Does the skbio PERMANOVA function have a pairwise option like in qiime2?

General Discussion
1

Hi all,

I know how to run the basic skbio permanova code in python:

import skbio as skb
skperm=skb.stats.distance.permanova(dm, host_md_test, column='Host1', permutations=999)

But I only get stats on the overall test. Is there a way to show the pairwise comparisons like in qiime2?
I am trying to keep this in python because I want to run a for loop on many permanovas.
My other option will be to go into R and use adonis's pairwise option.
Any info would be appreciated!!
Sam

2

Hi,
As far as I know there is no pairwise mode in skbio permanova implementation.
Workaround will be to filter the matrix in the loop to simulate pairwise comparisons and then adjust it for multiple comparisons, but if R is not an issue then adonis can be used in R.

2 Likes
3

@timanix appreciate the confirmation. Thanks!