[R] Neighborhood distance calculator
Antonio, Fabio Di Narzo
antonio.fabio at gmail.com
Wed Jan 28 22:14:48 CET 2009
The tseriesChaos package has an internal function "find_knearests"
which deals with a similar problem using a box-assisted search
strategy to alleviate time complexity explosion.
However, you will have to dig into the C sources, as these have no man pages.
HTH,
f.
2009/1/28 roger koenker <rkoenker at uiuc.edu>:
> 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
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>> 555792.81250000000 4825488.50000000000
>> 554144.81250000000 4825480.50000000000
>> 552537.81250000000 4825455.50000000000
>> 549324.81250000000 4825451.50000000000
>> 546093.81250000000 4825424.50000000000
>> 547705.81250000000 4825420.50000000000
>> 581566.87500000000 4824933.50000000000
>> 580760.87500000000 4824925.50000000000
>> 579954.87500000000 4824918.50000000000
>> 579153.87500000000 4824913.50000000000
>> 578353.87500000000 4824909.50000000000
>> 577544.87500000000 4824892.50000000000
>> 576736.87500000000 4824876.50000000000
>> 575928.87500000000 4824873.50000000000
>> 575120.87500000000 4824870.50000000000
>> 574325.87500000000 4824857.50000000000
>> 573530.87500000000 4824844.50000000000
>> 572726.87500000000 4824840.50000000000
>> 571923.87500000000 4824837.50000000000
>> 571121.87500000000 4824833.50000000000
>> 570319.87500000000 4824829.50000000000
>> 569514.87500000000 4824818.50000000000
>> 567106.87500000000 4824812.50000000000
>> 567907.87500000000 4824809.50000000000
>> 566302.87500000000 4824808.50000000000
>> 568709.87500000000 4824807.50000000000
>> 565499.87500000000 4824804.50000000000
>> 564676.87500000000 4824773.50000000000
>> 563854.87500000000 4824743.50000000000
>> 563053.87500000000 4824732.50000000000
>> 560648.87500000000 4824727.50000000000
>> 561450.87500000000 4824724.50000000000
>> 562252.87500000000 4824721.50000000000
>> 559835.81250000000 4824716.50000000000
>> 559023.81250000000 4824705.50000000000
>> 557410.81250000000 4824704.50000000000
>> 558216.81250000000 4824704.50000000000
>> 556600.81250000000 4824694.50000000000
>> 555791.81250000000 4824685.50000000000
>> 554971.81250000000 4824681.50000000000
>> 554151.81250000000 4824677.50000000000
>> 553346.81250000000 4824661.50000000000
>> 549337.81250000000 4824655.50000000000
>> 552541.81250000000 4824645.50000000000
>> 548522.81250000000 4824632.50000000000
>> 546095.81250000000 4824619.50000000000
>> 546901.81250000000 4824614.50000000000
>> 547708.81250000000 4824609.50000000000
>> 581576.87500000000 4824131.50000000000
>> 579957.87500000000 4824114.50000000000
>> 578352.87500000000 4824104.50000000000
>> 576744.87500000000 4824073.50000000000
>> 575129.87500000000 4824064.50000000000
>> 573538.87500000000 4824041.50000000000
>> 571927.87500000000 4824036.50000000000
>> 570323.87500000000 4824023.50000000000
>> 567100.87500000000 4824009.50000000000
>> 568715.87500000000 4824005.50000000000
>> 565496.81250000000 4823998.50000000000
>> 563861.81250000000 4823935.50000000000
>> 562256.81250000000 4823919.50000000000
>> 560644.81250000000 4823918.50000000000
>> 557409.81250000000 4823902.50000000000
>> 559026.81250000000 4823899.50000000000
>> 581587.87500000000 4823329.5000
>
> ...
>
> [Messaggio troncato]
--
Antonio, Fabio Di Narzo
Ph.D. student at
Department of Statistical Sciences
University of Bologna, Italy
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