[R] adonis help - (non-parametric (permutational) manova)

stephen sefick ssefick at gmail.com
Tue May 12 21:53:21 CEST 2009

I am trying to apply this technique (M.J Anderson 2001) to a dataset
of aquatic insect abundances.  There is a sample in the unrestored and
restored segement of a stream for every time period.  I would like to
compare the centroids of the distance matrices for the treatments up
(unrestored) and dn (restored) to see if there is a difference in
insect communities between the treatments.  I will not include the raw
data in this posting as it is large for posting to the list; however,
I would be happy to provide it off list if it would make this easier
(and reproducible).

my environmental matrix (or factor matrix I am not sure of the
terminology) is set up like this:

                date    site
0104 dn   0104   dn
0106 dn   0106   dn
0203 dn   0203   dn
0503 dn   0503   dn
0704 dn   0704   dn
0803 dn   0803   dn
0804 dn   0804   dn
0805 dn   0805   dn
1005 dn   1005   dn
1102 dn   1102   dn
1204 dn   1204   dn
0104 up   0104   up
0106 up   0106   up
0203 up   0203   up
0503 up   0503   up
0704 up   0704   up
0803 up   0803   up
0804 up   0804   up
0805 up   0805   up
1005 up   1005   up
1102 up   1102   up
1204 up   1204   up

my site x species matrix is called a, so here is the call to adonis:

adonis(a~site, data=b, strata=b[,"date"] ,Permutations=999)

Is this the correct way of testing the null hypothesis that :

There is no difference in community structure between treatments.

Thank you very much in advance, and anything that you need to make
this easier please don't hessitate to ask.


Stephen Sefick

Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods.  We are mammals, and have not exhausted the
annoying little problems of being mammals.

								-K. Mullis

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