How to accept the R^2 (R-Square) when running PERMANOVA or Krushkal-Wallis test?

#1

Uh…I just want to know that how to get the R^2 when calculating the p-values by PERMANOVA or Krushkal-Wallis test?
It confused me for several days. Thanks!

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(Colin Brislawn) #2

Great question. I’m not sure if the R-squared values are reported by the Qiime 2 plugins for these tests.

I’m pretty sure the adonis test can report R-squared values. Have you considered using that instead of PERMANOVA?
https://docs.qiime2.org/2019.1/plugins/available/diversity/adonis/

Colin

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#3

Thank you so much.
I reported R-squared values successfully!
However, in my opinion, this plugin (qiime diversity adonis) is called PERMANOVA.
It’s right?

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(Nicholas Bokulich) #4

This plugin is called diversity
This action is called adonis
vegan-R adonis is another implementation of the permanova test
permanova is also used in qiime diversity beta-group-significance, so when @colinbrislawn says:

He most likely means try adonis instead of beta-group-significance (which does not report R2 values).

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#5

Thank so much! I got it.:100:

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