interpreting adonis results

On Wed, 2011-11-16 at 03:43 +0100, Gian Maria Niccol? Benucci wrote:

Hi all,

I had 84 samples collected in 7 different sites.
In each sample were individuated the different fungal species and recorded.
I would test if exist a real difference between the sites and if exist a
sort of site effect that structure the fungal communities...
Then, I did adonis test

adonis(community.sq ~ location, data=env.table, permutations=999)

Call:
adonis(formula = community.sq ~ location, data = env.table, permutations =
999)

           Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)
location   6    12.593 2.09886  6.8867 0.34922  0.001 ***
Residuals 77    23.467 0.30477         0.65078
Total     83    36.060                 1.00000
---
Signif. codes:  0 *** 0.001 ** 0.01 * 0.05 . 0.1   1



The significance is  R2=0.349 at P=0.001
Can I assure that exist a strong site effect in structuring the communities
in each site?

Depends. The test is one of no effect of `location`. You have found
evidence against this hypothesis and thus could reject this hypothesis,
instead accepting the alternative hypothesis that there is an effect of
`location`. As to the strength of this effect? ~35% of the sums of
squares can be explained by `location`. Substantially more of the
variance remains unexplained. As I know nothing about your subject area,
I am unable to comment further on the strength of the relationship.

Seeing as many ecologists whose work I read would say an effect is
significant if the p-value was>= 0.05. Not that I subscribe to this way
or working, but by that criterion, you have identified a significant
`location` effect.

HTH

G

Thanks for helping,

G.

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