Gavin,
May I ask you if you have tutorial for the betadisper() function?
Maybe I did a mistake during the identification of the groups of samples...
The I tried to use the betadisper( ) function R gave me an error...
*******************************************************
> groups <- factor(c(rep(1,12),rep(13,24),
rep(25,36),rep(37,48),rep(49,60),rep(61,72),rep(73,84),+
labels=c("SIG","BA","SIMa","SIMb","SZV","BM","BRE")))
> betadiv <- betadisper(dist1, groups)
Error: (subscript) logical subscript too long
*******************************************************
I can't understand what is wrong...
Thank you help and patience,
Gian
2011/11/17 Gavin Simpson <[email protected]>
> 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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> > >> [email protected]
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> >
>
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> Dr. Gavin Simpson [t] +44 (0)20 7679 0522
> ECRC, UCL Geography, [f] +44 (0)20 7679 0565
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