[R-sig-eco] Need an algorithm to identify spatial clusters

[Julian Burgos]

Hi Mark,

What you are looking for is a connected component algorithm.  The algorithm
should receive a binary matrix (i.e. 0's and 1's for fire/no fire) and delineate
isolated groups of pixels following either a 4 or 8 neighbor rule.  Some time
ago I coded a function to do this (I couldn't find a package with this
functionality), and I would be happy to pass it along.  My function wasn't
extremely efficient but worked well enough to process thousand of matrices (each
100x100) in a relatively short time.  Let me know if you need it.

Julian Burgos, PhD
University of Washington



On Tue, 14 Apr 2009, Mark Andersen wrote:

> Hello, all,
>
> I am currently interested in simulating the initiation and spread of forest 
> fires in simulated landscapes consisting of 2 tree species (a native and an 
> invasive). I'm simulating fire seasons of fixed length; fires can start at any 
> time and in either tree species during this fire season, and spread through the 
> simulated forest according to a simple percolation-like process. I have 
> developed the algorithms for this in Matlab, and don't anticipate any problems 
> converting them to R if I need to.
>
> However, it's the next task that has me at a loss. At the end of each fire 
> season, there will be several burned patches on the simulated landscape; the 
> number of these patches won't necessarily correspond to the total number of 
> fires that season, because fires may coalesce. I need to count how many of 
> these burned patches there are, and find the size of each. It seems that there 
> should be an algorithm available to do this, but I haven't found one, possibly 
> because I haven't been using the right search criteria. I used 
> RSiteSearch("spatial cluster"), and got many references to the spatclus 
> package. However, from the spatclus documentation it appears that this is not 
> quite what I'm looking for. Spatclus looks like it picks out potential clusters 
> of occurrence of some phenomenon (such as earthqukes or cancer); I need 
> something that will delineate clusters of contiguous pixels with the same value 
> (i.e., burned in my simulations). Could anyone point me towards such an 
> algorithm, or help me get started finding one?
>
> -- 
> Dr. Mark C. Andersen, Professor
> Department of Fish, Wildlife, and Conservation Ecology
> New Mexico State University
> Las Cruces, NM 88003
> 575-646-8034
> fax: 575-646-1281
> web: web.nmsu.edu/~manderse
>
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