Hi Stefano, all,
same old question that emerges again:
What formula is used by IFEFFIT to calculate the number of independent points? Does it use the formula 2DkDR/pi? or 2DkDR/pi +1? or 2DkDR/pi +2? And how does it approximate the resulting number to integer?
Ifeffit uses an approximation of 2*delta_k * delta_R / pi. Well, it could use a better approximation -- see below. But Ifeffit does not use 2dKdR/pi + 2. The Stern paper considers "independent points" to be discrete, counts the endpoints of this discrete array of "independent points", and neglects the rather significant problem of the limit dk->0. I find each of these to be problematic. The dk->0 limit problem makes it especially hard to implement in a meaningful way. Ifeffit uses n_idp = 2*delta_k * delta_R / pi, but is cautious (and probably overly so) in determining delta_k and delta_R. First, it puts these on the k- and R- grids (0.05 Ang^-1 and ~0.03067Ang). It is also works to avoid rounding incorrectly. Thus, currently your ranges: kmin=2.0, kmax=12, rmin=1.0, rmax=6.0 get mapped to kmin = 2.05, kmax=12.00 , rmin=1.012427, rmax=5.98525 Thus you should have n_idp = 31.4824. You can confirm that with 'print n_idp' from the command line. It sounds like that's what you're getting. And yes, I do think that having "kmin=2.00" map to "kmin=2.05" for this part of the calculation is overly cautious, and I will fix that in the next release (and n_idp will equal ~31.64). I could be persuaded to just use the user-supplied values, but the round-off errors shouldn't matter much. In general, I agree with most of the answers to not take N_idp too seriously. I would say to report it to 1 decimal place, just to emphasize that it is understood to be an estimate and not a discrete number. Saying "n_idp=12" implies "I could fit up to 12 parameters with confidence". It's easy enough to show this is usually NOT the case, but some people sure like a hard and fast rule. And, sadly, n_idp does influence the error bars some, so it seems wise to get it as close as we can. That's sort of rambly, but hope that helps --Matt PS: For autobk/spline(), the number of knots is actually chosen as n = 2 * int( rbkg * (kmax-kmin)/pi ) + 1 It turns out that for the b-spline algorithm used, the number of knots used needs to be an odd number greater than 4. So, the formula is convenient. Is it right? Well, it seems to work pretty well. As fitting variables, the spline y-values are somewhat correlated, so you might argue that you could have a few more variables. That's easy enough to try with spline(data.chi, rbkg=1, nknots=17) In my experience, this rarely helps but it might be worth re-visiting.
Hi Matt,
Ifeffit uses an approximation of 2*delta_k * delta_R / pi.
OK. One nail down.
Well, it could use a better approximation -- see below. But Ifeffit does not use 2dKdR/pi + 2. The Stern paper considers "independent points" to be discrete, counts the endpoints of this discrete array of "independent points", and neglects the rather significant problem of the limit dk->0. I find each of these to be problematic. The dk->0 limit problem makes it especially hard to implement in a meaningful way.
OK
Ifeffit uses n_idp = 2*delta_k * delta_R / pi, but is cautious (and probably overly so) in determining delta_k and delta_R. First, it puts these on the k- and R- grids (0.05 Ang^-1 and ~0.03067Ang). It is also works to avoid rounding incorrectly. Thus, currently your ranges: kmin=2.0, kmax=12, rmin=1.0, rmax=6.0 get mapped to kmin = 2.05, kmax=12.00 , rmin=1.012427, rmax=5.98525
Now I get it...
Thus you should have n_idp = 31.4824. You can confirm that with 'print n_idp' from the command line. It sounds like that's what you're getting.
And yes, I do think that having "kmin=2.00" map to "kmin=2.05" for this part of the calculation is overly cautious, and I will fix that in the next release (and n_idp will equal ~31.64). I could be persuaded to just use the user-supplied values, but the round-off errors shouldn't matter much.
no, it is not a matter of rounding up or arguing whether the exact number will change the meaning or the analysis of the fit. I asked because being new to this I am trying to be rigorous and when I see a formula in a paper I would naively expect that the same formula is used to calculate output numbers from a program. Now everything is clearer. Thanks.
In general, I agree with most of the answers to not take N_idp too seriously. I would say to report it to 1 decimal place, just to emphasize that it is understood to be an estimate and not a discrete number.
will do
Saying "n_idp=12" implies "I could fit up to 12 parameters with confidence". It's easy enough to show this is usually NOT the case, but some people sure like a hard and fast rule. And, sadly, n_idp does influence the error bars some, so it seems wise to get it as close as we can.
ok
That's sort of rambly, but hope that helps
it does! Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"
participants (2)
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Matt Newville -
Stefano Ciurli