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lutteropp / NetRAX

Phylogenetic Network Inference without ILS
GNU General Public License v3.0
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Should we exclude datasets where the simulated network has worse BIC than the raxml-ng best tree? #40

Open lutteropp opened 3 years ago

lutteropp commented 3 years ago

It sometimes happens that the simulated network is rejected by BIC, in favor of the best tree inferred by raxml-ng. What should we do with these datasets?

A) Include them in our experiments, wasting hours on NetRAX calls that will infer a tree anyway. B) Re-simulate the dataset if this happens. Do not run NetRAX on it. Keep the problematic dataset in an extra folder (to use for post-analysis of simulation parameters). C) Re-simulate the dataset if this happens. Do not run NetRAX on it. Discard the problematic dataset.

I vote for B. (Or C, if we are ok with "well, likely it was an ultrametric network with a fake reticulation again")

lutteropp commented 3 years ago

(reopened because this still happens from time to time. It was not just due to some bug)

lutteropp commented 3 years ago

Or we can go with A, add writing to a logfile to NetRAX, and then post-evaluate whether NetRAX did encounter the correct network and just discarded it due to BIC issues.

stamatak commented 3 years ago

That (A) sounds like a good idea, but I wouldn't call it BIC issues, maybe just too weak signal/not enough data to infer the network, as, if I remember correctly, you said that with longer MSAs it's easier to infer the network correctly.

On 18.01.21 15:26, Sarah Lutteropp wrote:

Or we can go with A, add writing to a logfile to NetRAX, and then post-evaluate whether NetRAX did encounter the correct network and just discarded it due to BIC issues.

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