[R-sig-eco] Distinctiveness and contribdiv( )

Peter Solymos solymos at ualberta.ca
Wed Dec 1 20:56:30 CET 2010


Burak,

you can use contribdiv(x, scaled = TRUE) which in turn gives you C
values that are the relative contribution of diversity partitions. "A
positive value means that the contribution of a specific unit to
within-unit, among-unit or total species richness of the region is
higher than the average of all units, whereas a negative value
indicates a below average contribution." (quote from Lu et al,'s paper
cited in the ?contribdiv page). For further details and
interpretation, you should consult the paper:

Lu, H. P., Wagner, H. H. and Chen, X. Y. 2007. A contribution
diversity approach to evaluate species diversity. Basic and Applied
Ecology, 8, 1–12.

Cheers,

Peter

Péter Sólymos
Alberta Biodiversity Monitoring Institute
and Boreal Avian Modelling project
Department of Biological Sciences
CW 405, Biological Sciences Bldg
University of Alberta
Edmonton, Alberta, T6G 2E9, Canada
Phone: 780.492.8534
Fax: 780.492.7635
email <- paste("solymos", "ualberta.ca", sep = "@")



On Wed, Dec 1, 2010 at 12:34 PM, Pekin, Burak K <bpekin at purdue.edu> wrote:
> Yes Peter, I am looking for something that really conveys irreplaceability, in other words, the relative 'endemism' of species within a site. So, a site that contains species which are found only in a few other sites within a region is considered more 'irreplaceable' or 'distinct' than a site that contains more 'generalized' species which are found in many sites within the region, irrespective of the total number of species found within them. Does the beta component of contribdiv ( ) do this, or does it also take into account the total number of species within the sites?
> -Burak
>
> -----Original Message-----
> From: psolymos at gmail.com [mailto:psolymos at gmail.com] On Behalf Of Peter Solymos
> Sent: Wednesday, December 01, 2010 1:36 PM
> To: Pekin, Burak K
> Cc: r-sig-ecology at r-project.org
> Subject: Re: [R-sig-eco] Distinctiveness and contribdiv( )
>
> Burak,
> Not exactly clear what you want, but Lu et al. 2007 describes the differentiation coefficient D that is the sum(beta)/sum(gamma) and can be obtained as attributes(contribdiv(x))$diff.coef . Note also that there is a link between diversity partitions and distance indices so you might as well use the components from the contribution diversity approach. Or is it something like irreplaceability in the reserve selection literature you need?
> Cheers,
> Peter
>
> Péter Sólymos
> Alberta Biodiversity Monitoring Institute and Boreal Avian Modelling project Department of Biological Sciences CW 405, Biological Sciences Bldg University of Alberta Edmonton, Alberta, T6G 2E9, Canada
> Phone: 780.492.8534
> Fax: 780.492.7635
> email <- paste("solymos", "ualberta.ca", sep = "@")
>
>
>
> On Wed, Dec 1, 2010 at 11:17 AM, Pekin, Burak K <bpekin at purdue.edu> wrote:
>> Hello, Is there a diversity index similar to the 'contribution diversity approach' contribdiv()in vegan that reflects only  the compositional 'distinctiveness' of a site within a region. contribdiv()combines 'distinctiveness' with a within-site diversity measure such as richness, I on the other hand am looking for an index that measures only the relative number of species within a site that are 'distinct' or 'unique' within a region.
>>
>> Cheers,
>> Burak
>>
>>
>>        [[alternative HTML version deleted]]
>>
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