[R-sig-eco] Testing difference between diversity indices with vegan::oecosimu

[Gavin Simpson]

On Thu, 2012-04-26 at 00:36 -0400, David Valentim Dias wrote:
> Hello Cichini,
> 
> I cannot help with your code but seems like you have a silly hypothesis.
> Think about it: Probability of two communities to be identical?
> You need to restate it in some more useful way. We already know most things
> are different but with what magnitude? Which factors are causing these
> changes? How these changes matter from the environment and us?

Surely if we knew the two things were different there would be no need
to test if they were? Most statistics assumes a Null model as we can say
something specific about the magnitude of the difference (it is zero)
and we can then see if the observations are consistent with that model.

I agree that subsequent analysis is required to understand why there are
differences, but we still need a mechanism to say, given the data
collected and the error processes, are the diversities of these two
"samples" the same?

G

> 2012/4/25 Chris Howden <chris at trickysolutions.com.au>
> 
> > Why not try some type of ANOVA style glm?
> >
> > Chris Howden
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> > On 26/04/2012, at 7:19, Kay Cichini <kay.cichini at gmail.com> wrote:
> >
> > > Hello all,
> > >
> > > I'd like to test if total diversity differs between two communities. For
> > > each community several samples were taken and abundances collapsed over
> > > groups to compute total diversity for each group. I tried to use
> > > vegan::oecosimu to test non-randomness of my statisitc (difference in
> > > Simpson-Diversity indices of collapsed abundances) - however, I am not
> > > quite sure if I oversee posssible pitfalls:
> > >
> > > library(vegan)
> > > data(dune)
> > >
> > > # a grouping variable:
> > > gr <- gl(2, nrow(dune)/2)
> > >
> > > divdiff <- function(x) abs(diversity(colSums(x[gr == "1", ]), "simp") -
> > >                           diversity(colSums(x[gr == "2", ]), "simp"))
> > > # testing function:
> > > divdiff(dune)
> > >
> > > oecosimu(dune, divdiff, "r2dtable", nsimul = 1999)
> > > # oecosimu with 1999 simulations
> > > # simulation method r2dtable
> > > # alternative hypothesis: true mean is not equal to the statistic
> > > #           statistic        z     2.5%      50% 97.5% Pr(sim.)
> > > # statistic   0.00275 -0.20996  0.00013  0.00280  0.01     0.98
> > >
> > >    [[alternative HTML version deleted]]
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