[R-sig-Geo] how to do a principle component analysis with geo-referenced points

[Hufkens Koen]

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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