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

[Chris Howden]

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
>
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