[R-sig-eco] taxonomic diversity and distinctness - taxondive() in vegan package

[Jari Oksanen]

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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-- 
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
jari.oksanen at oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa