Dear Jari,

First thank you very much for your explanations. Indeed the confidence
funnel I mentioned is plotted with Delta+ and species values as you argued,
and not with Delta*. That was what I would mean but maybe I did a mistake
in writing, very sorry. I will try to plot the funnel from myself.
Lastly, I didn't read about the expected values calculation, maybe you can
give some brief clarification on how the work calculates these values.
Thanks a lot,

Gian



2012/2/16 Jari Oksanen <jari.oksanen@oulu.fi>

>
> On 16/02/2012, at 18:39 PM, Gian Maria Niccolò Benucci wrote:
>
> > Hi everybody,
> >
> > I am here for asking some kind of help about taxonimic diversity and
> > distinctness indices, from
> > taxondive()<http://127.0.0.1:25979/library/vegan/html/taxondive.html
> >function
> > in vegan.
> > The function produced also expected values for Delta, Dela* and Delta +
> > indices but no metodology about how these expected data are calculed is
> > reported. How are they calculated?
>
> Dear Giain Maria Niccolò Benucci,
>
> The ?taxondive help page reads:
>
>     Clarke & Warwick (1998, 2001) suggested several alternative
>     indices of taxonomic diversity or distinctness. Two basic indices
>     are called taxonomic diversity (Delta) and distinctness (Delta^*):
>
>             Delta = (sum sum_{i<j} omega_{ij} x_i x_j)/(n (n-1) / 2)
>       Delta^* = (sum sum_{i<j} omega_{ij} x_i x_j)/(sum sum_{i<j} x_i x_j)
>
>     The equations give the index value for a single site, and
>     summation goes over species i and j. Here omega are taxonomic
>     distances among taxa, and x are species abundances, and n is the
>     total abundance for a site.  With presence/absence data both
>     indices reduce to the same index Delta^+
>
> The intention of this passage was to give equations for Delta and Delta^*,
> and explanation of Delta^+ (and the pdf version has nicer formatting of
> equations). If this is not enough to explain the methodology of
> calculation, please consult the original publications referred to in the
> help page and the R code of taxondive().
>
> > According Clarke and Warwick (1998) it is also possible to plot a
> > confidence funnel of the result with plot.taxondive, where Delta * values
> > are plotted against corresponding number of species at each site.
>
> It is a long time since I read these papers, but I think C&W suggested
> plotting Delta^+ values (not Delta^*), and that plot is produced by plot()
> command for taxondive() results in vegan, like displayed in the examples of
> the help page of taxondive. However, the labels cannot be displayed with
> the standard plot() command: you have to do that yourself. Look at the
> model in vegan:::plot.taxondive to see how simple it is.
>
> Cheers, Jari Oksanen
>
>
> > I argued
> > that I only 15 points, instead of 24 that is the overall sample number,
> > becasue there is an overplotting...do is it possible?
> > Moreover, there is the possibility to plot in the funnel diagram the name
> > of the samples?
> > Thank you to everyone,
> > G.
> >
> > --
> > Gian Maria Niccolò Benucci, Ph.D.
> > Department of Applied Biology
> > University of Perugia
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > R-sig-ecology@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>
> --
> Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
> jari.oksanen@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa
>
>
>

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