Evaluation of HRR network

[proost]

Script at: PhyloNet\Fig - evaluating the network

Potential implementation. Import network with HRR cutoff of 100, then run test to check optimal setting and store that value in the database filter on the fly when constructing graphs. (Would allow users to request other values if they desire to do so, however extra data that needs to be pulled from DB creates overhead)

Faster would be to iterate once over the network and remove links with hrr > cutoff.

[mutwil]

ATTED uses a very similar rank metric (but not identical), and they set cutoff of 100, so we could theoretically get away with 100 just by citing it.
I observed that the performance of the network peaks around HRR 300 for multiple species, but there, network density is too high! We could argue that 100 is a good compromise between performance and density.

[proost]

Did you penalize the performance-score for increasing the neighborhoods size ?

[mutwil]

No. After collecting the genes in the neighborhood, they are treated equally regardless of being in 1st, 2nd, 3rd...

[mutwil]

But as discussed, let's stick to direct (i.e. 1st) neighborhoods, as this makes our lives so much easier.