[R-sig-eco] interpreting adonis results

[Gavin Simpson]

On Thu, 2011-11-17 at 10:01 +0100, gabriel singer wrote:
> ... dangerous wording, there could in fact be a location effect of 
> 'location' and/or a dispersion effect of 'location'.

Well of course, but I was assuming that the assumptions of the test were
met! ;-)

> Gian, I suggest you add a test of a dispersion effect using the function 
> betadisper(), then you know a bit more about the type of effect.

Indeed, and as the author of that function I too would suggest that the
homogeneity assumption be tested.

G

> gabriel
> 
> On 11/16/11 11:02 PM, Gavin Simpson wrote:
> > On Wed, 2011-11-16 at 03:43 +0100, Gian Maria Niccolò 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.
> >>
> >> 	[[alternative HTML version deleted]]
> >>
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> >> R-sig-ecology at r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> 

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