Is it possible to modify the log base used for calculating the Shannon index within the alpha diversity plugin? We typically use Past to calculate alpha diversity metrics - uses natural log for Shannon index. I'd like to change the base 2 to base e when running the following:
qiime diversity alpha
--i-table rarefied_table.qza
--p-metric 'shannon'
--o-alpha-diversity ./shannon.qza
Thanks!
There is not a way to do this within Qiime2 right now.
However, the scikit-bio function that Qiime2 uses does support this, which means that this is functionally we could add to the Qiime2 plugin!
We have discuss the base of Shannon's log before, and I think this sounds like a good feature to add. 
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.