The R Project SVN
R-packages
(root)/branches/cluster-2.1/tests/diana-ex.Rout.save – Rev 8500
Rev 7508 | Blame | Compare with Previous | Last modification | View Log | Download | RSS feed
R version 3.5.0 alpha (2018-03-28 r74481)Copyright (C) 2018 The R Foundation for Statistical ComputingPlatform: x86_64-pc-linux-gnu (64-bit)R is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain conditions.Type 'license()' or 'licence()' for distribution details.R is a collaborative project with many contributors.Type 'contributors()' for more information and'citation()' on how to cite R or R packages in publications.Type 'demo()' for some demos, 'help()' for on-line help, or'help.start()' for an HTML browser interface to help.Type 'q()' to quit R.> library(cluster)> options(digits = 6)> data(votes.repub)> di.votes <- daisy(votes.repub)>> .p00 <- proc.time()> summary(diana(votes.repub, metric = "manhattan", stand = TRUE))Merge:[,1] [,2][1,] -7 -32[2,] -13 -35[3,] -12 -50[4,] 1 -30[5,] -26 -28[6,] -5 -37[7,] -22 -38[8,] -21 -39[9,] -16 -27[10,] 4 2[11,] -25 -48[12,] -42 -46[13,] -6 -14[14,] -34 -41[15,] -8 -20[16,] 5 -31[17,] 10 7[18,] -17 -47[19,] -3 -44[20,] -33 12[21,] 15 18[22,] 17 -29[23,] 22 -49[24,] 21 11[25,] 23 -15[26,] -11 -19[27,] 3 9[28,] 8 -23[29,] 19 16[30,] 27 14[31,] 6 25[32,] -1 -10[33,] 31 13[34,] 29 -36[35,] -2 -45[36,] -9 -43[37,] 24 20[38,] 32 -4[39,] -24 -40[40,] 38 -18[41,] 33 30[42,] 34 37[43,] 35 26[44,] 41 28[45,] 40 36[46,] 42 44[47,] 45 39[48,] 43 46[49,] 47 48Order of objects:[1] Alabama Georgia Arkansas Louisiana Florida[6] Texas Mississippi South Carolina Alaska Vermont[11] Hawaii Maine Arizona Utah Montana[16] Nevada New Mexico Oklahoma Delaware Maryland[21] Kentucky Washington Missouri West Virginia North Carolina[26] Tennessee Virginia California Oregon Connecticut[31] New York New Jersey Illinois Ohio Michigan[36] Pennsylvania New Hampshire Wisconsin Iowa Colorado[41] Indiana Idaho Wyoming Kansas Nebraska[46] North Dakota South Dakota Massachusetts Rhode Island MinnesotaHeight:[1] 27.36345 33.96925 39.65826 48.53428 31.89965 72.59850 35.69152[8] 167.58020 31.58222 43.84601 24.48796 85.55248 18.39339 25.67631[15] 11.49397 17.45552 28.62550 42.54480 16.48510 20.04450 17.87516[22] 21.98373 14.21808 33.61071 18.39733 14.75762 56.55675 11.70132[29] 27.05887 8.38200 11.36820 13.25237 9.23004 17.83484 12.70819[36] 20.66714 21.03997 23.66586 28.60541 15.31703 40.33905 10.46294[43] 24.83525 12.80419 26.36292 16.25192 47.25773 12.79160 24.87206Divisive coefficient:[1] 0.8869181225 dissimilarities, summarized :Min. 1st Qu. Median Mean 3rd Qu. Max.8.38 25.54 34.51 45.06 56.02 167.60Metric : manhattanNumber of objects : 50Available components:[1] "order" "height" "dc" "merge" "diss" "call"[7] "order.lab" "data"> summary(diana(di.votes, keep.diss = FALSE))Merge:[,1] [,2][1,] -12 -50[2,] -13 -32[3,] -14 -35[4,] -7 -29[5,] -21 -39[6,] -3 -28[7,] -25 -48[8,] -16 -27[9,] -15 -41[10,] 2 -30[11,] 6 -26[12,] -33 -42[13,] 12 -46[14,] 1 -44[15,] 10 3[16,] -22 -38[17,] -11 -19[18,] -5 -47[19,] -17 -20[20,] -2 -45[21,] 14 -31[22,] -37 -49[23,] 9 8[24,] 4 15[25,] -8 19[26,] -6 21[27,] 5 -23[28,] 24 16[29,] 26 -36[30,] 11 29[31,] -1 -10[32,] 28 22[33,] 23 -34[34,] 7 13[35,] -4 -9[36,] 20 17[37,] -24 -40[38,] 31 -43[39,] 32 33[40,] 25 34[41,] 30 18[42,] 35 -18[43,] 38 42[44,] 39 27[45,] 41 40[46,] 36 44[47,] 43 37[48,] 46 45[49,] 47 48Order of objects:[1] Alabama Georgia Texas Arkansas Florida[6] Louisiana Mississippi South Carolina Alaska Vermont[11] Hawaii Maine Connecticut New Hampshire Illinois[16] New York New Jersey Indiana Ohio Michigan[21] Pennsylvania Oregon Wisconsin Iowa South Dakota[26] Kansas Nebraska North Dakota Massachusetts Rhode Island[31] Minnesota Arizona Nevada Montana Colorado[36] Idaho Wyoming Utah New Mexico Oklahoma[41] California Washington Delaware Kentucky Maryland[46] Missouri West Virginia North Carolina Tennessee VirginiaHeight:[1] 48.2397 63.1862 72.9221 56.1363 72.9221 116.7048 63.0951 281.9508[9] 33.8330 58.0384 32.7611 106.7448 20.5216 39.1728 19.8436 27.0243[17] 31.4966 20.2258 47.1690 31.6595 49.2428 36.7667 64.4821 26.1547[25] 37.4564 25.9221 50.7201 77.1184 22.6334 44.4594 178.4119 23.4206[33] 27.8273 48.0483 43.7055 17.1992 31.1988 34.0510 48.0483 70.4868[41] 33.2328 81.0764 43.3829 33.4744 66.7591 25.3953 54.7306 29.5099[49] 30.1541Divisive coefficient:[1] 0.878225Available components:[1] "order" "height" "dc" "merge" "diss" "call"[7] "order.lab"> cat('Time elapsed: ', proc.time() - .p00,'\n')Time elapsed: 0.006 0.003 0.008 0 0>> data(agriculture)> data(ruspini)>> .p0 <- proc.time()> dia.agr <- diana(agriculture)> drusp0 <- diana(ruspini, keep.diss=FALSE, keep.data=FALSE)> drusp1 <- diana(ruspini, metric = "manhattan")> cat('Time elapsed: ', proc.time() - .p0,'\n')Time elapsed: 0.002 0 0.003 0 0>> summary(dia.agr)Merge:[,1] [,2][1,] -1 -10[2,] -2 -9[3,] 1 -3[4,] -6 -8[5,] -5 -7[6,] 3 -12[7,] -4 -11[8,] 6 4[9,] 8 2[10,] 7 5[11,] 9 10Order of objects:[1] B NL D UK F I DK L GR P E IRLHeight:[1] 1.64924 2.43516 4.85077 6.72309 2.77308 8.05295 2.22036 24.03539[9] 5.16236 12.56742 3.14006Divisive coefficient:[1] 0.87110666 dissimilarities, summarized :Min. 1st Qu. Median Mean 3rd Qu. Max.1.65 4.36 7.99 9.59 13.25 24.04Metric : euclideanNumber of objects : 12Available components:[1] "order" "height" "dc" "merge" "diss" "call"[7] "order.lab" "data"> summary(drusp0)Merge:[,1] [,2][1,] -18 -19[2,] -55 -56[3,] -27 -28[4,] -49 -51[5,] -33 -34[6,] -23 -24[7,] -59 -60[8,] -29 -30[9,] -67 -69[10,] -36 -39[11,] -32 -35[12,] -50 -54[13,] -37 -38[14,] -70 -71[15,] -64 -68[16,] -62 -66[17,] -12 -13[18,] -16 1[19,] -9 -10[20,] -42 -43[21,] -15 -17[22,] -47 -48[23,] 12 -52[24,] -21 -22[25,] 9 14[26,] 2 -57[27,] -73 -74[28,] 6 -25[29,] -26 11[30,] 4 -53[31,] 3 8[32,] -11 17[33,] -6 -8[34,] -2 -3[35,] 10 -40[36,] -14 21[37,] -65 25[38,] -4 33[39,] 36 18[40,] 29 5[41,] 26 7[42,] -1 34[43,] 24 28[44,] 16 -63[45,] -46 22[46,] -31 35[47,] 27 -75[48,] 37 -72[49,] 43 31[50,] 30 23[51,] 13 20[52,] 15 48[53,] 32 -20[54,] 41 -58[55,] 42 -5[56,] 40 46[57,] -44 -45[58,] 19 39[59,] 38 -7[60,] 51 -41[61,] -61 44[62,] 50 54[63,] 52 47[64,] 61 63[65,] 49 56[66,] 59 53[67,] 55 58[68,] 57 62[69,] 65 60[70,] 67 66[71,] 68 45[72,] 69 71[73,] 70 64[74,] 73 72Order of objects:[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[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[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 48Height:[1] 10.04988 6.40312 16.12452 29.12044 4.12311 17.02939 8.48528[8] 4.24264 9.21954 4.12311 1.41421 40.24922 8.94427 6.32456[15] 19.02630 28.84441 6.32456 4.12311 14.14214 102.07840 21.40093[22] 4.12311 10.81665 27.07397 3.60555 13.60147 8.54400 2.82843[29] 5.09902 3.60555 12.80625 22.80351 5.65685 12.36932 154.49595[36] 4.47214 10.77033 2.23607 5.83095 13.03840 2.00000 6.32456[43] 2.82843 28.16026 6.08276 3.00000 9.43398 2.23607 16.27882[50] 11.04536 3.00000 6.70820 36.61967 3.60555 13.34166 4.24264[57] 20.02498 94.57801 17.02939 35.35534 2.23607 6.32456 13.15295[64] 3.16228 4.47214 22.20360 2.00000 5.38516 9.84886 2.82843[71] 15.29706 47.63402 11.00000 4.47214Divisive coefficient:[1] 0.960566Available components:[1] "order" "height" "dc" "merge" "diss" "call"[7] "order.lab"> summary(drusp1)Merge:[,1] [,2][1,] -55 -56[2,] -27 -28[3,] -18 -19[4,] -49 -51[5,] -33 -34[6,] -32 -35[7,] -23 -24[8,] -59 -60[9,] -50 -54[10,] -29 -30[11,] -67 -69[12,] -37 -38[13,] 11 -71[14,] -64 -68[15,] -62 -66[16,] -12 -13[17,] -16 3[18,] -9 -10[19,] -47 -48[20,] 9 -52[21,] -42 -43[22,] -39 -40[23,] -21 -22[24,] 13 -70[25,] -15 -17[26,] 1 -57[27,] -26 6[28,] 4 -53[29,] 7 -25[30,] 2 10[31,] -11 16[32,] -6 -8[33,] -31 -36[34,] -74 -75[35,] -2 -3[36,] -46 19[37,] -65 24[38,] -14 17[39,] -4 32[40,] 38 25[41,] -1 35[42,] 26 8[43,] 27 5[44,] 23 30[45,] 28 20[46,] 15 -63[47,] 43 33[48,] 44 29[49,] 46 -73[50,] 31 -20[51,] 42 -58[52,] -44 -45[53,] 12 22[54,] 37 -72[55,] 14 54[56,] 39 -7[57,] 41 -5[58,] 53 21[59,] 18 40[60,] 48 47[61,] -61 49[62,] 45 51[63,] 58 -41[64,] 55 34[65,] 61 64[66,] 57 59[67,] 56 50[68,] 52 62[69,] 60 63[70,] 66 67[71,] 68 36[72,] 69 71[73,] 70 65[74,] 73 72Order of objects:[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[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 48Height:[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 6Divisive coefficient:[1] 0.9580752775 dissimilarities, summarized :Min. 1st Qu. Median Mean 3rd Qu. Max.2.0 52.5 97.0 91.0 128.0 187.0Metric : manhattanNumber of objects : 75Available 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 elapsed0.192 0.044 0.292