Hi everyone, I am working on a community analysis project. I am very happy with a graph produced in package vegan using betadisper that is based off of a custom community distance matrix (uni.dist) and a species abundance by site table (shared). Betadisper produces a great PCoA plot of the communities clustered by habitat type (convex hull around communities belonging to the same habitat type, lines from community to the center of the cluster).
z <- with(enviro.variable.matrix, betadisper(as.dist(uni.dist), enviro.variable.matrix$habitat)) plot(z) What I would like to do now is to turn this into a biplot with the species most important in determining community relatedness represented as arrows. I can produce the PCoA plot without the convex hulls and centroids that contains ALL of the species arrows (~200) using package ape. uni.pcoa <- pcoa(uni.dist) biplot(uni.pcoa, Y=shared, plot.axes=c(1,2)) Unfortunately, I cannot find any way to extract the loadings from the biplot output. I've tried storing the biplot in a variable, but there does not appear to be anything produced by the function except the plot (I understand why uni.pcoa doesn't contain loadings). I've played with doing a NMDS with the weighted averages of the species displayed as points instead, but this does not communicate the same information that I was wanting. Any suggestions would be appreciated! Thank you, Jo [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology