In an ordination such as this, you have two sets of scores; i) one
pertaining to the (dis)similarity of your samples in terms of species
composition, and ii) one pertaining to the species and which species
co-occur. You can't display both sets of information and retain the
meaning of the scores on
code
rm(list=ls())
library(vegan)
library(MASS)
data(varespec)
print(varespec)
str(varespec)
#PCA
vare.pca <- rda(varespec)
vare.pca
plot(vare.pca)
sum(apply(varespec, 2, var))
biplot(vare.pca, scaling = -1)
Elaine
On Sat, Aug 14, 2010 at 10:48 AM, Ben Bolker wrote:
> elaine kuo gmail
elaine kuo gmail.com> writes:
> Pls kindly advise what scaling is in plot.
> Sometime it could be negative but sometimes it might be positive
> .(I guess it is the proportion between the plot and the margin)
Your question is unclear. Please give more context and/or details.
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