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.obr...@wsl.ch WWW http://www.wsl.ch/fe/biodiversitaet/
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