I am looking at various alpha diversity metrics using
qiime longitudinal volatility. The example used is shannon diversity and the metric to use is obviously
shannon. But when it comes to using the
evenness metric, it is unclear that the
--p-metric should actually be
pielou_e which is not intuitive. I figured this out by using
qiime tools extract to check the title of the vector. This should be clarified in the
--help docs and/or tutorial. It would also be nice to have some beta diversity examples. I was having trouble with that (possibly confusion with the metric as well) although I haven’t looked too much into it. That’s just a ‘nice to have’ I figured I’d mention too. Thank you!
Edit: to expand, I used
qiime diversity core-metrics-phylogenetic so the evenness vector is a standard output. If I created the evenness vector on my own, I might have seen the ‘pielou_e’ metric but I’m guessing most users will produce the core-metrics.