[R-sig-Geo] Neighborhood distance calculator
Kumudan
cybermails at gmail.com
Thu Jan 29 15:30:21 CET 2009
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
-----------------------------------------------------------------------------------
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