[R] Output of silhouette (cluster package)
Martin Maechler
maechler at stat.math.ethz.ch
Sun Jun 15 01:19:24 CEST 2008
>>>>> "CV" == Cristiano Varin <cristiano.varin at mac.com>
>>>>> on Fri, 13 Jun 2008 11:31:34 +0200 writes:
CV> Dear R users, I am mailing you about the graphical
CV> output of silhouette (cluster package)
CV> From the example of silhouette in help(silhouette):
>> ar <- agnes(ruspini)
>> si3 <- silhouette(cutree(ar, k = 5), # k = 4 gave the same as pam() above
CV> + daisy(ruspini))
>> plot(si3, nmax = 80, cex.names = 0.5)
CV> from which one may conclude that group 1 is composed by units from 1
CV> to 20, group 2 by units from 21 to 43, group 3 by units from 44 to 57,
CV> group 4 by units from 58 to 60 and, finally, group 5 by units from 61
CV> to 75.
CV> However, this seems to be in contrast with the output of silhouette
CV> where the fourth group is composed by units from 46 to 48 instead of
CV> units from 58 to 60 (belonging to the third cluster), see
You are right.
Indeed, I see that this has been a bug in sortSilhouette() ever
since that had been introduced in 2002.
It will be fixed in cluster_1.11.11
Martin Maechler, ETH Zurich
>> si3
CV> cluster neighbor sil_width
CV> [1,] 1 5 0.679838078
CV> [2,] 1 5 0.745615002
CV> [3,] 1 5 0.758796123
CV> [4,] 1 4 0.715554768
CV> [5,] 1 5 0.664657114
CV> [6,] 1 4 0.783993831
CV> [7,] 1 2 0.590057470
CV> [8,] 1 4 0.747969458
CV> [9,] 1 5 0.792304760
CV> [10,] 1 4 0.803547635
CV> [11,] 1 4 0.742402051
CV> [12,] 1 4 0.722302731
CV> [13,] 1 4 0.665412622
CV> [14,] 1 5 0.756910666
CV> [15,] 1 5 0.700685403
CV> [16,] 1 5 0.743601834
CV> [17,] 1 5 0.614854124
CV> [18,] 1 5 0.708007860
CV> [19,] 1 5 0.700093839
CV> [20,] 1 4 0.568989067
CV> [21,] 2 4 0.751866935
CV> [22,] 2 4 0.790783667
CV> [23,] 2 4 0.802659788
CV> [24,] 2 4 0.785895823
CV> [25,] 2 4 0.822943473
CV> [26,] 2 4 0.831313347
CV> [27,] 2 4 0.818043337
CV> [28,] 2 4 0.805454305
CV> [29,] 2 4 0.770547118
CV> [30,] 2 4 0.768289979
CV> [31,] 2 3 0.794485567
CV> [32,] 2 4 0.829925955
CV> [33,] 2 4 0.807379640
CV> [34,] 2 4 0.790626589
CV> [35,] 2 4 0.817427927
CV> [36,] 2 3 0.793572412
CV> [37,] 2 4 0.760561408
CV> [38,] 2 4 0.743170109
CV> [39,] 2 3 0.761413953
CV> [40,] 2 3 0.704193051
CV> [41,] 2 4 0.297007126
CV> [42,] 2 4 0.522049838
CV> [43,] 2 3 0.488556828
CV> [44,] 3 4 0.377632488
CV> [45,] 3 4 0.007214464
CV> [46,] 4 3 0.699407534
CV> [47,] 4 3 0.837451212
CV> [48,] 4 3 0.794349431
CV> [49,] 3 4 0.632862996
CV> [50,] 3 4 0.586149139
CV> [51,] 3 4 0.647326133
CV> [52,] 3 4 0.650020368
CV> [53,] 3 4 0.629131005
CV> [54,] 3 4 0.618843633
CV> [55,] 3 4 0.586439350
CV> [56,] 3 4 0.586788051
CV> [57,] 3 4 0.668108812
CV> [58,] 3 4 0.650074540
CV> [59,] 3 4 0.628444500
CV> [60,] 3 4 0.591393005
CV> [61,] 5 1 0.770110294
CV> [62,] 5 1 0.815309198
CV> [63,] 5 4 0.771622667
CV> [64,] 5 1 0.806125429
CV> [65,] 5 1 0.850310507
CV> [66,] 5 1 0.822984066
CV> [67,] 5 1 0.852743923
CV> [68,] 5 1 0.762055943
CV> [69,] 5 1 0.839180986
CV> [70,] 5 1 0.854894699
CV> [71,] 5 1 0.838106473
CV> [72,] 5 1 0.774812117
CV> [73,] 5 1 0.795021304
CV> [74,] 5 1 0.759681469
CV> [75,] 5 1 0.742553847
CV> attr(,"Ordered")
CV> [1] FALSE
CV> attr(,"call")
CV> silhouette.default(x = cutree(ar, k = 5), dist = daisy(ruspini))
CV> attr(,"class")
CV> [1] "silhouette"
CV> Thanks for your attention,
CV> Cristiano
CV> ---------------------------------
CV> Cristiano Varin
CV> sammy at unive.it
CV> http://www.dst.unive.it/~sammy/
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