[R-sig-Geo] how to do a principle component analysis with geo-referenced points
Hufkens Koen
koen.hufkens at ua.ac.be
Mon Nov 13 10:15:27 CET 2006
Some articles:
>From fields to objects: A review of geographic boundary analysis
http://www.springerlink.com/content/q1kxcfqegmrmjv92/
Integrating Edge Detection and Dynamic Modeling in Quantitative Analyses of Ecological Boundaries
http://www.bioone.org/perlserv/?request=get-abstract&issn=0006-3568&volume=053&issue=08&page=0730
Measuring the abruptness of patchy ecotones - A simulation-based comparison of landscape pattern statistics
http://www.springerlink.com/content/k556v88m62g02462/
Edge effects in fragmented landscapes: a generic model for
delineating area of edge influences (D-AEI)
http://scholar.google.com/url?sa=U&q=http://research.eeescience.utoledo.edu/lees/pubs/zheng2000.pdf
I've got a lot more in my endnote database, I can send you the file if you want to because this copy pasting isn't exactly efficient.
regards,
Koen
--
Koen Hufkens, Phds
Department of Biology
Research Group of Plant and Vegetation Ecology
University of Antwerp
Universiteitsplein 1
B-2610 Wilrijk, Belgium
Koen.Hufkens at ua.ac.be
> -----Original Message-----
> From: r-sig-geo-bounces at stat.math.ethz.ch
> [mailto:r-sig-geo-bounces at stat.math.ethz.ch] On Behalf Of
> Nicholas Lewin-Koh
> Sent: zondag 12 november 2006 4:23
> To: Carlos A. Bastos M.Guerra
> Cc: r-sig-geo at stat.math.ethz.ch
> Subject: Re: [R-sig-Geo] how to do a principle component
> analysis with geo-referenced points
>
> Hi Carlos,
> I think that there are tools in the sp package for dealing with grids.
> If I am understanding you correctly and you want to do
> "zoning" of your region than you probably are not looking to
> do pca, but some sort of clustering.
> Marie Jose Fortin had some nice papers on a technique called
> wombling, for finding regions of abrupt ecological change.
> There are some other techniques for spatial partitioning, but
> I am not sure if they are implemented in R. It has been a
> long time since I worked on ecological problems.
>
> For more information on the spatial tools in R a good place
> to start is http://cran.r-project.org/src/contrib/Views/Spatial.html
> the CRAN task view for spatial statistics, and
> http://cran.r-project.org/src/contrib/Views/Environmetrics.html
> has some more pointers.
>
> Hope this helps,
>
> Nicholas
> On Sat, 11 Nov 2006 20:24:59 -0000, "Carlos A. Bastos M.Guerra"
> <carlosguerra at esa.ipvc.pt> said:
> >
> > Dear Nicholas,
> >
> > First of all thanks for the references, I think they will
> help me with
> > my current problem. :) The thing is that I am used to work
> with AcrGIS
> > to do the spatial analysis, but the statistical methods in
> ArcGIS are
> > a bit "dummy", namely in spatial PCA. I am used to work with R with
> > the ade4 package :) but when I heard that I could do
> spatial analysis
> > with R I ad to try it...but its more difficult that it seams (at
> > first)...
> >
> > What I did was: (in ArcGIS) convert the centroids of a grid into a
> > point shape file, than I have integrated all the information into
> > different columns. I converted the dbf file into a txt an then I
> > imported the file into R ... and my problems began... :)
> >
> > My objective is to do a PCA and extract the different
> groups of points
> > in order to make an ecological zoning.
> >
> > I am still starting with R and "the Geo tools" can you
> point me some
> > reading material that I can use?
> >
> > Best regards,
> >
> > Carlos
> >
> >
> > -----Mensagem original-----
> > De: Nicholas Lewin-Koh [mailto:nikko at hailmail.net]
> > Enviada: sábado, 11 de Novembro de 2006 19:06
> > Para: r-sig-geo at stat.math.ethz.ch
> > Cc: Carlos GUERRA
> > Assunto: [R-sig-Geo] RE: how to do a principle component
> analysis with
> > geo-referenced points
> >
> > Hi Carlos,
> > There are a couple of ways to do this, but you have to be a little
> > more specific about what your goals/intentions are. I
> assume you have
> > points p(x1,y1), ...., p(xn,yn), where p is a vector of
> observations.
> >
> > If the goal is interpolation than you have to model the spatial
> > covariance of the orthognal factors, and you should look at
> > waekernagel's book.
> > if your goal is to extract principal components and account for the
> > variance induced by a spatial process, a quick and dirty
> approach is
> > to include polynomials of the xy coordinates in the data
> and do pca on
> > the augmented matrix. Take a look at
> >
> > Borcard, D., P. Legendre & P. Drapeau. 1992. Partialling out the
> > spatial component of ecological variation. Ecology 73: 1045-1055
> >
> > Méot, A., P. Legendre & D. Borcard. 1998. Partialling out
> the spatial
> > component of ecological variation: questions and
> propositions in the
> > linear modeling framework. Environmental and Ecological Statistics 5
> > (1): 1-27.
> >
> > Another approach is spatial factor analysis
> >
> > Christensen, WF, and Amemiya, Y (2001). "Generalized
> shifted-factor
> > analysis method for multivariate geo-referenced data," Mathematical
> > Geology, 33, 801-824.
> >
> > Christensen, WF, and Amemiya, Y (2002). "Latent variable
> analysis of
> > multivariate spatial data," Journal of the American Statistical
> > Association, 97, 302-317
> >
> > If your question is there R code to do this, I think the
> ade4 package
> > can to the spatial variance partitioning, but for factor
> analysis, you
> > are on your own.
> >
> > Nicholas
>
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