Hi Clément, Mathiew, I'm sorry I haven't replied earlier, I'm abroad and I have been a little off...
Thank you very very much for your answers and tips. I agree with Mathiew, the enfa it's a very elegant way of exploring the data. That's why I want to use it in my paper. Again, about the tolerance, using the code you told me: pc3 <- dudi.pca(kasc2df(map)$tab, scan=FALSE) sum(dudi.pca(pc3$tab, scale=FALSE, row.w = dataenfa1$pr/sum(dataenfa1$pr), scan=FALSE)$eig) I got* 3.129783*, is this correct? But I don't understand, shouldn't tolerance have a value ranging from 0 to 1? I thougth that was the idea, since specialization varies from 1 to infinite, right? [i.e. Reutter et al 2003***] In the other hand, I have estimated the global specializations using Hirzel et al (2002) formula, like this: S <- (sqrt(sum(enfa1$s)))/1.96 Does it seem correct? I got this value S = 0.996322 (<1 though), and then, my tolerance (1/S) was 1.003692 (>1). It bothers me that we don't have the same values! grrr What do you think? About my other question about the scatter plot of enfa, the scores and so on... I think I haven't been able to explain myself... I have uploaded a picture http://img808.imageshack.us/i/scatter.jpg/. I hope you can see what I mean there. Thanks again guys!!! Consuelo *** Reutter, B.A, V. Helfer, A.H. Hirzel1 & P. Vogel. 2003. Modelling habitat-suitability using museum collections: an example with three sympatric Apodemus species from the Alps. Journal of Biogeography, 30, 581590 ------------- Consuelo Hermosilla PhD student Departamento de Ecología y Biología Animal Departamento de Bioquímica, Genética e Inmunología, Área de Genética Facultad de Ciencias del Mar Campus de As Lagoas-Marcosende Universidad de Vigo 36310 Vigo SPAIN Mobile: +34 692 633 298 oooO ( ) Oooo ( ( ) _) ) / (_/ Stop Gaza Massacre 2010/6/9 Clément Calenge <clement.cale...@gmail.com> > On 06/09/2010 09:05 AM, Clément Calenge wrote: > >> >> >>> sum(dudi.pca(kasc2df(map), row.w = dataenfa1$pr/sum(dataenfa1$pr), >>> scan=FALSE)$eig) >>> >>> which gives you 5 only. The weights should sum to 1 (i.e. they are >>> proportions). But then, how would you interpret this? This is the same >>> as for the "global specialization". >>> >> >> Yes, but be careful: kasc2df returns a list with one component "tab" (the >> component of interest) and one component "index" (the component allowing to >> rebuild the original kasc), so that the correct code is: >> >> sum(dudi.pca(kasc2df(map)$tab, row.w = dataenfa1$pr/sum(dataenfa1$pr), >> scan=FALSE)$eig) >> > > I was a bit too hasty for this reply. Actually the code is incorrect. > Consider the following code: > > pc <- dudi.pca(kasc2df(map)$tab, row.w = dataenfa1$pr/sum(dataenfa1$pr)) > > This code performs a *centered and scaled* PCA of the environmental > variables: this analysis first centers and scales the table containing the > value of the environmental variables. Therefore, for each variable of > pc$tab, the mean *weighted by the utilization weights* is equal to zero and > the variance *weighted by the utilization weights* is equal to 1. Therefore, > the sum of the eigenvalues of the PCA on this transformed table is equal to > the number of environmental variables. This code is incorrect (thanks > Mathieu for noting the inconsistency). First, to calculate the global > tolerance, you would need to calculate: > > pc <- dudi.pca(kasc2df(map)$tab, scan=FALSE) > > This preliminary analysis is performed just to center/scale the variables > with uniform weighting. This allows to compare the different variables in > pc$tab (they all have the same average and the same scale). *Then*, > calculate the weighted and *unscaled* PCA of the table pc$tab: > > sum(dudi.pca(pc$tab, scale=FALSE, row.w = dataenfa1$pr/sum(dataenfa1$pr), > scan=FALSE)$eig) > > This gives the tolerance of the species on the area, > Sorry for the confusion, > HTH, > > Clément Calenge > > -- > Clément CALENGE > Cellule d'appui à l'analyse de données > Office national de la chasse et de la faune sauvage > Saint Benoist - 78610 Auffargis > tel. (33) 01.30.46.54.14 > > [[alternative HTML version deleted]]
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