How to perform a pairwise adonis test with unifrac distance?

[Stabilo12]

I would like to perform a pairwise adonis test with phyloseq object and a unifrac distance matrix but I don't know how?

Example:
data(GlobalPatterns)
metadata <- as(sample_data(GlobalPatterns), "data.frame")
dist.uf <- phyloseq::distance(GlobalPatterns, method = "unifrac")
ps.adonis <- adonis(dist.uf ~ SampleType, data = metadata, perm=9999)

SampleType 8 3.4957 0.43696 4.2046 0.66427 1e-04 ***

The adonis test showed that SampleType does explain part of the variation, but I want to know which Samples are different from each other.. With betadisper paired test is easy to perform, but I don't know how to do this within the adonis function with a uf distance matrix?

ps.disper <- betadisper(dist.uf, metadata$SampleType)
permutest(ps.disper, pair=TRUE)

Response: Distances
Df Sum Sq Mean Sq F N.Perm Pr(>F)
Groups 8 0.042397 0.0052996 2.9572 999 0.027 *
Residuals 17 0.030466 0.0017921

Signif. codes: 0 ‘’ 0.001 ‘’ 0.01 ‘’ 0.05 ‘.’ 0.1 ‘ ’ 1

Pairwise comparisons:

The pairwise.adonis function does only include Bray-curtis and Jaccard distance..

Thank you in advance!

[antagomir]

As far as I can see, none of the above-mentioned functions are maintaiend in the microbiome R pkg. This functionality and examples would be useful, though, but not currently implemented. We could welcome & incorporate new examples on this in the tutorial

[Stabilo12]

Thank for your reaction, it would be great if it could be implemented. I think many people would need such a function, right? Or are you currently only testing between two groups (without correction for multiple testing)? (Sorry, probably this is not the place for those questions, but i dont know were to ask otherwise)

[antagomir]

I agree, this would be useful. If you could afford the time to prepare an example, we could add it in the tutorial? Otherwise, I'll leave this open for now and we could return to this later when time allows to expand the tutorials.