Tim, I've used mvpart to cluster, and then rpart.pca the resulting
regression clustering.
mvpart requires a corresponding environmental data set.
The pca plot has what you require, polygons like ordihull based on and
showing plots (rows in your data), and vectors to named species.
I have assumed that the distance from the centroid to each species
corresponds to its importance in configuring the output, but I'm a
novice andwould like more information on that.
Mike Marsh
On 9/26/2015 3:00 AM, r-sig-ecology-requ...@r-project.org wrote:
get species within sites ordihull polys
Date: Fri, 25 Sep 2015 18:58:19 +0000
From: "Howard, Tim G (DEC)"<tim.how...@dec.ny.gov>
To:"r-sig-ecology@r-project.org" <r-sig-ecology@r-project.org>
Subject: [R-sig-eco] get species within sites ordihull polys
Message-ID:
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All -
Consider clusters of points in an NMDS with those clusters determined in some
way (I'll use hclust below).
Then consider plotting the species on that ordination. I'd like to
automatically find which species are 'most associated' with each cluster.
Perhaps that translates to finding those species that fall within an ordihull
of each group. Before I stumble down into the world of the sp package and
spatial overlaps perhaps this is already a part of vegan or another package.
###Example:
library(vegan)
data(dune)
ord <- metaMDS(dune)
# get some groups based on hclust
dis <- vegdist(dune)
clus <- hclust(dis, "average")
plot(clus)
rect.hclust(clus, 3)
grp <- cutree(clus, 3)
#plot the mds with the groups
mdsPlot <- plot(ord, type="n", display = "sites")
points(ord, display = "sites", col="red", pch=19)
ordihull(ord, grp)
#plot the species
points(ord, display = "species", col = "blue", pch=19)
###End example
This isn't the best example because species points don't fall in more than one
of the black polygons. But, my question: Can I easily identify which blue
points (species) fall within the polygon? Or can I easily identify which
species are 'most important' (most abundant?) for defining each of the three
groups?
Thanks for any pointers
Tim Howard
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