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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