Sarah Lutteropp

This issue is going into that direction: https://github.com/lutteropp/NetRAX/issues/33 There we have an example with a 4-taxon 1-reticulation network. Both displayed trees have the same topology, only one branch length can...

One tricky thing: There can be displayed trees for which the current branch we want to optimize is inactive. What happens to their sumtables? Since here we care about derivatives,...

I made a mistake in the partition loglikelihood formulas above. New image coming soon.

Do we really need the correct derivative of phylogenetic network likelihood? It is apparently pretty ugly: https://en.wikipedia.org/wiki/Product_rule#Product_of_more_than_two_factors

Now I did the Math correctly, and it does not look good for Newton-Raphson on phylogenetic networks :-( We can still do it as it is known to converge quicker,...

Or maybe we can still do something here? I need to dig into how the Math is done for derivative of tree likelihood. After all, there is a product involved...

Whichever trick is used for trees there should also work for the networks. Because with the approach I used here, I get into the same problem if there is only...

Okay... now I understand the text in Alexeys thesis (https://cme.h-its.org/exelixis/pubs/dissAlexey.pdf, page 26). What this sumtable gives us is fast computation of: - L(b) - L'(b) - L''(b) My problem was...

My confusion originated from this: For trees, we end up getting and using these: - (loglL(T))' -> first derivative of loglikelihood of tree T - (logL(T))'' -> second derivative of...

I got it all together now. The main difference (compared to the tree case) is that in order to compute network loglikelihood derivatives, we also need to use the sumtables...