What are the most important functions in d2d? - Data2Dynamics/d2d GitHub Wiki

Summary of the most frequently used methods, functions and configuration options. For full description of the available functionality as well as for further configuration options, we refer to the comments in the matlab functions (e.g. help arPrint) as well to the configuration struct ar.config.

Further information on the functions in the image

Parameters

The parameter values are stored in ar.p and their labels in ar.pLabel. Calling arPrint gives a summary. arSetPars can be used to change parameter values, set linear or logarithmic scale and define if a parameter should be fitted or not. arSetParsPattern does the same for a group of parameters with a name pattern.

Data

If the steady state cannot be calculated pre-equillibration can be done using arSteadyState. In case of a simulation study arSimuData can be used.

Plotting

arPlot and arPlot2 give the current data together with the best fit. The waterfall plot after a multi start fit can be shown with arPlotChi2s. Using arPlotter different plot options are available using a graphical interface. The fluxes can be found there by plotting v, the dynamics of the states by plotting x and y gives the observables. arPlotMulti gives the fit results for different parameter sets in one plot and can be used after a multi start.

Fitting

A general, first fit can be started with arFit, arFitLHS(number of fits) does a multi start. There clicking stop fits will finish the current fit and stop the procedure afterwards, so the current results are not lost. Using arMergeFits different fits and multi starts can be merged, e.g. after calculating on a cluster. Lower and upper bounds for parameters can be set in ar.ub and ar.lb. Numerical issues can usually be addressed by changing integrator settings in ar.config, this sometimes is a trial and error procedure.

Profile Likelihood

After a best fit is found, the calculation of profiles has to be initialized with arPLEInit. Calling ple calculates profiles for all fitted parameters, plePlot shows each profile in a single plot and the parameter dependencies underneath, plePlotMulti gives all profiles in one plot. If the calculation of the profile broke up too early pleExtend can be called for that parameter to extend the profile to one or both sides.

Loading and Saving

arSave save the current fits, the settings and the parameter values, thus the whole workspace. This can be loaded again by using arLoad. arLoadPars Loads the parameters and parameter settings from a file, but matches this to the currently loaded model by parameter names.