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

Dear Stephane,

thanks very much for your quick and helpful answer. Now it is clear that

lw are the row weights and cw the column weights.

Of course, I meant ca$lw instead of ca$li, that was my mistake, sorry.

The manual I mentioned, is the complete ade4-package manual ("The ade-4

package, version 1.2-2, 21 May 2004"), page 65 description of "dudi"

(page 52 in the older version1.1-2)

However, I still fail to do the randtest. The error message is:

"Error in randtest.coinertia(coinert, nrepet = 9999) :

Equal row weights expected"

I would very much appreciate any suggestions, what could have gone wrong!?

Best wishes from Leipzig (well, -3, but cold enough for me),

Frank

Stephane Dray schrieb:

*>
*

*> 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 CA of 155 species and 11 trait variables with 59 trait
*

*>> categories. The other datatable has 155 species and 37 sites.
*

*>>
*

*>> FCA was performed on the traits-species table (traits) with traits in
*

*>> columns and species in lines/rows
*

*>> CA was performed on the transposed species-sites table (artentranspo)
*

*>> with sites in columns and species in lines/rows
*

*>>
*

*>> ######################
*

*>> blocks <- c(4,11,3,4,3,4,4,7,3,9,7) ##no. of categories per variable
*

*>> traits <- read.table ("c:/1
*

*>> Daten/Sachsen-Anhalt/Ergebnisse/Analysen/traits.txt", sep="\t")
*

*>>
*

*>> artentranspo<-data.frame(t(arten))
*

*>> ca<-dudi.coa(artentranspo, scan=F, nf=2)
*

*>> traits2<-prep.fuzzy.var(traits, blocks, row.w=ca$lw) ## new FCA with
*

*>> row weights ca$lw from the CA
*

*>>
*

*>> fca <- dudi.fca(traits2, scann=F, nf=4)
*

*>> coinert<-coinertia(fca,ca,scannf=F, nf=4)
*

*>> plot(coinert)
*

*>> randtest.coinertia(coinert,nrepet=9999)
*

*>> ######################
*

*>>
*

*>> In the manual (p. 52) it says that in "dudi" cw are row weights, but
*

*>> this doesnt work for my coinertia, so I took "lw", which is said to
*

*>> be column weights, which I doubt!?
*

*>>
*

*>> The co-inertia seems to have worked with my data and using ca$li as
*

*>> row 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 eitther setting "fixed=0" or 1 or 2.
*

*>>
*

*>> I would be delighted if someone could help me by telling me what is
*

*>> "lw" 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
*

*> = FALSE, nf = 3)
*

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

*>
*

*> > 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,
*

*>>
*

*>> With best wishes from sunny Leipzig,
*

*>>
*

*>> 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
*

*> --------------------------------------------------------------------------------------------------
*

*>
*

*> Web
*

*> http://www.steph280.freesurf.fr/
*

*> --------------------------------------------------------------------------------------------------
*

*>
*

*>
*

*>
*

*>
*

-- / *NEW EMAIL-ADRESS, PLEASE CHANGE IN YOUR ADRESS-BOOK*/_________________________________________________________________________________________________

Dr. Frank Dziock Umweltforschungszentrum Leipzig-Halle GmbH - Centre for Environmental Research Leipzig-Halle Department Naturschutzforschung - Department of Conservation Biology Permoser Str. 15 D - 04318 Leipzig Germany Telefon - Phone ++49 - 341 235 2533 Fax ++49 - 341 235 3191 E-mail Frank.Dziock@ufz.de homepage http://www.ufz.de/index.php?de=1897

_________________________________________________________________________________________________

God in his wisdom made the fly, and then forgot to tell us why /

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

*
This archive was generated by hypermail 2b30
: Tue Dec 21 2004 - 16:10:07 MET
*