[R-sig-eco] scaling issues with vegan's envfit()

[ADuranel]

Hello

I am running a PCA of some environmental variables. I have a second set of
environmental variables that I would like to project passively onto the
ordination plot, but with the same arrow length scaling as that used for the
first dataset. I used envfit() in vegan for that purpose. To check that I
get the same arrow length scaling in plot.envfit() as in plot.cca(), I
fitted the same dataset:  

require(vegan)
data(varechem)
pca1<-rda(varechem, scale=T)

ef<-envfit(pca1, scale(varechem))
plot(pca1, type="points")
sp.sc<-scores(pca1, display="species")
ef.sc<-scores(ef, display="vectors")
plot(ef, arrow.mul=abs(sp.sc[1,1]/ef.sc[1,1]), col="red")
# equivalent to:
plot(ef, arrow.mul=vegan:::ordiArrowMul(ef.sc)/vegan:::ordiArrowMul(sp.sc))

The last two lines are the only two ways I managed to get the same length
scaling for the plot.cca() "species" and plot.envfit() vectors.
However if I want to use another scaling (scaling=1 or 3) for the PCA plot,
I can't get similar coordinates for the plot.cca() "species" and
plot.envfit() vectors:

ef1<-envfit(pca1, scale(varechem), scaling=1)
plot(pca1, scaling=1, type="points")
sp.sc1<-scores(pca1, scaling=1, display="species")
ef.sc1<-scores(ef1, scaling=1, display="vectors")
plot(ef1, arrow.mul=abs(sp.sc1[1,1]/ef.sc1[1,1]), col="red") # wrong: the
ratio sp.sc/ef.sc varies according to "species" in this case...
plot(ef1,
arrow.mul=vegan:::ordiArrowMul(ef.sc1)/vegan:::ordiArrowMul(sp.sc1)) # the
arrow length scaling varies according to "species".

Can somebody tell me what I am doing wrong here?

I use R version 3.1.1 (2014-07-10) with vegan_2.0-10
Platform: x86_64-w64-mingw32/x64 (64-bit)

Many thanks

Arnaud





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