The output file, as well as an optional initialisation file, is a vector file.
mds 2 difmatrix > resultsThis command performs Kruskal's Non-metric Multidimensional Scaling into 3 dimensions on the difference matrix stored in the file difmatrix and stores the result in the file results3:
mds -K 3 difmatrix > results3
With the option -K the program does Kruskal's Non-metric Multidimensional Scaling.
With the option -S the program does Sammon's Non-Linear Mapping.
Kruskal's Method and Sammon Mapping require a pre-initialisation. By default, this is done by Classical Multidimensional Scaling. However, you can use the result of a previous run of the program as an initialisation. For example:
mds -o tmp -S 3 difmatrix mds -o result -i tmp -K 3 difmatrixIn this case, initialisation is first done by Classical Multidimensional Scaling, then a Sammon Mapping is performed, and then this Sammon Mapping is used as the initialisation for doing Kruskal's Method.