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vignette("discoCVI")).disco_samples() and disco_score() no
longer build any n x n matrix. The minimum spanning tree of the
mutual-reachability graph is computed in compiled code (Rcpp) with
distances evaluated on the fly, and all quantities needed by DISCO (sums
and minima of density-connectivity distances per cluster) are obtained
in a single pass over the resulting single-linkage merge tree. Memory
now grows linearly with the number of points (times the number of
clusters) instead of quadratically. On synthetic benchmarks, 0.2.0 is 23
to 138 times faster than 0.1.1 (n = 500 to 4,000; 1,222 MB vs 93 MB peak
memory at n = 4,000), and 100,000 points can be scored in about 50
seconds with about 200 MB peak memory for the whole R process.extract_dc_distances_from_mst() fills the DC-distance
matrix block by block in Kruskal order instead of running a
breadth-first search from every point.compute_dc_distances() no longer builds the
mutual-reachability matrix.p_cluster() is vectorised (one matrix product instead
of nested loops).silhouette_samples(). Version
0.1.1 gave them a score of 1, which inflated disco_score()
for labelings containing singleton clusters (for example from DBSCAN
with a small minPts). Labelings without singleton clusters
are not affected.tests/testthat).These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.