1

I don't understand how the scaling works in Vegan, when plotting ordinations.

I found this question which will help clarify my point. For what I can read on the "Numerical ecology with R" book, there is differences between scaling = 1 and scaling = 2. In particular, with scaling 1 "The angles among descriptor vectors do not reflect their correlations" while with scaling 2 "The angles between descriptors in the biplot reflect their correlations".

So, I run this code (partially copy-pasted from the cited question) and I get two different plots (the axis span is different, so maybe the scaling parameter is doing something) but I don't see much difference between the angles of the descriptor vectors so I am trying to understand what, if anything, is wrong.

What I am missing, here?

library("vegan")
data(varespec)
data(varechem)

ord <- rda(varespec)

set.seed(1)
(fit <- envfit(ord, varechem, perm = 999))

## make up a fake `status`
status <- factor(rep(c("Class1","Class2"), times = nrow(varespec) / 2))

## manual version with extra things
colvec <-  c("red","green")
scl <- 1
plot(ord, type = "n", scaling = scl, main="Scaling 1")
points(ord, display = "sites", col = colvec[status], pch = (1:2)[status])
points(ord, display = "species", pch = "+")
plot(fit, add = TRUE, col = "black")

dev.new()
scl <- 2
plot(ord, type = "n", scaling = scl, main="Scaling 2")
points(ord, display = "sites", col = colvec[status], pch = (1:2)[status])
points(ord, display = "species", pch = "+")
plot(fit, add = TRUE, col = "black")
gabt
  • 668
  • 1
  • 6
  • 20
  • Have you read `vignette("decision-vegan", "vegan")`, section 3: Scaling in redundancy analysis? – Jari Oksanen Jun 14 '22 at 17:29
  • no, i did not read it and thank you for the source. now that I did, though, I still don't understand how this is related with the vectors representing explanatory variables. should they be scaled, too, to follow the reasoning in NumEcWithR? Since the angles do not change but the positions of species and sites do...is this the whole point? Changing position change the relation with the vectors? – gabt Jun 15 '22 at 06:16

0 Answers0