I'm going to perform MDS by means of
cmdscale function of standard
R library. I spent several hours googling it and finally have a number of questions (some of them more general, some could be more specific to its implementations in
- I have a matrix of non-metric distances, e.g. based on Sorensen-Dice coefficient.
Can I use the matrix for
cmdscalefunction? As I understand, the function will perform "metric MDS"; so, metric MDS for non-metric distances.
- How can I estimate the quality of my model? I've found the
GOFcomponent of output of
cmdscalefunction, but I am confused with their interpretation. Could you clarify it for me please? Is there anything else?
- In PCA one often calculates the percentage of explained variance. Is this term applicable in MDS as well? How can I interpret it?