Thanks Gavin. That's actually very nice and I suspect just what Andy
was looking for.
Dave
On 05/23/2011 04:33 AM, Gavin Simpson wrote:
require(vegan)
require(labdsv)
data(dune)
data(dune.env)
## Indicators of Management type
set.seed(38)
inds<- with(dune.env, indval(dune, Management))
## ordinate
dune.pca<- rda(dune, scale = TRUE)
## exract scores you want to plot presume species and sites
dune.site<- scores(dune.pca, display = "sites", scaling = 3)
dune.spp<- scores(dune.pca, display = "species",
scaling = 3)[inds$pval<= 0.05, ]
## plot
plot(dune.pca, display = c("sites","species"), type = "n",
scaling = 3)
points(dune.site)
arrows(0, 0, dune.spp[,1], dune.spp[,2], col = "red", length = 0.05)
lab.xloc<- dune.spp[,1] * 1.2
lab.yloc<- dune.spp[,2] * 1.2
text(lab.xloc, lab.yloc, rownames(dune.spp), col = "red", cex = 0.8)
--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
David W. Roberts office 406-994-4548
Professor and Head FAX 406-994-3190
Department of Ecology email drobe...@montana.edu
Montana State University
Bozeman, MT 59717-3460
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