Fast C++ implementation of the Jarvis-Patrick clustering which first builds a shared nearest neighbor graph (k nearest neighbor sparsification) and then places two points in the same cluster if they are in each other's nearest neighbor list and they share at least kt nearest neighbors.
jpclust(x, k, kt, ...)
- a data matrix/data.frame (Euclidean distance is used), a precomputed
dist object or a kNN object created with
- Neighborhood size for nearest neighbor sparsification. If
xis a kNN object then
kmay be missing.
- threshold on the number of shared nearest neighbors (including the points themselves) to form clusters.
- additional arguments are passed on to the k
nearest neighbor search algorithm. See
kNNfor details on how to control the search strategy.
Note: Following the original paper, the shared nearest neighbor list is
constructed as the k neighbors plus the point itself (as neighbor zero).
Therefore, the threshold
kt can be in the range [1, k]. Fast nearest neighbors search with
kNN() is only used if
x is a matrix. In this case Euclidean distance is used.
A object of class 'general_clustering' with the following components:
R. A. Jarvis and E. A. Patrick. 1973. Clustering Using a Similarity Measure Based on Shared Near Neighbors. IEEE Trans. Comput. 22, 11 (November 1973), 1025-1034.
data("DS3") # use a shared neighborhood of 20 points and require 12 shared neighbors cl <- jpclust(DS3, k = 20, kt = 12) cl plot(DS3, col = cl$cluster+1L, cex = .5) # Note: JP clustering does not consider noise and thus, # the sine wave points chain clusters together. # use a precomputed kNN object instead of the original data. nn <- kNN(DS3, k = 30) nn cl <- jpclust(nn, k = 20, kt = 12) cl # cluster with noise removed (use low pointdensity to identify noise) d <- pointdensity(DS3, eps = 25) hist(d, breaks = 20) DS3_noiseless <- DS3[d > 110,] cl <- jpclust(DS3_noiseless, k = 20, kt = 10) cl plot(DS3_noiseless, col = cl$cluster+1L, cex = .5)