Dr. Stevens,
Hi, my name is Trey Scott, and I'm a grad student of Brian McCarthy's. He
referred me to you because of your expertise in handling complex R problems.
We were hoping you could help us solve a nagging problem that is prohibiting
me from producing graphicl output.
Here is a simple mock-up of the matrix I'm using
a b c d e f
1i 1 4 7 9 2 5
2i 12 17 6 2 3 7
3i 2 5 8 1 3 2
1c 0 2 4 7 2 1
2c 0 1 4 6 9 10
3c 13 15 19 10 8 9
Where: 1i-3i are "infested" sites, and 1c-3c are "control sites". A-F are
species found at each site. I have several of these ordinations to perform
on different variables (BA, density, RIV, cover, etc..., all in different
matrices). I'm running NMDS (metaMDS) ordinations on each matrices, and
producing ordination graphs for each cloud of points. The problem I have is
that I cannot devise a way to split the cloud of points into infested and
control so that I can deduce any significant groupings. A simple difference
in symbols/color (Ex. gray triangles for infested, black circles for
control) would do. Also, I understand the use of pch/col/cex, I just need
to apply them to the "split".
So:
+ How would I split these out in R after I run the metaMDS in vegan?
+ What code would be necessary to bring this about?
McCarthy and I are at the end of our preoverbial rope on this; nothing has
worked.
--
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