Dear Edward, Thanks for your early suggestion regarding different model selections. I have been busy on other stuff and only recently got time to focus on this subject again. I have run all the diffusion models e.g. isotropic, prolate, oblate and ellipsoid and model selections were made within each model (in aic directory). I am not sure how to write a script to select different models using 'model_selection()'. Could you please do me a favor? Your help is highly appreciated! Best wishes, Hongyan
Quoting Edward d'Auvergne <[EMAIL PROTECTED]>: > Hi, > > To compare the results what you need to employ is a technique from the > statistical field of model selection. The spherical diffusion > (isotropic) + all model-free models of all selected residues is one > single mathematical model. The prolate and oblate spheroids (prolate > and oblate axially symmetric anisotropic diffusion tensors) + all > model-free models, and the ellipsoid (fully anisotropic or three > different eigenvalues) + all model-free models, are three additional > mathematical models. Therefore to compare these four different models > you need to select the model which best represents your relaxation > data. These models are, however, not nested and therefore cannot be > compared using ANOVA F-tests! Firstly the three types of diffusion > tensor are not nested (there is a reference from Dominique Marion's > group in which they say ANOVA statistics cannot be used but I can't > find it at the moment (although it shouldn't be too hard to track > down, it's related to Tensor)). Secondly the model-free models > selected will be different between the four models. Hence chi-squared > and F-tests cannot be used. > > A useful reference (I'm not at all biased ;) for this problem is my > paper d'Auvergne, E. J. and Gooley, P. R. (2003), (see > http://www.nmr-relax.com/refs.html for the full reference). On page > 37 at the end of that paper I discuss how AIC model selection is > perfect for selecting between these non-nested models. The AIC > criterion is still > > AIC = chi2 + 2k, > > however chi2 is the minimised chi-squared value for the complete model > and k is the sum of the number of diffusion parameters and number of > model-free parameters for all spin systems. BIC model selection is > likely to work quite well as well. If you have four runs, one for > each of the diffusion models, then the relax user function > 'model_selection()' is designed to select between these models. I > hope this helps and hasn't been too biased. > > Cheers, > > Edward > > > P.S. Prior to model selection between the diffusion models, the > diffusion models must have fully converged. Multiple iterations of > optimisation of the model-free models, AIC model selection, and > optimisation of all parameters together (diffusion tensor + model-free > parameter of all residues) must be executed. Convergence is when two > iterations possess identical chi-squared values, identical model-free > models, and identical parameter values. > > > On 3/2/07, Hongyan Li <[EMAIL PROTECTED]> wrote: > > Dear relax users, > > I have managed to use Relax to run my dynamics data by both isotropic and > > axial-oblate models. My qestion is how to compare the results, by > chi-square?? > > what is the criteria to make judgment that which residues is beter > simulated > > with which model? > > > > Thanks for your kind help! > > > > Best wishes, > > > > Hongyan > > > > Dr. Hongyan Li > > Department of Chemistry > > The University of Hong Kong > > Pokfulam Road > > Hong Kong > > > > > > _______________________________________________ > > relax (http://nmr-relax.com) > > > > This is the relax-users 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-users > > > Dr. Hongyan Li Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong _______________________________________________ relax (http://nmr-relax.com) This is the relax-users 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-users
