I want to display species coordinates relative to an environmental variable using ordination surface (
vegan package). In order to do this, I guess I have take the scaling of species scores into consideration.
plot.cca function in
vegan package seems to scale species proportional to eigenvalues (see example below) and leave site scores unscaled:
library(vegan) data(varechem) data(varespec) mod <- cca(varespec ~ Al + P + K, varechem) summary(mod, display = "species") # Scaling 2 for species and site scores # * Species are scaled proportional to eigenvalues # * Sites are unscaled: weighted dispersion equal on all dimensions plot(mod, type = "n") points(mod, display = "sites", pch = 19, cex = 0.1) ordisurf(mod, varechem$Al, add = TRUE) text(mod, display = "species")
Species scores seem aligned correctly. Now if I specify another scaling:
scal <- "sites" plot(mod, type = "n", scaling = scal) points(mod, display = "sites", pch = 19, cex = 0.1, scalin = scal) ordisurf(mod, varechem$Al, add = TRUE, scaling = scal) text(mod, display = "species", scaling = scal, cex = 0.7)
Species scores get higher values than site scores. The ordination surface, however, seems linked to the site scores.
- Does the default scaling plot species scores such that they are correctly related to the ordination surface model?
- (Why) can(not) I specify other scaling such as "sites" (row scores) and still get the species scores correctly aligned related to ordination surface if I consequently specify this for all layers (as above)?