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.