**Previous message:**Frank Dziock: "row weights in co-inertia"**In reply to:**Frank Dziock: "row weights in co-inertia"**Next in thread:**Frank Dziock: "Re: row weights in co-inertia"**Reply:**Frank Dziock: "Re: row weights in co-inertia"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ]

Hi !

At 07:55 21/12/2004, you wrote:

*>Dear ADE-colleagues,
*

*>
*

*>I am trying to perform a co-inertia in ADE-4 with R 2.0.0 based on a Fuzzy
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*>CA of 155 species and 11 trait variables with 59 trait categories. The
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*>other datatable has 155 species and 37 sites.
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*>
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*>FCA was performed on the traits-species table (traits) with traits in
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*>columns and species in lines/rows
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*>CA was performed on the transposed species-sites table (artentranspo) with
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*>sites in columns and species in lines/rows
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*>
*

*>######################
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*>blocks <- c(4,11,3,4,3,4,4,7,3,9,7) ##no. of categories per variable
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*>traits <- read.table ("c:/1
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*>Daten/Sachsen-Anhalt/Ergebnisse/Analysen/traits.txt", sep="\t")
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*>
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*>artentranspo<-data.frame(t(arten))
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*>ca<-dudi.coa(artentranspo, scan=F, nf=2)
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*>traits2<-prep.fuzzy.var(traits, blocks, row.w=ca$lw) ## new FCA with row
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*>weights ca$lw from the CA
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*>
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*>fca <- dudi.fca(traits2, scann=F, nf=4)
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*>coinert<-coinertia(fca,ca,scannf=F, nf=4)
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*>plot(coinert)
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*>randtest.coinertia(coinert,nrepet=9999)
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*>######################
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*>
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*>In the manual (p. 52) it says that in "dudi" cw are row weights, but this
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*>doesnt work for my coinertia, so I took "lw", which is said to be column
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*>weights, which I doubt!?
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*>
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*>The co-inertia seems to have worked with my data and using ca$li as row
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*>weights, because I got a summary plot.
*

I am not sure to really understand what you say. It seems there is an error

which must be corrected but can you tell us about which "manual" are you

talking ?

row weights are in lw (line weights)

column wights in cw (column weights)

for all objects of the class dudi.

Your example seems correct, but I suppose that there is a mistake in your

text when you say ca$li as row weights, it is ca$lw I suppose ??

*>But in the Monte-Carlo test an error occured "non-equal row weights" with
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*>eitther setting "fixed=0" or 1 or 2.
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*>
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*>I would be delighted if someone could help me by telling me what is "lw"
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*>and "cw" and maybe a hint on what went wrong in the Monte-Carlo test.
*

you do not receive an error but a warning, It is quite different. You must

fix the table on which you apply COA because row weights are computed from

this analysis. And the real message that you obtain is:

* > dudi2 <- dudi.coa(doubs$poi, scan = FALSE, nf = 2)
*

* > dudi1 <- dudi.pca(doubs$mil, scale = TRUE, row.w=dudi2$lw,scan =
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FALSE, nf = 3)

* > coin1 <- coinertia(dudi1,dudi2, scan = FALSE, nf = 2)
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* > rnd1=randtest(coin1,fixed=2)
*

Warning: non uniform weight. The results from permutations

are valid only if the row weights come from the fixed table.

The fixed table is table Y : doubs$poi

Here is is correct, I fix the table on which coa is applied.

*>Thanks very much in advance,
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*>
*

*>With best wishes from sunny Leipzig,
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*>
*

*>Frank
*

Here in Montreal it is sun, snow and cold (-25, -38 with the wind).

Stéphane DRAY

--------------------------------------------------------------------------------------------------

Département des Sciences Biologiques

Université de Montréal, C.P. 6128, succursale centre-ville

Montréal, Québec H3C 3J7, Canada

Tel : (514) 343-6111 poste 1233 Fax : (514) 343-2293

E-mail : stephane.dray@umontreal.ca

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Web http://www.steph280.freesurf.fr/

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