Dear all,
I have a species (phyllosphere microfungi)-sample matrix "spec.its1.s" and an
environmental matrix "env.its1" with several parameters, such as setting
("phytometer" and "natural"), elevation ("valley", "mountain" and "top") or
substrate ("living" and "dead" [leaves]).
My species matrix therefore contains samples with different environmental
combinations, e.g. phytometer-valley-living, phytometer-mountain-living, etc.
Instead of extracting several subsets and calculating metaMDS independently for
every subset, I seek a solution to manage all data simultaneously.
Whereas I know how to plot subsets of samples with points(...) in different
colours, I have no idea about how to do this with ordiellipse, ordihull,
ordiclust, etc. Of course, I did my best to search the www for a solution.
Here are my commands:
nms.its1<-metaMDS(spec.its1.s, autotransform=F, distance="bray")
fig.nms.its1<-ordiplot(nms.its1, type="none", main="Phyllosphere community -
relative abundances")
points(fig.nms.its1, "species", pch=20, col="blue", cex=0.25)
points(fig.nms.its1, "sites", pch=19, col="green",
select=env.its1$elevation=="valley" & env.its1$setting=="phytometer" &
env.its1$substrate=="living")
points(fig.nms.its1, "sites", pch=19, col="darkgreen",
select=env.its1$elevation=="mountain" & env.its1$setting=="phytometer" &
env.its1$substrate=="living")
points(fig.nms.its1, "sites", pch=19, col="orange",
select=env.its1$elevation=="valley" & env.its1$setting=="natural" &
env.its1$substrate=="living")
points(fig.nms.its1, "sites", pch=19, col="red",
select=env.its1$elevation=="mountain" & env.its1$setting=="natural" &
env.its1$substrate=="living")
points(fig.nms.its1, "sites", pch=19, col="violet",
select=env.its1$elevation=="top" & env.its1$setting=="natural" &
env.its1$substrate=="living")
And then I got stuck: How can I draw a ordihull, ordiellipse for the green,
orange, violet, etc. groups?
Next I want to apply e.g. "anosim" to check for significant community
compositions. For instance, I want to compare the phytometer-VALLEY-living
community with the phytometer-MOUNTAIN-living community with the (null)
hypothesis that both communities do not overlap.
This brings me to the next question: How can I extract subsets of my
species-sample matrix by using information from the environmental data: e.g.
"extract only those samples (and species) from the species-sample dataframe,
that have the combination setting=phytometer, elevation=valley, and
substrate=living, etc..
I hope that someone out there can help me though I do not provide some of the
data at the moment.
Best wishes
Martin
__________
Dr. Martin Unterseher
Ernst-Moritz-Arndt University
Institute of Botany and Landscape Ecology
Dept. of Systematic Botany
Soldmannstr. 15
D-17487 Greifswald
http://www.botanik.uni-greifswald.de/100.html
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