How to set --p-max-depth for alpha rarefaction?

Hello @DannyBoi97,
Great Question and Welcome to the forum!
This is a hard question because there is no optimum value. It is all just what you think is best for your data. I think that Colin gave a really great answer on this post. They explained how they choose their max-depth.

I also would suggest looking at the description of the Parkinson's mouse tutorial . It really helped me understand.

Hope that helps!

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