Feature/similarity_threshold #12
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This branch adds the similarity_threshold argument
-st=, which allows the user to define a value in range [0, 1] above which aligned pairs are included in the output. For computational complexity reasons, our alignment algorithm finds a complete (rather than partial) matching between two networks. This means that certain nodes may be matched by the algorithm, even if they obviously bear no relation (have a very low similarity). Hence, the value of this argument. This does not impact base functionality, it is completely optional, and the default value of 0 keeps the same logic that existed previously.The other notable addition (and source of bloat) on this PR is the rewrite to the examples. All have been pulled out of the root README in favor of deeper explanation with actual inputs (using real-world data) and outputs in the
example/folder. The previous single example in that folder has been removed, as it was essentially a duplicate of one single network pair from the Simulation data. Again, no impact on base functionality.