Could you then create a table of the nested models, with one row per model? This will have to be documented. Why do you break away for this logic? This might be better explained by a one-to-one nested model table. The CR72 model is very useful due to its speed and accuracy. And numerical models should definitely not come first, as the entire point of the nesting is for speed by avoiding the grid search. I find the changed nesting an extremely worrying development!
Cheers, Edward On 18 August 2014 15:59, Troels Emtekær Linnet <[email protected]> wrote: > Hi Edward. > > Yep, the placement of the "nesting functions" in variables.py was not > the best place. > > But I could not figure out where to do it better. > > So model.py sound good. > > Unit tests are implemented, and function fine. > > > One should note, that this nesting is breaking away from the method > described in the paper: > > Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., > Tollinger, M., Teilum, K., Gagné, S., Marion, D., Griesinger, C., > Blackledge, M., and d'Auvergne, E. J. (2014). relax: the analysis of > biomolecular kinetics and thermodynamics using NMR relaxation > dispersion data. Bioinformatics. > http://dx.doi.org/10.1093/bioinformatics/btu166 > > It will not always nest from CR72 for example. > But it depends on which earlier models have already been analysed. > > Order is: > Numerical, analytical > Same parameter / partial parameters > > > Best > Troels > > 2014-08-18 15:41 GMT+02:00 Edward d'Auvergne <[email protected]>: >> A table might be the best way to document this. It should include all >> models and the table can be added to the manual (as a new section or >> an expansion of the current nested parameter description). I would >> highly recommend that unit tests are created, one for each model, to >> make sure that the nesting occurs correctly and as expected for all >> models. >> >> Cheers, >> >> Edward >> >> >> >> On 18 August 2014 15:36, Edward d'Auvergne <[email protected]> wrote: >>> Hi Troels, >>> >>> This change requires a bit of work. Firstly the functions would be >>> better in their own module, as in the case of the >>> specific_analyses.model_free.model module. Secondly could you >>> document the parameter nesting you implemented in the nesting_model() >>> function? Is this different to the nesting() method of the Relax_disp >>> auto-analysis? What is its purpose? There are many ways to nest test >>> dispersion models, but here I am confused as to what is happening and >>> why. >>> >>> Cheers, >>> >>> Edward >>> >>> >>> >>> On 12 August 2014 10:54, <[email protected]> wrote: >>>> Author: tlinnet >>>> Date: Tue Aug 12 10:54:39 2014 >>>> New Revision: 24984 >>>> >>>> URL: http://svn.gna.org/viewcvs/relax?rev=24984&view=rev >>>> Log: >>>> Implemented nesting function, which will determine which model to nest >>>> from. >>>> >>>> sr #3135(https://gna.org/support/?3135): Optimisation of the R1 relaxation >>>> rate for the off-resonance R1rho relaxation dispersion models. >>>> >>>> Modified: >>>> branches/R1_fitting/specific_analyses/relax_disp/variables.py >>>> >>>> branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py >>>> >>>> [This mail would be too long, it was shortened to contain the URLs only.] >>>> >>>> Modified: branches/R1_fitting/specific_analyses/relax_disp/variables.py >>>> URL: >>>> http://svn.gna.org/viewcvs/relax/branches/R1_fitting/specific_analyses/relax_disp/variables.py?rev=24984&r1=24983&r2=24984&view=diff >>>> >>>> Modified: >>>> branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py >>>> URL: >>>> http://svn.gna.org/viewcvs/relax/branches/R1_fitting/test_suite/unit_tests/_specific_analyses/_relax_disp/test_variables.py?rev=24984&r1=24983&r2=24984&view=diff >>>> >>>> >>>> _______________________________________________ >>>> relax (http://www.nmr-relax.com) >>>> >>>> This is the relax-commits mailing list >>>> [email protected] >>>> >>>> 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 >> [email protected] >> >> 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 [email protected] 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
