[R-sig-eco] relative compositional dissimilarity among sites against a continuous variable

[Jari Oksanen]

Burak,

I just wonder how this turned out to being an adonis() case. Your original
idea was quite different: you asked about mean dissimilarities of
observations. Some messages suggested you how to get it. Then you asked
would analysing these mean dissimilarities be the same as NPMANOVA, and got
an answer that you cannot use mean dissimilarities for this, but you could
use adonis(). So what do you actually want to achieve?

Here a simple and extreme example of symmetric dissimilarity matrix of four
observations:
d =
0011
0011
1100
1100

That is, there are two blocks of observations: first two are an identical
set, last two are another identical set (dissimilarities = 0), and these
sets have nothing in common (dissimilarities = 1), and diagonal is = 0. All
these observations have the same row means, but adonis(d ~ c(0,0,1,1)) finds
that these sets are as different as you can get. If you want to analyse the
mean dissimilarities (that are identical above), then vegan function
betadisper() is a tool. In general, adonis() studies differences in
multivariate location, betadisper() differences in multivariate dispersion
(approximately similar to mean dissimilarity). However, you should be
careful in interpreting adonis(): although it is used to study multivariate
location, it is sensitive to other differences in the data, such as
differences in multivariate dispersion.

There are many things you can do in vegan, but that does not mean you should
do them.

We do not know what was your problem, so we have no idea if you had a
meaningful analysis.

Cheers, Jari Oksanen