Dear all
I have used permutational multivariate analysis of variance (adonis in package
vegan) based on Bray-Curtis distances to assess the signifance of carbon,
nitrogen and more complex nutrient amendments on soil microbial community
structure (microbial fatty acids).
I have identified signifant effects of nutrients and would like to know how to
identify the fatty acids (microbial markers) that are associated with these
differences. So far I have used Pierre Legrendre's "Dufrene-Legendre Indicator
Species Analysis" duleg in package 'labdsv' to do this (Calculates the
indicator value (fidelity and relative abundance) of species in
clusters or types). However, I am not familiar with the implementation of this
method and am concerned about the relevance of the output as the 'indicator
species' are not probably not based on Bray-Curtis distances.
Is there another way to identify fatty acids contributing to differences
between my nutrient amendment groups? For example, the output of the
permutational multivariate analysis of variance (adonis) has the following
attributes:
aov.tab 6 data.frame list
call 2 -none- call
coefficients 74 -none- numeric
coef.sites 28 -none- numeric
f.perms 999 -none- numeric
model.matrix 28 -none- numeric
terms 3 terms call
Can I use the coefficients to select fatty acids that contribute to the
differences between treatment?
Thanks
Paul
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