[R] Output of silhouette (cluster package)

From: Cristiano Varin <cristiano.varin_at_mac.com>
Date: Fri, 13 Jun 2008 11:31:34 +0200


Dear R users,
I am mailing you about the graphical output of silhouette (cluster package)

 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

+                    daisy(ruspini))

 > plot(si3, nmax = 80, cex.names = 0.5)

from which one may conclude that group 1 is composed by units from 1 to 20, group 2 by units from 21 to 43, group 3 by units from 44 to 57, group 4 by units from 58 to 60 and, finally, group 5 by units from 61 to 75.

However, this seems to be in contrast with the output of silhouette where the fourth group is composed by units from 46 to 48 instead of units from 58 to 60 (belonging to the third cluster), see  > si3

       cluster neighbor   sil_width
  [1,]       1        5 0.679838078
  [2,]       1        5 0.745615002
  [3,]       1        5 0.758796123
  [4,]       1        4 0.715554768
  [5,]       1        5 0.664657114
  [6,]       1        4 0.783993831
  [7,]       1        2 0.590057470
  [8,]       1        4 0.747969458
  [9,]       1        5 0.792304760

[10,] 1 4 0.803547635
[11,] 1 4 0.742402051
[12,] 1 4 0.722302731
[13,] 1 4 0.665412622
[14,] 1 5 0.756910666
[15,] 1 5 0.700685403
[16,] 1 5 0.743601834
[17,] 1 5 0.614854124
[18,] 1 5 0.708007860
[19,] 1 5 0.700093839
[20,] 1 4 0.568989067
[21,] 2 4 0.751866935
[22,] 2 4 0.790783667
[23,] 2 4 0.802659788
[24,] 2 4 0.785895823
[25,] 2 4 0.822943473
[26,] 2 4 0.831313347
[27,] 2 4 0.818043337
[28,] 2 4 0.805454305
[29,] 2 4 0.770547118
[30,] 2 4 0.768289979
[31,] 2 3 0.794485567
[32,] 2 4 0.829925955
[33,] 2 4 0.807379640
[34,] 2 4 0.790626589
[35,] 2 4 0.817427927
[36,] 2 3 0.793572412
[37,] 2 4 0.760561408
[38,] 2 4 0.743170109
[39,] 2 3 0.761413953
[40,] 2 3 0.704193051
[41,] 2 4 0.297007126
[42,] 2 4 0.522049838
[43,] 2 3 0.488556828
[44,] 3 4 0.377632488
[45,] 3 4 0.007214464
[46,] 4 3 0.699407534
[47,] 4 3 0.837451212
[48,] 4 3 0.794349431
[49,] 3 4 0.632862996
[50,] 3 4 0.586149139
[51,] 3 4 0.647326133
[52,] 3 4 0.650020368
[53,] 3 4 0.629131005
[54,] 3 4 0.618843633
[55,] 3 4 0.586439350
[56,] 3 4 0.586788051
[57,] 3 4 0.668108812
[58,] 3 4 0.650074540
[59,] 3 4 0.628444500
[60,] 3 4 0.591393005
[61,] 5 1 0.770110294
[62,] 5 1 0.815309198
[63,] 5 4 0.771622667
[64,] 5 1 0.806125429
[65,] 5 1 0.850310507
[66,] 5 1 0.822984066
[67,] 5 1 0.852743923
[68,] 5 1 0.762055943
[69,] 5 1 0.839180986
[70,] 5 1 0.854894699
[71,] 5 1 0.838106473
[72,] 5 1 0.774812117
[73,] 5 1 0.795021304
[74,] 5 1 0.759681469
[75,] 5 1 0.742553847

attr(,"Ordered")
[1] FALSE

attr(,"call")
silhouette.default(x = cutree(ar, k = 5), dist = daisy(ruspini)) attr(,"class")
[1] "silhouette"

Thanks for your attention,
Cristiano



Cristiano Varin
sammy_at_unive.it
http://www.dst.unive.it/~sammy/

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