Could you please help me to understand what is the difference between Permutational multivariate analysis of variance (PERMANOVA,adonis) and Variance partitioning (permutest).

I understood that permutest is used to confirm the PERMANOVA result that differences in PERMANOVA is not due to dispersion.

BC <- phyloseq::distance(phyloseq_prop, "bray")
pmv =adonis(BC ~Season*Region, as(sample_data(physeqN3), "data.frame"),permutations = 5000)

adonis(formula = BC ~ Season * Region, data = as(sample_data(physeqN3),      "data.frame"), permutations = 5000) 

Permutation: free
Number of permutations: 5000

Terms added sequenti         
Total         99   19.8578                 1.00000 ally (first to last)

              Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)    
Season         1    1.8586 1.85862  12.036 0.09360  2e-04 ***
Region         1    2.4218 2.42183  15.682 0.12196  2e-04 ***
Season:Region  1    0.7522 0.75222   4.871 0.03788  2e-04 ***
Residuals     96   14.8251 0.15443         0.74656  

Many thanks

  • $\begingroup$ Fair question, but I do think it would use some references and reasoning why you think they should (not) be the same thing. Also could be better suited for cross-validated (the statistical Stack Exchange web). $\endgroup$ – Kamil S Jaron Jan 15 at 14:45
  • $\begingroup$ Thanks, I understand that permutest can be done to validate the permanova (adonis) result, and if permutest result is not significant then this means we can be more confident that our adonis result is a real result, and not due to differences in group dispersions. $\endgroup$ – bioinfonext Jan 18 at 11:40
  • 1
    $\begingroup$ Great, I recommend to edit the question. Also, your comment kind of sound you know the answer already. Is you just need a confirmation, you could really make it easier for someone to answer if you provide relevant links. $\endgroup$ – Kamil S Jaron Jan 18 at 11:56
  • $\begingroup$ This is done; thanks! $\endgroup$ – bioinfonext Jan 18 at 22:18

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