I am trying to apply a permuation-based MANOVA (Anderson 2001) to a set of
morphological data from three ecomorphs of fish reared under two different
conditions and measured at two points during ontogeny. I will supply a
distance matrix based on Procrustes distances calculated outside of vegan.

I have not found an example of a design such as this for adonis. However, I
have designed my factors for this test which hopefully will work.

This design is just to understand the principals of this test, my real data
set is comprised of over a thousand specimens. Column 1 represents the
ecomorph, column 2 respresents diet, column 3 represents family (nested in
ecomorph). This example would have 9 individuals, but being that measures
are repeated

1 1 5
1 2 5
1 2 6
2 1 7
2 2 7
2 2 8
3 1 9
3 2 9
3 1 10
1 1  5
1 2  5
1 2  6
2 1  7
2 2  7
2 2  8
3 1  9
3 2  9
3 1 10

my factor matrix is called Z, so the call to adonis is

adonis (Z~ecomorph+diet+family(ecomorph) +
ecomorph*diet+ecomorph*family(ecomorph)+ecomorph*diet*family(ecomorph), data
=b, permuations =999)

However, I'm not confident this is the correct way as I would like time to
be incorporated as a factor. I have seen the strata command, would this
allow me to incorporate time by including a column for time in my matrix?
I'm guessing this is how it would go?

adonis (Z~ecomorph+diet+family(ecomorph) +
ecomorph*diet+ecomorph*family(ecomorph)+ecomorph*diet*family(ecomorph),
strata =b [,"time"], permuations =999)

Thank you in advance for any help you may provide. If you have further
questions please ask.

best,


Kevin Parsons

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