[R] finding euclidean proximate points in two datasets
Alexander Shenkin
ashenkin at ufl.edu
Thu May 20 17:12:19 CEST 2010
On 5/20/2010 9:18 AM, David Winsemius wrote:
>
> On May 20, 2010, at 10:02 AM, Alexander Shenkin wrote:
>
>> Hello all,
>>
>> I've been pouring through the various spatial packages, but haven't come
>> across the right thing yet.
>
> There is a SIG for such questions.
thanks - just joined it.
>> Given a set of points in 2-d space X, i'm trying to find the subset of
>> points in Y proximate to each point in X. Furthermore, the proximity
>> threshold of each point in X differs (X$threshold). I've constructed
>> this myself already, but it's horrificly slow with a dataset of 40k+
>> points in one set, and a 700 in the other.
>>
>> A very inefficient example of what I'm looking for:
>
> Not really a reproducible example. If euclidean_dist is a function ,
> then it is not one in any of the packages I have installed.
it's not reproducible - i'll make a better effort to include
reproducible code in the future. and that function is just one i would
have written, but didn't want to clog the email with code. Anyway, here
is a reproducible example:
X = data.frame(x=c(1,2,3), y=c(2,3,1), threshold=c(1,2,4))
Y = data.frame(x=c(5,2,3,4,2,5,2,3), y=c(5,2,2,4,1,2,3,1))
proximate=list()
i=1
for (pt in 1:length(X$x)) {
proximate[[i]] <- sqrt((X[pt,]$x - Y$x)^2 + (X[pt,]$y - Y$y)^2) >
X[pt,]$threshold
i=i+1
}
proximate
>>
>> for (pt in X$idx) {
>> proximity[i] = euclidian_dist(X[pt]$x, X[pt]$y, Y$x, Y$y) <
>> X$threshold
>> i = i+1
>> }
>>
>
> Have you considered first creating a subset of candidate points that are
> within "threshold" of each reference point on both coordinates. That
> might sidestep a lot of calculations on points that are easily
> eliminated on a single comparison. Then you could calculate distances
> within that surviving subset of points. On average that should give you
> an over 50% "hit rate":
>
>> (4/3)*pi*0.5^3
> [1] 0.5235988
That's a nice idea. I'll still be waiting quite a while while my
machine cranks, but not as long. Still - I suspect there would be much
bigger gains if there were tailored packages. I'll re-post over on
sig-geo about that. thanks.
>> Perhaps crossdist() in spatstat is what I should use, and then code a
>> comparison with X$threshold after the cross-distances are computed.
>> However, I was wondering if there was another tool I should be
>> considering. Any and all thoughts are very welcome. Thanks in advance.
>>
>> Thanks,
>> Allie
>> --
>> Alexander Shenkin
>> PhD Candidate
>> School of Natural Resources and Environment
>> University of Florida
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