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
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