Hello,
I'm looking for a function that groups elements below a certain distance threshold, based on a distance matrix. In other words, I'd like to group samples without using a standard clustering algorithm on the distance matrix. For example, let the distance matrix be :
A B C D
A 0 0.03 0.77 1.12
B 0.03 0 1.59 1.11
C 0.77 1.59 0 0.09
D 1.12 1.11 0.09 0
Two clusters would be found with a cutoff of 0.1. The first contains A,B. The second has C,D. Is there an efficient function that does this ? I can think of how to do this recursively, but am hoping it's already been considered.
--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
Grouping on a Distance Matrix
2 messages · Dario Strbenac, Bert Gunter
You need to re-think. What you said is nonsense. Use an appropriate clustering algorithm. (a can be near b; b can be near c; but a is not near c, using "near" = closer than threshhold) Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." H. Gilbert Welch On Thu, Feb 13, 2014 at 12:00 AM, Dario Strbenac
<dstr7320 at uni.sydney.edu.au> wrote:
Hello,
I'm looking for a function that groups elements below a certain distance threshold, based on a distance matrix. In other words, I'd like to group samples without using a standard clustering algorithm on the distance matrix. For example, let the distance matrix be :
A B C D
A 0 0.03 0.77 1.12
B 0.03 0 1.59 1.11
C 0.77 1.59 0 0.09
D 1.12 1.11 0.09 0
Two clusters would be found with a cutoff of 0.1. The first contains A,B. The second has C,D. Is there an efficient function that does this ? I can think of how to do this recursively, but am hoping it's already been considered.
--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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