Re: [R] Output of silhouette (cluster package)

From: Martin Maechler <maechler_at_stat.math.ethz.ch>
Date: Sun, 15 Jun 2008 01:19:24 +0200

>>>>> "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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