[R] Neighborhood distance calculator

[roger koenker]

If you are willing to dig into the adjacency information returned from
tri.mesh in the tripack package, this could be done quite efficiently.

url:    www.econ.uiuc.edu/~roger            Roger Koenker
email    rkoenker at uiuc.edu            Department of Economics
vox:     217-333-4558                University of Illinois
fax:       217-244-6678                Champaign, IL 61820

On Jan 28, 2009, at 2:33 PM, Kumudan wrote:

> Hi all,
>
> I am new to R, hence this question. I have a set of points with X and
> Y coordinates. I would like to build an R code to calculate the
> distances of points within a specified neighborhood (circular range)
> for each point. I would like the code to be a function, so that I can
> call the function, specifying parameters (data file, distance), from
> another piece of code. Also, I would like the output to be as:
>
> output = list(array)
> .........code...........
> ........new code.....
> return(output)
>
> Something like this--
> [[1496]]
> [1] 1490 1491 1492 1493 1494 1495
>
> The most important thing, however, is that I want to run the code for
> 100,000+ points. The current code I have calculates the neighborhood
> distances for all the points with ever point, and then selects only
> those points within the specified distance parameter. This code
> crashes when I have over 40,000 points. Therefore, I need to figure
> out a way to preclude the step where it calculates all of the paired
> distances, and rather only those points within the specified distance
> parameter. Please, see below for the existing code, and a sample data.
> Thanks a lot for your time and effort.
>
> Best,
> Kumudan
>
> Kumudan Grubh
> EEB Graduate student
> Iowa State University
>
> -------------------------------------------------------------------------------------------------------------------------------------------------------
> #--Code--
> #transform coordinates in kilometers, and redefine origin
> newx=(XCOORD-min(XCOORD))/1000
> newy=(YCOORD-min(YCOORD))/1000
> plot(newx,newy,pch=20,xlab="X coordinate (km)",ylab="Y coordinate  
> (km)")
>
> #set of new locations to be used from here on
> tr.locs=cbind(newx,newy)
>
> #the functions necessary for estimation are written in an external
> program. All you need to do is to run this program one. To do this,
> you could "source" this code
> source("D:/...../Functions_distance.R")
>
> #define distance-based neighborhood
> nb.tr=dist.neighbors(tr.locs,2)
> ----------------------------------------------------------------------------------------------------------------------------------------------------------
> #---Function_distance.R   <- Function to calculate distance of pairs
> of neighbors
> #start by defining neighbors
> library(spatstat)#need this to compute distances between all points  
> in a data
>
> dist.neighbors=function(data,distance)
> #distance is set by user
> {
> #data has the x and y on the first two columns. Could have more than
> two columns, or exactly two columns, it doesn't matter.
> #produces a "list" object with a vector of the neighbors for each  
> location
> #distance defines the range within which we define neighbors
> nd=length(data[,1])
> nbmat=list(array)
> dist=pairdist(data[,1:2])
>  for(i in 1:nd){
>  nbmat[[i]]=0
> 	for(j in 1:nd) if((dist[i,j]<distance)&(i!=j))  
> nbmat[[i]]=c(nbmat[[i]],j)
> 	nbmat[[i]]=nbmat[[i]][nbmat[[i]]!=0]}
> return(nbmat)		
> }
> ------------------------------------------------------------------------------------------------------------------------------------
>
> Data
> -----------------------------------------------------------------------------------
> XCOORD	YCOORD
> 544312.87500000000	4851169.00000000000
> 542705.87500000000	4851165.00000000000
> 541068.87500000000	4851155.00000000000
> 537861.81250000000	4851123.00000000000
> 536246.81250000000	4851118.00000000000
> 539476.87500000000	4851116.00000000000
> 534612.81250000000	4851113.00000000000
> 533004.75000000000	4851095.00000000000
> 542714.87500000000	4850363.00000000000
> 543516.87500000000	4850360.00000000000
> 544319.93750000000	4850358.00000000000
> 541883.87500000000	4850353.00000000000
> 541053.87500000000	4850342.50000000000
> 540268.87500000000	4850326.50000000000
> 537866.81250000000	4850313.50000000000
> 538674.87500000000	4850311.50000000000
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> 536255.81250000000	4850307.00000000000
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> 533809.81250000000	4850297.00000000000
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> 542716.87500000000	4849553.50000000000
> 541074.87500000000	4849537.50000000000
> 539486.87500000000	4849508.50000000000
> 537867.87500000000	4849507.50000000000
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> 555838.75000000000	4816629.50000000000
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.