CODEWITHSUNDEEP
rvegan
outside842
outside842

Reputation: 51

Options for multiple comparisons in vegan::simper

I am using the adonis function in the vegan package to determine differences in dissimilarities in a community (PCB congeners) between several different factors. I also have decided to use the simper function to assess which community members contributed most to the observed differences. Is there a way for to include multiple factors in the simper function? I ran the adonis model shown below successfully, but the corresponding code for the simper function doesn't work. Many thanks.

# Adonis model
pcbtest3 <- adonis(pcbcong ~ FISH_CLASS+REACH+BASIN,
                   data=pcbcov,
                   method="bray",
                   permutations=999
                   )
# pcbcong=matrix of community dissimilarities
# FISH_CLASS,REACH, BASIN are factors
# Simper
simp <- with(pcbcov, simper(pcbcong,(FISH_CLASS, BASIN, REACH)))

Upvotes: 2

Views: 1936

Answers (1)

EDi
EDi

Reputation: 13280

simper can be used only with one grouping variable.

A workaround would be to use interaction() to create a new grouping variable from all three factors.

Interpretation of this will be awkward (depending how many factor levels you have) and I don't know if that`s meaningful at all - so be careful.

Upvotes: 1

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