core-metrics-phylo
core-metrics-phylogenetic produces all of the non-phylogenetic metrics from core-metrics with some phylo metrics thrown in for spice (faith’s pd, weighted, and unweighted unifrac). Non-phylo metrics included:
Alpha Diversity:
- Shannon’s diversity index
- Observed Features
- Pielou’s evenness
Beta Diversity:
- Jaccard distance
- Bray-Curtis distance
Bray-Curtis
Though bray_curtis doesn’t currently accept relative frequency (RF) data, I don’t think passing relative frequency data breaks any assumptions of Bray Curtis, @nathaniel_hubert. McMurdie & Holmes used RF with Bray Curtis with no issues, and I didn’t see any reason not to implement it when I was tinkering with the formula.
If I remember correctly, expediency was the main reason Bray Curtis doesn’t accept RF data yet - there were some unexpected test failures with RF data and that method, and we opted to ship what we had rather than delaying release of other methods in favor of that feature.
I’d love to see this enhancement made available in q2-diversity-lib, and have opened an issue to track progress. This isn’t currently a high priority for me, but I would be super happy to lend a hand if it’s something you’re interested in working on!