Dear all

we'd like to optimize rarefactions in a species group with imperfect identifications.

To illustrate, let's say we have evidence for

Species A
Species B
Species_aggregate C/D

in a sample. Despite only having two species identified, and an additional species complex (where we are not sure if it is C or D) we actually can be sure to have three species detected.

However, if we have a list

Species A
Species B
Species_aggregate B/C

we can only be certain of two species, as species B, already counted, could also be present in the complex of B and C.

I'm aware, that I would need a matrix somewhere to check if n is contained in k, e.g.

(column contains row)

 \ n A  B  C  D
k \
A    1  0  0  0
B    0  1  0  0
C    0  0  1  0
D    0  0  0  1
CD   0  0  1  1
BC   0  1  1  0

We would like to use this improved counting in randomized sample extractions (e.g. in rarefy or specaccum in package vegan), thus search for a function that could be called.

Does anybody know of such a functionality in any of the ecological packages? Vegan does not seem to be able to account for such mechanisms...

Any tips are appreciated!

Regards

Martin


      Dr. Martin K. Obrist                    ^v^
                                                                     ^v^
   Swiss Federal Research Institute WSL
   Biodiversity and Conservation Biology
   CH-8903 Birmensdorf, Switzerland                                    
   MG D 52        phone: ++41 44 739 24 66        fax: ++41 44 739 22 15 
   E- mailto:martin.obrist@wsl.ch   WWW http://www.wsl.ch/fe/biodiversitaet/




	[[alternative HTML version deleted]]

