Dear Adrien and Ted,

thank you for your suggestions. For now I do not care about elegance and the simple solution worked perfectly enough for me:
I "cbinded" a group-vector to my environmental data and plotted the oridiellipse accordingly:

points(fig.nms.its1, "sites", pch=19, col="green", select=env.its1$group==1)
with(env.its1, ordiellipse(fig.nms.its1, env.its1$group, kind="se",label=T, conf=0.95, col="green", show.groups=1))
with(env.its1, ordihull(fig.nms.its1$site, group, col="green", lty=2, show.groups=1))

Thanks also for the second answer!

With best wishes
Martin



> From: "Donn, Ted" <Ted.Donn@tetratech.com>
> Subject: RE: [R-sig-eco] ordiellipse with more than one environmental factor??
> Date: 21 May 2014 01:05:48 CEST
> To: Martin Unterseher <martin.unterseher@uni-greifswald.de>
> 
> Dr. Unterseher,
> Although this is not very elegant, I generally add a column that identifies my groups and then use that to select the group for the hull or ellipse that I want to plot. You can place that column in a separate variable (array) or add it to the environmental variable matrix.
> Regards,
> Ted
> 
> Theodore E. Donn, Jr, PhD | Principal Ecologist (E.S.A. Certified)
> Direct: 925.280-7419 | Main: 925.280.7411 | Fax: 925.283.0780
> ted.donn@tetratech.com
> 
> Tetra Tech | Research and Development
> 3746 Mt. Diablo Blvd., Suite 300 | Lafayette, CA 94549| www.tetratech.com
> 
> PLEASE NOTE:  This message, including any attachments, may include privileged, confidential and/or inside information. Any distribution or use of this communication by anyone other than the intended recipient is strictly prohibited and may be unlawful. If you are not the intended recipient, please notify the sender by replying to this message and then delete it from your system.
> 
> 
> -----Original Message-----
> From: r-sig-ecology-bounces@r-project.org [mailto:r-sig-ecology-bounces@r-project.org] On Behalf Of Martin Unterseher
> Sent: Tuesday, May 20, 2014 2:54 PM
> To: r-sig-ecology@r-project.org
> Subject: [R-sig-eco] ordiellipse with more than one environmental factor??
> 
> 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
> 
> 
> 	[[alternative HTML version deleted]]
> 
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> 
> 
Begin forwarded message:

> From: Adrien Vetterli <adrien.vetterli@helsinki.fi>
> Subject: Re: [R-sig-eco] ordiellipse with more than one environmental factor??
> Date: 21 May 2014 08:20:25 CEST
> To: Martin Unterseher <martin.unterseher@uni-greifswald.de>
> 
> Hello Martin ,
> 
> for your first question, you should definitely give ggplot2 a go:
> 
> http://stackoverflow.com/questions/13794419/plotting-ordiellipse-function-from-vegan-package-onto-nmds-plot-created-in-ggplo
> 
> It's easy to learn how to deal with facets in ggplot2 and if I understood correctly, that's the way you want to go about plotting your subsets nmds plots with ordiellipse.
> 
>        http://docs.ggplot2.org/0.9.3.1/facet_grid.html
> 
> As for the last question, you can either use the function "subset", or subset directly like this:
> 
> yourdataframe[yourdataframe$yourcolumn=='yourmatch',]
> 
> StackOverflow is a wonderful resource fall all these questions, they should pop up on Google search.
> 
> a.
> 

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