Hi Edward. I actually think that I have created local minima in my dataset, which is not caught.
I am looking into it. 2015-01-19 10:30 GMT+01:00 Edward d'Auvergne <edw...@nmr-relax.com>: > Hi, > > Maybe we should discuss on the original thread the problem in detail > and see if there is a solution. I wonder why the kex errors are so > different? > > Regards, > > Edward > > > > On 19 January 2015 at 09:51, Troels Emtekær Linnet > <tlin...@nmr-relax.com> wrote: > > Hi Edward. > > > > I was through sor (sum of residuals), sos(sum of squares), and now > sse(sum > > of squared errors). > > > > I agree with sse being the best, but I have reverted all my commits, and > > found a solution through the API. > > > > Just using the chi2 value, and finding degrees of freedom with the API. > > > > If one wants .sse, one can just quickly do > > > > value.set(val=1.0, param="r2eff", error=True) > > minimise.calculate(verbosity=1) > > > > Anyway, in the end, the new method did not solve my problem. > > STD_fit = sqrt(chi2 / dof) > > > > Since dof is so big (many datapoints, small amounts of parameters for > > clustered fitting), STD_fit becomes close to 1. > > > > > > Best > > Troels > > > > > > 2015-01-19 9:35 GMT+01:00 Edward d'Auvergne <edw...@nmr-relax.com>: > >> > >> Hi Troels, > >> > >> Could you rename spin.sos to spin.sse? This is the acronym used in > >> the field and by other software - the sum of squared errors > >> (https://en.wikipedia.org/wiki/Residual_sum_of_squares, > >> http://www.palmer.hs.columbia.edu/software/modelfree_manual.pdf). If > >> the individual SSE elements are divided by the experimental error > >> sigma_i, then this is the chi2 value. The SSE and chi2 statistics are > >> related, and are identical in the case of unit errors. Other > >> acronyms, much less used in the NMR field, are SSR or RSS. I don't > >> think I've ever encountered SOS before, outside of emergencies > >> (https://en.wikipedia.org/wiki/SOS). > >> > >> Cheers, > >> > >> Edward > >> > >> On 16 January 2015 at 23:19, <tlin...@nmr-relax.com> wrote: > >> > Author: tlinnet > >> > Date: Fri Jan 16 23:19:50 2015 > >> > New Revision: 27203 > >> > > >> > URL: http://svn.gna.org/viewcvs/relax?rev=27203&view=rev > >> > Log: > >> > Implemented storing of sum of squares and the standard deviation of > >> > these for relaxation dispersion, when doing a point calculation. > >> > > >> > Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo > >> > simulation, where errors are generated with width of standard > deviation or > >> > residuals. > >> > > >> > Modified: > >> > trunk/specific_analyses/relax_disp/optimisation.py > >> > > >> > Modified: trunk/specific_analyses/relax_disp/optimisation.py > >> > URL: > >> > > http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/optimisation.py?rev=27203&r1=27202&r2=27203&view=diff > >> > > >> > > ============================================================================== > >> > --- trunk/specific_analyses/relax_disp/optimisation.py (original) > >> > +++ trunk/specific_analyses/relax_disp/optimisation.py Fri Jan 16 > >> > 23:19:50 2015 > >> > @@ -119,7 +119,7 @@ > >> > @type spin_lock_nu1: list of lists of numpy rank-1 float > >> > arrays > >> > @keyword relax_times_new: The interpolated experiment specific > >> > fixed time period for relaxation (in seconds). The dimensions are > {Ei, Mi, > >> > Oi, Di, Ti}. > >> > @type relax_times_new: rank-4 list of floats > >> > - @keyword store_chi2: A flag which if True will cause the > >> > spin specific chi-squared value to be stored in the spin container. > >> > + @keyword store_chi2: A flag which if True will cause the > >> > spin specific chi-squared value to be stored in the spin container > together > >> > with the sum of squares of the residuals and the standard deviation > of the > >> > sum of squares of the residuals. > >> > @type store_chi2: bool > >> > @return: The back-calculated R2eff/R1rho value > >> > for the given spin. > >> > @rtype: numpy rank-1 float array > >> > @@ -215,10 +215,15 @@ > >> > # Make a single function call. This will cause back calculation > >> > and the data will be stored in the class instance. > >> > chi2 = model.func(param_vector) > >> > > >> > - # Store the chi-squared value. > >> > + # Get the sum of squares 'sos' of the residuals between the > fitted > >> > values and the measured values. Get the std deviation of these, > std_sos. > >> > + sos, sos_std = model.get_sum_of_squares() > >> > + > >> > + # Store the chi-squared value, sums of squares of residual and > the > >> > standard deviation of sums of squares of residual. > >> > if store_chi2: > >> > for spin in spins: > >> > spin.chi2 = chi2 > >> > + spin.sos = sos > >> > + spin.sos_std = sos_std > >> > > >> > # Return the structure. > >> > return model.get_back_calc() > >> > > >> > > >> > _______________________________________________ > >> > relax (http://www.nmr-relax.com) > >> > > >> > This is the relax-commits mailing list > >> > relax-comm...@gna.org > >> > > >> > To unsubscribe from this list, get a password > >> > reminder, or change your subscription options, > >> > visit the list information page at > >> > https://mail.gna.org/listinfo/relax-commits > >> > >> _______________________________________________ > >> relax (http://www.nmr-relax.com) > >> > >> This is the relax-devel mailing list > >> relax-devel@gna.org > >> > >> To unsubscribe from this list, get a password > >> reminder, or change your subscription options, > >> visit the list information page at > >> https://mail.gna.org/listinfo/relax-devel > > > > > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
