MATLAB: Is there a method to better organize functions for experiments?

I will run a set of experiments. The main method evaluated has the following signature:

[Model threshold] = detect(...
    TrainNeg, TrainPos, nf, nT, factors, ...
    removeEachStage, applyEstEachStage, removeFeatures);

where removeEachStage, applyEstEachStage, and removeFeatures are booleans. You can see that if I reverse the order of any of these boolean parameters I may get wrong results.

Is there a method in MATLAB that allows better organization in order to minimize this kind of error? Or is there any tool I can use to protect me against these errors?