[R-sig-eco] get species within sites ordihull polys

[Howard, Tim G (DEC)]

Eduard,
Yes, indicator species may help - and indeed, perhaps all I need are some pointers from the community table produced in vegan: vegemite and tabasco. I'm working down that path now. 

Mike,
Aha - yes, distance from the centroid to each species looks very promising too. Excellent!

Thank you both for your replies and help. 
Best, 
Tim


> Date: Sat, 26 Sep 2015 14:07:07 +0200
> From: Eduard Sz?cs <szoecs at uni-landau.de>
> To: r-sig-ecology at r-project.org
> Subject: Re: [R-sig-eco] get species within sites ordihull polys
> Message-ID: <56068A6B.4040000 at uni-landau.de>
> Content-Type: text/plain; charset=windows-1252
> 
> Dear Tim,
> 
> Sound's like your looking for indicator species ?
> 
> Maybe the indicspecies packages suites your needs.
> 
> Dufr?ne, M and P. Legendre. 1997. Species assemblages and indicator
> species: the need for a flexible assymetrical approach. Ecological
> Monographs 67: 345 - 366.
> 
> De C?ceres, M., P. Legendre, and M. Moretti, 2010. Improving indicator
> species analysis by combining groups of sites. Oikos 119: 1674 -1684.
> 
> Cheers,
> 
> Eduard
> 
> On 25/09/15 20:58, Howard, Tim G (DEC) wrote:
> > 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
> 
> --
> Eduard Sz?cs
> Quantitative Landscape Ecology
> Institute for Environmental Sciences
> University Koblenz-Landau
> Tel. +49 6341 280 31552
> http://www.uni-koblenz-landau.de/en/campus-
> landau/faculty7/environmental-sciences/landscape-
> ecology/Staff/eduardszoecs
> 
> 
> ------------------------------
> 
> Date: Sat, 26 Sep 2015 21:18:24 -0700
> From: Michael Marsh <swamp at blarg.net>
> To: r-sig-ecology at r-project.org
> Subject: Re: [R-sig-eco] get species within sites ordihull polys
> Message-ID: <56076E10.4050301 at blarg.net>
> Content-Type: text/plain; charset=windows-1252; format=flowed
> 
> 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-request at 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.howard at dec.ny.gov>
> To:"r-sig-ecology at r-project.org"  <r-sig-ecology at r-project.org>
> Subject: [R-sig-eco] get species within sites ordihull polys
> Message-ID:
> 	<CY1PR09MB0266DBF8A724047334E58D6CA8420 at CY1PR09MB0266.n
> amprd09.prod.outlook.com>
> 
> Content-Type: text/plain; charset="us-ascii"
> 
> 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
>