[R-sig-Geo] Neighborhood distance calculator
Roger Bivand
Roger.Bivand at nhh.no
Thu Jan 29 16:21:46 CET 2009
On Thu, 29 Jan 2009, 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.
By crash, you mean stops because you have run out of memory, right?
Try dnearneigh() and nbdists() in spdep, they should work OK.
Roger
PS. Please don't attach large data sets to messages to the list, sending
85K to 1000+ addressees is environmentally unfriendly (big carbon
footprint) I believe.
>
> 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
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>
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>
--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no
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