Sorry, I can not understand your reply very clearly.
How to compute the number of unique sites ?
Can you give me a simply example or do a simply analyse using one data?
Thanks very much.
                                       Jian Zhang


On 7/7/07, Sarah Goslee <sarah.goslee@gmail.com> wrote:
>
> It should be the number of unique sites. In this case, the number of
> unique columns in the data frame. See ?unique. (Interestingly,
> convention is usually that species are columns and sites are rows.)
>
> For your sample data you only see 10 of the 2^17 possible combinations
> of 17 species (not 2n).
>
> Sarah
>
> On 7/7/07, Zhang Jian <jzhang1982@gmail.com> wrote:
> > I want to analyze the co-occurrence of some species. In some papers, the
> > authors said that the index"the number of species combinations (COMBO)"
> is a
> > good index. I try to calculate the index by R language. But I can not
> get
> > the right value. I think that I do not understand the concept of the
> index
> > because my english is not good.
> >
> > The concept:
> > *The number of species combinations   *This index scans the columns of
> the
> > presence-absence matrix and keeps track of the number of unique species
> > combinations that are represented in different sites. For an assemblage
> of n
> > species, there are 2n possible species combinations, including the
> > combination of no species being present (Pielou and Pielou 1968). In
> most
> > real matrices, the number of sites (= columns) is usually substantially
> less
> > than 2n, which places an upper bound on the number of species
> combinations
> > that can be found in both the observed and the simulated matrices.
> >
> > Presence-absence Data (Each row represents different species and each
> column
> > represents a different site. A "1" indicates a species is present at a
> > particular site, and a "0" indicates that a species is absent from a
> > particular site):
> > Species Cuba Hispaniola Jamaica Puerto_Rico Guadeloupe Martinique
> Dominica
> > St._Lucia Barbados St._Vincent Grenada Antigua St._Croix Grand_Cayman
> > St._Kitts Barbuda Montserrat St._Martin St._Thomas
> > Carduelis_dominicensis 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> > Loxia_leucoptera 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> > Volatinia_jacarina 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
> > Sporophila_nigricollis 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
> > Melopyrrha_nigra 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
> > Loxigilla_portoricensis 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> > Loxigilla_violacea 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> > Loxigilla_noxis 0 0 0 0 1 1 1 1 1 1 1 1 0 0 1 1 1 1 0
> > Melanospiza_richardsoni 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
> > Tiara_olivacea 1 1 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
> > Tiara_bicolor 0 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1
> > Tiara_canora 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> > Loxipasser_anoxanthus 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> > Saltator_albicollis 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0
> > Torreornis_inexpectata 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> > Ammodramus_savannarum 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> > Zonotrichia_capensis 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> >
>
> --
> Sarah Goslee
> http://www.functionaldiversity.org
>

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