548 lines
17 KiB
Plaintext
548 lines
17 KiB
Plaintext
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R version 3.5.0 alpha (2018-03-28 r74481)
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Copyright (C) 2018 The R Foundation for Statistical Computing
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Platform: x86_64-pc-linux-gnu (64-bit)
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R is free software and comes with ABSOLUTELY NO WARRANTY.
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You are welcome to redistribute it under certain conditions.
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Type 'license()' or 'licence()' for distribution details.
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R is a collaborative project with many contributors.
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Type 'contributors()' for more information and
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'citation()' on how to cite R or R packages in publications.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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'help.start()' for an HTML browser interface to help.
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Type 'q()' to quit R.
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> library(cluster)
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> options(digits = 6)
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> data(votes.repub)
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> di.votes <- daisy(votes.repub)
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>
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> .p00 <- proc.time()
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> summary(diana(votes.repub, metric = "manhattan", stand = TRUE))
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Merge:
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[,1] [,2]
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[1,] -7 -32
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[2,] -13 -35
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[3,] -12 -50
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[4,] 1 -30
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[5,] -26 -28
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[6,] -5 -37
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[7,] -22 -38
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[8,] -21 -39
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[9,] -16 -27
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[10,] 4 2
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[11,] -25 -48
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[12,] -42 -46
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[13,] -6 -14
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[14,] -34 -41
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[15,] -8 -20
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[16,] 5 -31
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[17,] 10 7
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[18,] -17 -47
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[19,] -3 -44
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[20,] -33 12
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[21,] 15 18
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[22,] 17 -29
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[23,] 22 -49
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[24,] 21 11
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[25,] 23 -15
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[26,] -11 -19
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[27,] 3 9
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[28,] 8 -23
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[29,] 19 16
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[30,] 27 14
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[31,] 6 25
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[32,] -1 -10
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[33,] 31 13
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[34,] 29 -36
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[35,] -2 -45
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[36,] -9 -43
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[37,] 24 20
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[38,] 32 -4
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[39,] -24 -40
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[40,] 38 -18
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[41,] 33 30
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[42,] 34 37
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[43,] 35 26
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[44,] 41 28
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[45,] 40 36
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[46,] 42 44
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[47,] 45 39
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[48,] 43 46
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[49,] 47 48
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Order of objects:
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[1] Alabama Georgia Arkansas Louisiana Florida
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[6] Texas Mississippi South Carolina Alaska Vermont
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[11] Hawaii Maine Arizona Utah Montana
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[16] Nevada New Mexico Oklahoma Delaware Maryland
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[21] Kentucky Washington Missouri West Virginia North Carolina
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[26] Tennessee Virginia California Oregon Connecticut
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[31] New York New Jersey Illinois Ohio Michigan
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[36] Pennsylvania New Hampshire Wisconsin Iowa Colorado
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[41] Indiana Idaho Wyoming Kansas Nebraska
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[46] North Dakota South Dakota Massachusetts Rhode Island Minnesota
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Height:
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[1] 27.36345 33.96925 39.65826 48.53428 31.89965 72.59850 35.69152
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[8] 167.58020 31.58222 43.84601 24.48796 85.55248 18.39339 25.67631
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[15] 11.49397 17.45552 28.62550 42.54480 16.48510 20.04450 17.87516
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[22] 21.98373 14.21808 33.61071 18.39733 14.75762 56.55675 11.70132
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[29] 27.05887 8.38200 11.36820 13.25237 9.23004 17.83484 12.70819
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[36] 20.66714 21.03997 23.66586 28.60541 15.31703 40.33905 10.46294
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[43] 24.83525 12.80419 26.36292 16.25192 47.25773 12.79160 24.87206
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Divisive coefficient:
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[1] 0.886918
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1225 dissimilarities, summarized :
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Min. 1st Qu. Median Mean 3rd Qu. Max.
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8.38 25.54 34.51 45.06 56.02 167.60
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Metric : manhattan
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Number of objects : 50
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Available components:
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[1] "order" "height" "dc" "merge" "diss" "call"
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[7] "order.lab" "data"
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> summary(diana(di.votes, keep.diss = FALSE))
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Merge:
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[,1] [,2]
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[1,] -12 -50
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[2,] -13 -32
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[3,] -14 -35
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[4,] -7 -29
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[5,] -21 -39
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[6,] -3 -28
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[7,] -25 -48
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[8,] -16 -27
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[9,] -15 -41
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[10,] 2 -30
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[11,] 6 -26
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[12,] -33 -42
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[13,] 12 -46
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[14,] 1 -44
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[15,] 10 3
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[16,] -22 -38
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[17,] -11 -19
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[18,] -5 -47
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[19,] -17 -20
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[20,] -2 -45
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[21,] 14 -31
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[22,] -37 -49
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[23,] 9 8
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[24,] 4 15
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[25,] -8 19
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[26,] -6 21
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[27,] 5 -23
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[28,] 24 16
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[29,] 26 -36
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[30,] 11 29
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[31,] -1 -10
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[32,] 28 22
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[33,] 23 -34
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[34,] 7 13
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[35,] -4 -9
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[36,] 20 17
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[37,] -24 -40
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[38,] 31 -43
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[39,] 32 33
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[40,] 25 34
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[41,] 30 18
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[42,] 35 -18
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[43,] 38 42
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[44,] 39 27
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[45,] 41 40
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[46,] 36 44
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[47,] 43 37
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[48,] 46 45
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[49,] 47 48
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Order of objects:
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[1] Alabama Georgia Texas Arkansas Florida
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[6] Louisiana Mississippi South Carolina Alaska Vermont
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[11] Hawaii Maine Connecticut New Hampshire Illinois
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[16] New York New Jersey Indiana Ohio Michigan
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[21] Pennsylvania Oregon Wisconsin Iowa South Dakota
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[26] Kansas Nebraska North Dakota Massachusetts Rhode Island
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[31] Minnesota Arizona Nevada Montana Colorado
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[36] Idaho Wyoming Utah New Mexico Oklahoma
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[41] California Washington Delaware Kentucky Maryland
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[46] Missouri West Virginia North Carolina Tennessee Virginia
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Height:
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[1] 48.2397 63.1862 72.9221 56.1363 72.9221 116.7048 63.0951 281.9508
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[9] 33.8330 58.0384 32.7611 106.7448 20.5216 39.1728 19.8436 27.0243
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[17] 31.4966 20.2258 47.1690 31.6595 49.2428 36.7667 64.4821 26.1547
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[25] 37.4564 25.9221 50.7201 77.1184 22.6334 44.4594 178.4119 23.4206
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[33] 27.8273 48.0483 43.7055 17.1992 31.1988 34.0510 48.0483 70.4868
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[41] 33.2328 81.0764 43.3829 33.4744 66.7591 25.3953 54.7306 29.5099
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[49] 30.1541
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Divisive coefficient:
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[1] 0.878225
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Available components:
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[1] "order" "height" "dc" "merge" "diss" "call"
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[7] "order.lab"
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> cat('Time elapsed: ', proc.time() - .p00,'\n')
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Time elapsed: 0.006 0.003 0.008 0 0
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>
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> data(agriculture)
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> data(ruspini)
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>
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> .p0 <- proc.time()
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> dia.agr <- diana(agriculture)
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> drusp0 <- diana(ruspini, keep.diss=FALSE, keep.data=FALSE)
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> drusp1 <- diana(ruspini, metric = "manhattan")
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> cat('Time elapsed: ', proc.time() - .p0,'\n')
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Time elapsed: 0.002 0 0.003 0 0
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>
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> summary(dia.agr)
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Merge:
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[,1] [,2]
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[1,] -1 -10
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[2,] -2 -9
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[3,] 1 -3
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[4,] -6 -8
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[5,] -5 -7
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[6,] 3 -12
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[7,] -4 -11
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[8,] 6 4
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[9,] 8 2
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[10,] 7 5
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[11,] 9 10
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Order of objects:
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[1] B NL D UK F I DK L GR P E IRL
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Height:
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[1] 1.64924 2.43516 4.85077 6.72309 2.77308 8.05295 2.22036 24.03539
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[9] 5.16236 12.56742 3.14006
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Divisive coefficient:
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[1] 0.871106
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66 dissimilarities, summarized :
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Min. 1st Qu. Median Mean 3rd Qu. Max.
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1.65 4.36 7.99 9.59 13.25 24.04
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Metric : euclidean
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Number of objects : 12
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Available components:
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[1] "order" "height" "dc" "merge" "diss" "call"
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[7] "order.lab" "data"
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> summary(drusp0)
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Merge:
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[,1] [,2]
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[1,] -18 -19
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[2,] -55 -56
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[3,] -27 -28
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[4,] -49 -51
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[5,] -33 -34
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[6,] -23 -24
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[7,] -59 -60
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[8,] -29 -30
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[9,] -67 -69
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[10,] -36 -39
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[11,] -32 -35
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[12,] -50 -54
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[13,] -37 -38
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[14,] -70 -71
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[15,] -64 -68
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[16,] -62 -66
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[17,] -12 -13
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[18,] -16 1
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[19,] -9 -10
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[20,] -42 -43
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[21,] -15 -17
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[22,] -47 -48
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[23,] 12 -52
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[24,] -21 -22
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[25,] 9 14
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[26,] 2 -57
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[27,] -73 -74
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[28,] 6 -25
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[29,] -26 11
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[30,] 4 -53
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[31,] 3 8
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[32,] -11 17
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[33,] -6 -8
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[34,] -2 -3
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[35,] 10 -40
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[36,] -14 21
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[37,] -65 25
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[38,] -4 33
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[39,] 36 18
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[40,] 29 5
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[41,] 26 7
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[42,] -1 34
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[43,] 24 28
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[44,] 16 -63
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[45,] -46 22
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[46,] -31 35
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[47,] 27 -75
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[48,] 37 -72
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[49,] 43 31
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[50,] 30 23
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[51,] 13 20
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[52,] 15 48
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[53,] 32 -20
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[54,] 41 -58
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[55,] 42 -5
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[56,] 40 46
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[57,] -44 -45
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[58,] 19 39
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[59,] 38 -7
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[60,] 51 -41
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[61,] -61 44
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[62,] 50 54
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[63,] 52 47
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[64,] 61 63
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[65,] 49 56
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[66,] 59 53
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[67,] 55 58
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[68,] 57 62
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[69,] 65 60
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[70,] 67 66
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[71,] 68 45
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[72,] 69 71
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[73,] 70 64
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[74,] 73 72
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Order of objects:
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[1] 1 2 3 5 9 10 14 15 17 16 18 19 4 6 8 7 11 12 13 20 61 62 66 63 64
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[26] 68 65 67 69 70 71 72 73 74 75 21 22 23 24 25 27 28 29 30 26 32 35 33 34 31
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[51] 36 39 40 37 38 42 43 41 44 45 49 51 53 50 54 52 55 56 57 59 60 58 46 47 48
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Height:
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[1] 10.04988 6.40312 16.12452 29.12044 4.12311 17.02939 8.48528
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[8] 4.24264 9.21954 4.12311 1.41421 40.24922 8.94427 6.32456
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[15] 19.02630 28.84441 6.32456 4.12311 14.14214 102.07840 21.40093
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[22] 4.12311 10.81665 27.07397 3.60555 13.60147 8.54400 2.82843
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[29] 5.09902 3.60555 12.80625 22.80351 5.65685 12.36932 154.49595
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[36] 4.47214 10.77033 2.23607 5.83095 13.03840 2.00000 6.32456
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[43] 2.82843 28.16026 6.08276 3.00000 9.43398 2.23607 16.27882
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[50] 11.04536 3.00000 6.70820 36.61967 3.60555 13.34166 4.24264
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[57] 20.02498 94.57801 17.02939 35.35534 2.23607 6.32456 13.15295
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[64] 3.16228 4.47214 22.20360 2.00000 5.38516 9.84886 2.82843
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[71] 15.29706 47.63402 11.00000 4.47214
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Divisive coefficient:
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[1] 0.960566
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Available components:
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[1] "order" "height" "dc" "merge" "diss" "call"
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[7] "order.lab"
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> summary(drusp1)
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Merge:
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[,1] [,2]
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[1,] -55 -56
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[2,] -27 -28
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[3,] -18 -19
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[4,] -49 -51
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[5,] -33 -34
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[6,] -32 -35
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[7,] -23 -24
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[8,] -59 -60
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[9,] -50 -54
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[10,] -29 -30
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[11,] -67 -69
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[12,] -37 -38
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[13,] 11 -71
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[14,] -64 -68
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[15,] -62 -66
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[16,] -12 -13
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[17,] -16 3
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[18,] -9 -10
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[19,] -47 -48
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[20,] 9 -52
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[21,] -42 -43
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[22,] -39 -40
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[23,] -21 -22
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[24,] 13 -70
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[25,] -15 -17
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[26,] 1 -57
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[27,] -26 6
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[28,] 4 -53
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[29,] 7 -25
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[30,] 2 10
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[31,] -11 16
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[32,] -6 -8
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[33,] -31 -36
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[34,] -74 -75
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[35,] -2 -3
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[36,] -46 19
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[37,] -65 24
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[38,] -14 17
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[39,] -4 32
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[40,] 38 25
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[41,] -1 35
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[42,] 26 8
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[43,] 27 5
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[44,] 23 30
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[45,] 28 20
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[46,] 15 -63
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[47,] 43 33
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[48,] 44 29
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[49,] 46 -73
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[50,] 31 -20
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[51,] 42 -58
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[52,] -44 -45
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[53,] 12 22
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[54,] 37 -72
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[55,] 14 54
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[56,] 39 -7
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[57,] 41 -5
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[58,] 53 21
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[59,] 18 40
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[60,] 48 47
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[61,] -61 49
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[62,] 45 51
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[63,] 58 -41
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[64,] 55 34
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[65,] 61 64
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[66,] 57 59
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[67,] 56 50
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[68,] 52 62
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[69,] 60 63
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[70,] 66 67
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[71,] 68 36
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[72,] 69 71
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[73,] 70 65
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[74,] 73 72
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Order of objects:
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[1] 1 2 3 5 9 10 14 16 18 19 15 17 4 6 8 7 11 12 13 20 61 62 66 63 73
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||
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[26] 64 68 65 67 69 71 70 72 74 75 21 22 27 28 29 30 23 24 25 26 32 35 33 34 31
|
||
|
[51] 36 37 38 39 40 42 43 41 44 45 49 51 53 50 54 52 55 56 57 59 60 58 46 47 48
|
||
|
Height:
|
||
|
[1] 12 9 22 36 5 24 11 5 2 12 6 54 12 8 20 40 8 5 16
|
||
|
[20] 142 30 5 15 16 33 5 19 11 4 5 6 18 32 9 187 6 14 2
|
||
|
[39] 8 4 16 3 8 26 7 3 13 3 16 9 51 5 18 6 24 6 32
|
||
|
[58] 123 18 48 3 8 15 4 6 31 2 7 13 4 18 67 11 6
|
||
|
Divisive coefficient:
|
||
|
[1] 0.958075
|
||
|
|
||
|
2775 dissimilarities, summarized :
|
||
|
Min. 1st Qu. Median Mean 3rd Qu. Max.
|
||
|
2.0 52.5 97.0 91.0 128.0 187.0
|
||
|
Metric : manhattan
|
||
|
Number of objects : 75
|
||
|
|
||
|
Available components:
|
||
|
[1] "order" "height" "dc" "merge" "diss" "call"
|
||
|
[7] "order.lab" "data"
|
||
|
> str (drusp1)
|
||
|
List of 8
|
||
|
$ order : int [1:75] 1 2 3 5 9 10 14 16 18 19 ...
|
||
|
$ height : num [1:74] 12 9 22 36 5 24 11 5 2 12 ...
|
||
|
$ dc : num 0.958
|
||
|
$ merge : int [1:74, 1:2] -55 -27 -18 -49 -33 -32 -23 -59 -50 -29 ...
|
||
|
$ diss : 'dissimilarity' num [1:2775] 11 12 29 13 25 43 33 22 27 39 ...
|
||
|
..- attr(*, "Size")= int 75
|
||
|
..- attr(*, "Metric")= chr "manhattan"
|
||
|
..- attr(*, "Labels")= chr [1:75] "1" "2" "3" "4" ...
|
||
|
$ call : language diana(x = ruspini, metric = "manhattan")
|
||
|
$ order.lab: chr [1:75] "1" "2" "3" "5" ...
|
||
|
$ data : int [1:75, 1:2] 4 5 10 9 13 13 12 15 18 19 ...
|
||
|
..- attr(*, "dimnames")=List of 2
|
||
|
.. ..$ : chr [1:75] "1" "2" "3" "4" ...
|
||
|
.. ..$ : chr [1:2] "x" "y"
|
||
|
- attr(*, "class")= chr [1:2] "diana" "twins"
|
||
|
>
|
||
|
> ## From system.file("scripts/ch11.R", package = "MASS")
|
||
|
> data(swiss)
|
||
|
> swiss.x <- as.matrix(swiss[,-1])
|
||
|
> .p1 <- proc.time()
|
||
|
> dCH <- diana(swiss.x)
|
||
|
> cat('Time elapsed: ', proc.time() - .p1,'\n')
|
||
|
Time elapsed: 0.001 0 0.001 0 0
|
||
|
> str(as.dendrogram(as.hclust(dCH)))# keep back-compatible
|
||
|
--[dendrogram w/ 2 branches and 47 members at h = 127]
|
||
|
|--[dendrogram w/ 2 branches and 31 members at h = 99.2]
|
||
|
| |--[dendrogram w/ 2 branches and 11 members at h = 60.9]
|
||
|
| | |--[dendrogram w/ 2 branches and 8 members at h = 29.1]
|
||
|
| | | |--[dendrogram w/ 2 branches and 5 members at h = 22.7]
|
||
|
| | | | |--[dendrogram w/ 2 branches and 4 members at h = 17.4]
|
||
|
| | | | | |--[dendrogram w/ 2 branches and 3 members at h = 11.7]
|
||
|
| | | | | | |--leaf "Courtelary"
|
||
|
| | | | | | `--[dendrogram w/ 2 branches and 2 members at h = 7.48]
|
||
|
| | | | | | |--leaf "Le Locle"
|
||
|
| | | | | | `--leaf "ValdeTravers"
|
||
|
| | | | | `--leaf "La Chauxdfnd"
|
||
|
| | | | `--leaf "La Vallee"
|
||
|
| | | `--[dendrogram w/ 2 branches and 3 members at h = 19]
|
||
|
| | | |--[dendrogram w/ 2 branches and 2 members at h = 11.5]
|
||
|
| | | | |--leaf "Lausanne"
|
||
|
| | | | `--leaf "Neuchatel"
|
||
|
| | | `--leaf "Vevey"
|
||
|
| | `--[dendrogram w/ 2 branches and 3 members at h = 56.1]
|
||
|
| | |--leaf "V. De Geneve"
|
||
|
| | `--[dendrogram w/ 2 branches and 2 members at h = 21.4]
|
||
|
| | |--leaf "Rive Droite"
|
||
|
| | `--leaf "Rive Gauche"
|
||
|
| `--[dendrogram w/ 2 branches and 20 members at h = 48.4]
|
||
|
| |--leaf "Moutier"
|
||
|
| `--[dendrogram w/ 2 branches and 19 members at h = 44.3]
|
||
|
| |--[dendrogram w/ 2 branches and 18 members at h = 39.1]
|
||
|
| | |--[dendrogram w/ 2 branches and 6 members at h = 21.9]
|
||
|
| | | |--[dendrogram w/ 2 branches and 4 members at h = 12.1]
|
||
|
| | | | |--[dendrogram w/ 2 branches and 2 members at h = 10.8]
|
||
|
| | | | | |--leaf "Neuveville"
|
||
|
| | | | | `--leaf "Boudry"
|
||
|
| | | | `--[dendrogram w/ 2 branches and 2 members at h = 4.56]
|
||
|
| | | | |--leaf "Grandson"
|
||
|
| | | | `--leaf "Val de Ruz"
|
||
|
| | | `--[dendrogram w/ 2 branches and 2 members at h = 13.5]
|
||
|
| | | |--leaf "Nyone"
|
||
|
| | | `--leaf "Yverdon"
|
||
|
| | `--[dendrogram w/ 2 branches and 12 members at h = 20.4]
|
||
|
| | |--[dendrogram w/ 2 branches and 7 members at h = 15.1]
|
||
|
| | | |--[dendrogram w/ 2 branches and 5 members at h = 11.6]
|
||
|
| | | | |--[dendrogram w/ 2 branches and 4 members at h = 8.05]
|
||
|
| | | | | |--[dendrogram w/ 2 branches and 3 members at h = 6.79]
|
||
|
| | | | | | |--[dendrogram w/ 2 branches and 2 members at h = 4.79]
|
||
|
| | | | | | | |--leaf "Aigle"
|
||
|
| | | | | | | `--leaf "Morges"
|
||
|
| | | | | | `--leaf "Rolle"
|
||
|
| | | | | `--leaf "Avenches"
|
||
|
| | | | `--leaf "Orbe"
|
||
|
| | | `--[dendrogram w/ 2 branches and 2 members at h = 6.04]
|
||
|
| | | |--leaf "Moudon"
|
||
|
| | | `--leaf "Payerne"
|
||
|
| | `--[dendrogram w/ 2 branches and 5 members at h = 17.3]
|
||
|
| | |--[dendrogram w/ 2 branches and 4 members at h = 11.2]
|
||
|
| | | |--[dendrogram w/ 2 branches and 2 members at h = 7.57]
|
||
|
| | | | |--leaf "Aubonne"
|
||
|
| | | | `--leaf "Oron"
|
||
|
| | | `--[dendrogram w/ 2 branches and 2 members at h = 6.35]
|
||
|
| | | |--leaf "Cossonay"
|
||
|
| | | `--leaf "Lavaux"
|
||
|
| | `--leaf "Paysd'enhaut"
|
||
|
| `--leaf "Echallens"
|
||
|
`--[dendrogram w/ 2 branches and 16 members at h = 56.2]
|
||
|
|--[dendrogram w/ 2 branches and 5 members at h = 20.4]
|
||
|
| |--[dendrogram w/ 2 branches and 3 members at h = 12.7]
|
||
|
| | |--leaf "Delemont"
|
||
|
| | `--[dendrogram w/ 2 branches and 2 members at h = 9.4]
|
||
|
| | |--leaf "Franches-Mnt"
|
||
|
| | `--leaf "Porrentruy"
|
||
|
| `--[dendrogram w/ 2 branches and 2 members at h = 13]
|
||
|
| |--leaf "Gruyere"
|
||
|
| `--leaf "Sarine"
|
||
|
`--[dendrogram w/ 2 branches and 11 members at h = 30]
|
||
|
|--[dendrogram w/ 2 branches and 5 members at h = 12.9]
|
||
|
| |--[dendrogram w/ 2 branches and 4 members at h = 11.9]
|
||
|
| | |--[dendrogram w/ 2 branches and 3 members at h = 8.45]
|
||
|
| | | |--leaf "Broye"
|
||
|
| | | `--[dendrogram w/ 2 branches and 2 members at h = 4.14]
|
||
|
| | | |--leaf "Glane"
|
||
|
| | | `--leaf "Veveyse"
|
||
|
| | `--leaf "Sion"
|
||
|
| `--leaf "Monthey"
|
||
|
`--[dendrogram w/ 2 branches and 6 members at h = 16]
|
||
|
|--[dendrogram w/ 2 branches and 4 members at h = 7.42]
|
||
|
| |--[dendrogram w/ 2 branches and 3 members at h = 5.94]
|
||
|
| | |--[dendrogram w/ 2 branches and 2 members at h = 2.05]
|
||
|
| | | |--leaf "Conthey"
|
||
|
| | | `--leaf "Sierre"
|
||
|
| | `--leaf "Herens"
|
||
|
| `--leaf "Entremont"
|
||
|
`--[dendrogram w/ 2 branches and 2 members at h = 5.09]
|
||
|
|--leaf "Martigwy"
|
||
|
`--leaf "St Maurice"
|
||
|
>
|
||
|
> proc.time()
|
||
|
user system elapsed
|
||
|
0.192 0.044 0.292
|