insight into this approach.
Best regards, Jatin
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request@millenia.cars.aps.anl.gov Sent: 22 March, 2015 18:00 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 145, Issue 40
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--------------------------------------------------------------------- -
Message: 1 Date: Sun, 22 Mar 2015 11:52:30 -0500 From: Matt Newville
To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Breaking down correlationships between parameters Message-ID:
Content-Type: text/plain; charset="utf-8" Hi Jatin,
On Sat, Mar 21, 2015 at 10:41 AM, Rana, Jatinkumar Kantilal < jatinkumar.rana@helmholtz-berlin.de> wrote:
Hi Matt,
Thanks a lot for your prompt reply. The method I am referring to is not the multiple k-weight fits by constraining N*S02. My apologies for not being clear enough. Let's do it again. I am actually referring to an approach where we take an advantage of a different k-dependence of various parameters to breakdown correlations between them. For example, S02 and sigma2. S02 is k-independent and Sigma2 has k^2 dependence. Yes, I am familiar with this approach, and I understand that this is what you are using. What I am saying is that this does not work nearly as well as (sometimes) claimed, and is sort of cheating. It ignores the measures of statistical significance.
In this case, to breakdown correlation between S02 and sigma2,
The correlation between N*S02 and sigma2 is inherent to the finite k-range of the EXAFS signal. It cannot be "broken", though it might be reduced.
one can assume a series of S02 values and perform fits using a single k-weight each time (say k-weight 1,2 and 3) and record corresponding sigma2 values.
Let us say for k-weight =1, a series of preset S02 values will result in a
series of corresponding sigma2 values refined in fits, which can be plotted as a straight line in sigma2 vs. S02 plot.
OK, one can fit sigma2 with a series of preset values on N*S02. That's fine. But it does NOT lead to an infinitely thin line of sigma2 vs. N*S02. Each sigma2 value on that line has a width, corresponding to its uncertainty. In fact, the line you produce nicely demonstrates and measures the correlation of N*S02 and sigma2 as the slope of this line.
Similar straight lines can be obtained for fits using k-weight = 2 and then 3.
Now, these three lines may intersect at or near some point, which will
determine the "true" value of parameters independent of k-weight.
The different lines (each with finite thickness) will give a *range of values* for N*S02 and sigma2, not a single value.
The biggest problem with this approach is that it ignores the relative goodness-of-fits (let's just assume that is 'chi-square' for the purpose of this discussion) for the fits along these lines. Some fits are better than others, and this approach completely ignores that fact, and equally importantly ignores the fact that there is a range of values for chi-square that are consistent with "good". If you include these values, your linear plot will become contours of chi-square as a function of N*S02 and sigma2. And, yes, by using different k-weights and k-ranges and so on you can get overlapping contour plots which may reduce the correlation a small amount when looked at as an ensemble. And you can find a best set of values for N*S02 and sigma2, but *each* of these will have an uncertainty.
So, you can use this approach to find a good value for N*S02, but it is not breaking the correlation. You can do this by hand. Or you can just do a fit with datasets with different k-weights and k-ranges. When you do this as a fit, you will see that the correlation is still fairly large.
Also, just to be clear, this is absolutely not a "true" value. It is a measured value. Not at all the same thing.
One can then constrain S02 to a value obtained from the point of
intersection of three lines and vary sigma2 in a fit.
Well, one can certainly set N*S02 to some value and fit sigma2. As I said earlier, this ignores the correlation of N*S02 and sigma2, but does not remove that correlation.
In this particular case, however, the advantage is, S02 does not depend on changes inside sample and we have very good estimate of its range (say 0.7 - 1.0).
Now suppose instead of S02 (which i now set to a reasonable value), I am interested in determining N, but it is highly correlated with sigma2. Each time when disorder in the sample increases, the sigma2 increases and due to its high correlation, N is also overestimated. On the other hand, when the disorder in the sample decreases, the sigma2 decreases and I can have a "true" estimation of N in the sample. Can I still apply the above mentioned approach to break the correlationship between N and sigma2 and get a "true" estimation of N, even if disorder is high in my samples ? or it is simply not possible due to the fact that both N and sigma2 varies with changes inside the sample. N and S02 are always 100% correlated (mathematically, not merely by the finite k range). So, to the extent that the approach works at all, you can use it for "N" or "S02". Really, the approach is comparing N*S02 and sigma2, in one case you asserted a value of "N" and projected all changes to "S02" -- you can equally assert "S02" and project all changes to "N".
To be clear, this is not going to find the "true" value of anything, because no analysis is ever going to find the "true" value -- it's going to find a measured value.
Finally, the correlation of N*S02 and sigma2 does not imply a bias in the values for N*S02. N*S02 is NOT overestimated because it is highly correlated with sigma2.
Hope that helps,
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participants (1)
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Rana, Jatinkumar Kantilal