Re: Including No-Species Samples for CCA?

From: Stéphane Dray (dray@biomserv.univ-lyon1.fr)
Date: Fri Feb 24 2006 - 19:16:13 MET

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    Hi,
    if you want, you can include these samples. But, this has no effect on
    the analysis :

    > data(doubs)
    > cca1=cca(doubs$poi,doubs$mil,scannf=F,nf=2)
    > apply(doubs$poi,1,sum)
     1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
    25 26
     3 12 16 21 34 21 16 0 14 14 11 18 19 28 33 40 44 42 46 56 62 72 4 15
    11 43
    27 28 29 30
    63 70 87 89

    There is no fish in the 8th site. And this site has no effect and is
    positionned at the origin of the biplot :

    > cca1$li[8,]
      Axis1 Axis2
    8 0 0

    If you remove this site, results do not change:

    > cca2=cca(doubs$poi[-8,],doubs$mil[-8,],scannf=F,nf=2)
    > cor(cca1$eig,cca2$eig)
    [1] 1
    > cor(cca1$li[-8,],cca2$li)
              Axis1 Axis2
    Axis1 1.0000000 0.2032862
    Axis2 0.2032862 1.0000000

    Cheers,

    Kathleen Beyer wrote:

    >Hello Everyone,
    >maybe you could help?
    >
    >I want to run a CCA to examine the habitat use in fish (of different species/ages).
    >For the analysis do I include samples without fish?
    >
    >Thanks very much for your help.
    >
    >Regards,
    >Kathleen Beyer.
    >
    >
    >
    > 

    -- 
Stéphane DRAY (dray@biomserv.univ-lyon1.fr )
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - Lyon I
43, Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
Tel: 33 4 72 43 27 57       Fax: 33 4 72 43 13 88
http://www.steph280.freesurf.fr/

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