Replying to
@DrPen@mastodon.social
@DrPen Looks interesting. But what's it going to catch that Google Scholar doesn't already have? Is it best seen as a backup in case GS ever goes down?
Remote
Rob Noble
@robjohnnoble@ecoevo.social
Senior Lecturer (≡ associate professor) in applied mathematics at City St George's, University of London, investigating the evolution and ecology of cancer. Dad of two small kids.
307
Followers
324
Following
6
Posts
Joined November 03, 2022
Website:
Twitter:
Bluesky:
@robjohnnoble.bsky.social
Official profile:
Posts
Replying to
@ryneches@ecoevo.social
@ryneches@ecoevo.social No, I hadn't considered that. And I'd love to discuss further. I'll drop you an email.
Replying to
@plektix@mathstodon.xyz
@plektix@mathstodon.xyz For the entropy/diversity indices, yes, that's a nice way to put it (but the evenness denominators depend only on non-zero-sized branches). I hope we convey that this is just a tweak of prior work by you and others. Our more original contribution is in defining evenness indices (including tree balance indices) that account for branch lengths and node sizes and are consistent with the entropy/diversity indices.
Replying to
@robjohnnoble@ecoevo.social
As explained in the preprint, we're building here on fifty years of pioneering work by Mark Hill, Daniel Faith, Anne Chao, Chun Huo Chiu, Lou Jost, Benjamin Allen, and many others. Although I'm convinced that our indices should supersede prior approaches, I very much doubt they'll be the last word.
Replying to
@robjohnnoble@ecoevo.social
Unlike currently popular phylogenetic diversity, phylogenetic entropy, and tree balance indices, our definitions assign interpretable values to all rooted trees and enable meaningful comparison of any pair of trees.
For example, this preprint figure compares the shapes of trees representing the evolution of HIV and of Uralic languages. If we ignore branch lengths then the trees are indistinguishable (a-d). But our new indices accounting for branch lengths capture important differences (e-h).
V2 of my preprint with PhD student Kim Verity is now online: https://www.biorxiv.org/content/10.1101/2023.07.17.549219v2
tldr: If you want to assess the shape (e.g. balance, diversity) of a rooted tree then generally you're better off using our new indices than Sackin's index, phylogenetic entropy, etc.
The article is long mainly because we provide lots of examples. I plan soon to write a shorter #mathonco blog post explaining why these indices are better than prior approaches. Meanwhile, here's a poster.