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CircosHeatmap-aardio/dist/lib/r-library/cluster/tests/agnes-ex.Rout.save

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2025-01-12 00:52:51 +08:00
R version 4.0.3 Patched (2021-01-18 r79850) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: 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)
>
> ## IGNORE_RDIFF_BEGIN
> source(system.file("test-tools.R", package = "cluster"), keep.source = FALSE)
Loading required package: tools
doExtras <- cluster:::doExtras() : TRUE
> ## IGNORE_RDIFF_END
> ## -> showProc.time() ... & doExtras
>
> agn1 <- agnes(votes.repub, metric = "manhattan", stand = TRUE)
> summary(agn1)
Object of class 'agnes' from call:
agnes(x = votes.repub, metric = "manhattan", stand = TRUE)
Agglomerative coefficient: 0.797756
Order of objects:
[1] Alabama Georgia Arkansas Louisiana Mississippi
[6] South Carolina Alaska Vermont Arizona Montana
[11] Nevada Colorado Idaho Wyoming Utah
[16] California Oregon Washington Minnesota Connecticut
[21] New York New Jersey Illinois Ohio Indiana
[26] Michigan Pennsylvania New Hampshire Wisconsin Delaware
[31] Kentucky Maryland Missouri New Mexico West Virginia
[36] Iowa South Dakota North Dakota Kansas Nebraska
[41] Maine Massachusetts Rhode Island Florida North Carolina
[46] Tennessee Virginia Oklahoma Hawaii Texas
Merge:
[,1] [,2]
[1,] -7 -32
[2,] -13 -35
[3,] -12 -50
[4,] 1 -30
[5,] 2 -14
[6,] -26 -28
[7,] -5 -37
[8,] -15 -41
[9,] -22 -38
[10,] -25 -31
[11,] 7 -47
[12,] -21 -39
[13,] -16 -27
[14,] 4 5
[15,] -42 -46
[16,] -20 10
[17,] 14 9
[18,] -3 6
[19,] -6 3
[20,] -33 15
[21,] 17 -29
[22,] -17 16
[23,] 8 -34
[24,] 21 -49
[25,] 22 -48
[26,] -8 25
[27,] 19 -44
[28,] 11 -23
[29,] 28 24
[30,] -11 -43
[31,] 18 27
[32,] 23 13
[33,] 29 26
[34,] 20 -36
[35,] -1 -10
[36,] 32 -19
[37,] 31 33
[38,] -9 34
[39,] 37 36
[40,] 35 -4
[41,] -2 -45
[42,] 40 -18
[43,] -24 -40
[44,] 39 12
[45,] 44 38
[46,] 41 45
[47,] 42 43
[48,] 46 30
[49,] 47 48
Height:
[1] 27.36345 31.15453 35.61832 51.44421 35.69152 87.45523 31.58222 47.53682
[9] 16.34184 11.49397 22.11426 16.35662 10.46294 19.03961 28.41137 11.70132
[17] 12.72838 19.07671 20.90246 8.38200 11.10094 12.92659 9.23004 11.37867
[25] 15.97442 12.70819 16.91515 17.74499 24.83533 18.78225 17.03525 15.77893
[33] 12.71848 18.52818 30.74557 12.55524 17.14634 22.33846 12.80419 27.38835
[41] 37.23685 12.79160 38.76377 29.38432 16.63215 14.75762 25.59605 53.03627
[49] 21.07684
1225 dissimilarities, summarized :
Min. 1st Qu. Median Mean 3rd Qu. Max.
8.38 25.54 34.51 45.06 56.02 167.60
Metric : manhattan
Number of objects : 50
Available components:
[1] "order" "height" "ac" "merge" "diss" "call"
[7] "method" "order.lab" "data"
> Dvr <- daisy(votes.repub)
> agn2 <- agnes(Dvr, method = "complete")
> summary(agn2)
Object of class 'agnes' from call:
agnes(x = Dvr, method = "complete")
Agglomerative coefficient: 0.88084
Order of objects:
[1] Alabama Georgia Louisiana Arkansas Florida
[6] Texas Mississippi South Carolina Alaska Michigan
[11] Connecticut New York New Hampshire Indiana Ohio
[16] Illinois New Jersey Pennsylvania Minnesota North Dakota
[21] Wisconsin Iowa South Dakota Kansas Nebraska
[26] Arizona Nevada Montana Oklahoma Colorado
[31] Idaho Wyoming Utah California Oregon
[36] Washington Missouri New Mexico West Virginia Delaware
[41] Kentucky Maryland North Carolina Tennessee Virginia
[46] Hawaii Maine Massachusetts Rhode Island Vermont
Merge:
[,1] [,2]
[1,] -12 -50
[2,] -7 -32
[3,] -14 -35
[4,] -13 -30
[5,] -25 -31
[6,] -37 -47
[7,] -21 -39
[8,] -3 -28
[9,] 4 -38
[10,] -16 -27
[11,] -15 -41
[12,] 8 -26
[13,] -2 -22
[14,] -33 -42
[15,] 14 -46
[16,] 1 -44
[17,] -11 -19
[18,] 2 -29
[19,] -5 6
[20,] -17 -20
[21,] -34 -49
[22,] 5 -48
[23,] 18 3
[24,] 11 10
[25,] 23 9
[26,] -23 21
[27,] -8 20
[28,] 12 -36
[29,] -6 16
[30,] 13 25
[31,] 28 29
[32,] -1 -10
[33,] 19 22
[34,] 17 7
[35,] -4 -9
[36,] 30 26
[37,] 35 -43
[38,] 32 -18
[39,] -24 -40
[40,] 36 24
[41,] 27 15
[42,] 31 33
[43,] 38 37
[44,] 40 42
[45,] 34 -45
[46,] 43 39
[47,] 44 41
[48,] 47 45
[49,] 46 48
Height:
[1] 48.2397 60.8984 72.9221 56.1363 58.8227 116.7048 63.0951 281.9508
[9] 28.1437 47.1690 19.4218 32.9438 36.7643 20.2258 39.1728 20.8792
[17] 25.3229 56.3813 42.2230 33.6978 64.5254 26.1547 37.4564 25.9221
[25] 80.4894 23.4206 27.8273 43.4492 48.0483 43.7055 17.1992 31.1988
[33] 70.4868 33.2328 22.1831 54.3057 21.1413 35.1129 121.4022 43.3829
[41] 33.4744 66.7591 29.5099 30.1541 178.4119 32.7611 55.3633 22.6334
[49] 83.1040
1225 dissimilarities, summarized :
Min. 1st Qu. Median Mean 3rd Qu. Max.
17.2 48.3 64.7 82.2 105.5 282.0
Metric : euclidean
Number of objects : 50
Available components:
[1] "order" "height" "ac" "merge" "diss" "call"
[7] "method" "order.lab"
> ## almost same:
> (ag2. <- agnes(Dvr, method= "complete", keep.diss=FALSE))
Call: agnes(x = Dvr, method = "complete", keep.diss = FALSE)
Agglomerative coefficient: 0.88084
Order of objects:
[1] Alabama Georgia Louisiana Arkansas Florida
[6] Texas Mississippi South Carolina Alaska Michigan
[11] Connecticut New York New Hampshire Indiana Ohio
[16] Illinois New Jersey Pennsylvania Minnesota North Dakota
[21] Wisconsin Iowa South Dakota Kansas Nebraska
[26] Arizona Nevada Montana Oklahoma Colorado
[31] Idaho Wyoming Utah California Oregon
[36] Washington Missouri New Mexico West Virginia Delaware
[41] Kentucky Maryland North Carolina Tennessee Virginia
[46] Hawaii Maine Massachusetts Rhode Island Vermont
Height (summary):
Min. 1st Qu. Median Mean 3rd Qu. Max.
17.2 28.1 39.2 52.3 58.8 282.0
Available components:
[1] "order" "height" "ac" "merge" "diss" "call"
[7] "method" "order.lab"
> ag22 <- agnes(votes.repub, method= "complete", keep.diss=FALSE,keep.data=FALSE)
> stopifnot(identical(agn2[-5:-6], ag2.[-5:-6]),
+ identical(Dvr, daisy(votes.repub)), # DUP=FALSE (!)
+ identical(ag2.[-6], ag22[-6])
+ )
>
> data(agriculture)
> summary(agnes(agriculture))
Object of class 'agnes' from call:
agnes(x = agriculture)
Agglomerative coefficient: 0.781893
Order of objects:
[1] B NL D F UK DK L I GR P E IRL
Merge:
[,1] [,2]
[1,] -1 -10
[2,] -2 -9
[3,] 1 -3
[4,] 3 -6
[5,] -5 -7
[6,] 4 -12
[7,] 6 2
[8,] -4 -11
[9,] 7 -8
[10,] 8 5
[11,] 9 10
Height:
[1] 1.64924 2.24836 2.76918 4.02677 4.78835 2.22036 5.29409 14.77963
[9] 5.16236 8.55075 3.14006
66 dissimilarities, summarized :
Min. 1st Qu. Median Mean 3rd Qu. Max.
1.65 4.36 7.99 9.59 13.25 24.04
Metric : euclidean
Number of objects : 12
Available components:
[1] "order" "height" "ac" "merge" "diss" "call"
[7] "method" "order.lab" "data"
>
> data(ruspini)
> summary(ar0 <- agnes(ruspini, keep.diss=FALSE, keep.data=FALSE))
Object of class 'agnes' from call:
agnes(x = ruspini, keep.diss = FALSE, keep.data = FALSE)
Agglomerative coefficient: 0.947954
Order of objects:
[1] 1 2 3 5 4 6 8 7 9 10 14 15 17 16 18 19 11 12 13 20 61 62 66 63 64
[26] 68 65 67 69 70 71 72 75 73 74 21 22 23 24 27 28 29 30 25 26 32 35 31 36 39
[51] 40 33 34 37 38 41 42 43 44 45 49 51 53 50 54 52 55 56 57 59 60 58 46 47 48
Merge:
[,1] [,2]
[1,] -18 -19
[2,] -55 -56
[3,] -27 -28
[4,] -49 -51
[5,] -33 -34
[6,] -23 -24
[7,] -67 -69
[8,] -59 -60
[9,] -29 -30
[10,] -36 -39
[11,] -32 -35
[12,] -50 -54
[13,] -25 -26
[14,] -16 1
[15,] -70 -71
[16,] -64 -68
[17,] -37 -38
[18,] 12 -52
[19,] -62 -66
[20,] -12 -13
[21,] -9 -10
[22,] -42 -43
[23,] -15 -17
[24,] -47 -48
[25,] -21 -22
[26,] 7 15
[27,] 2 -57
[28,] 4 -53
[29,] 10 -40
[30,] 3 9
[31,] -73 -74
[32,] -72 -75
[33,] -11 20
[34,] 13 11
[35,] -6 -8
[36,] -14 23
[37,] -2 -3
[38,] -65 26
[39,] 5 17
[40,] 25 6
[41,] 36 14
[42,] 34 -31
[43,] -4 35
[44,] 28 18
[45,] 27 8
[46,] 19 -63
[47,] -46 24
[48,] -1 37
[49,] 16 38
[50,] 40 30
[51,] 42 29
[52,] 33 -20
[53,] 49 32
[54,] 51 39
[55,] 21 41
[56,] 48 -5
[57,] 45 -58
[58,] 53 31
[59,] 43 -7
[60,] 50 54
[61,] 44 57
[62,] -41 22
[63,] -61 46
[64,] 55 52
[65,] 63 58
[66,] -44 -45
[67,] 59 64
[68,] 56 67
[69,] 66 61
[70,] 60 62
[71,] 69 47
[72,] 70 71
[73,] 68 65
[74,] 73 72
Height:
[1] 9.26758 6.40312 12.13789 22.37868 7.63441 6.32456 14.58991
[8] 21.63544 4.12311 12.07902 6.36396 4.24264 7.23741 3.56155
[15] 1.41421 16.38921 5.85486 4.12311 10.69547 67.75052 15.48443
[22] 4.12311 8.94386 17.00500 3.60555 9.53375 6.46443 2.82843
[29] 4.48680 3.60555 10.91541 5.83095 14.34411 5.65685 101.14200
[36] 4.47214 6.98022 2.23607 9.56136 2.00000 5.61339 2.82843
[43] 14.95692 3.16228 6.19728 3.00000 7.28356 9.97147 3.00000
[50] 5.47542 11.07404 2.23607 6.60456 3.60555 24.90532 15.45463
[57] 4.24264 64.42555 17.02939 22.56493 2.23607 5.22383 8.28122
[64] 3.16228 3.81721 15.20808 2.00000 5.19258 8.51123 2.82843
[71] 12.62990 34.72475 9.14005 4.47214
Available components:
[1] "order" "height" "ac" "merge" "diss" "call"
[7] "method" "order.lab"
> summary(ar1 <- agnes(ruspini, metric = "manhattan"))
Object of class 'agnes' from call:
agnes(x = ruspini, metric = "manhattan")
Agglomerative coefficient: 0.946667
Order of objects:
[1] 1 2 3 5 4 6 8 7 9 10 14 16 18 19 15 17 11 12 13 20 61 62 66 63 73
[26] 74 64 68 65 67 69 70 71 72 75 21 22 23 24 27 28 29 30 25 26 32 35 31 36 39
[51] 40 33 34 37 38 41 42 43 44 45 49 51 53 50 54 52 55 56 57 59 60 58 46 47 48
Merge:
[,1] [,2]
[1,] -55 -56
[2,] -27 -28
[3,] -18 -19
[4,] -49 -51
[5,] -36 -39
[6,] -33 -34
[7,] -32 -35
[8,] -23 -24
[9,] -67 -69
[10,] -59 -60
[11,] -50 -54
[12,] -29 -30
[13,] -25 -26
[14,] -16 3
[15,] -70 -71
[16,] -64 -68
[17,] -62 -66
[18,] 11 -52
[19,] -37 -38
[20,] -12 -13
[21,] -9 -10
[22,] 9 15
[23,] 1 -57
[24,] -47 -48
[25,] -42 -43
[26,] -21 -22
[27,] -15 -17
[28,] 4 -53
[29,] 2 12
[30,] 5 -40
[31,] 6 19
[32,] 13 7
[33,] -11 20
[34,] -73 -74
[35,] -72 -75
[36,] -6 -8
[37,] -65 22
[38,] -14 14
[39,] -2 -3
[40,] 32 -31
[41,] 38 27
[42,] 26 8
[43,] 28 18
[44,] -46 24
[45,] -4 36
[46,] 23 10
[47,] -1 39
[48,] 42 29
[49,] 33 -20
[50,] 37 35
[51,] 40 30
[52,] 17 -63
[53,] 16 50
[54,] 51 31
[55,] 46 -58
[56,] 21 41
[57,] 47 -5
[58,] 45 -7
[59,] 52 34
[60,] -44 -45
[61,] 48 54
[62,] 43 55
[63,] 59 53
[64,] 56 49
[65,] -41 25
[66,] -61 63
[67,] 57 58
[68,] 67 64
[69,] 60 62
[70,] 61 65
[71,] 69 44
[72,] 70 71
[73,] 68 66
[74,] 73 72
Height:
[1] 11.50000 9.00000 16.00000 26.25000 10.00000 8.00000 16.66667
[8] 28.70833 5.00000 15.50000 8.66667 4.00000 2.00000 9.25000
[15] 6.00000 20.50000 7.50000 5.00000 12.33333 94.33333 22.78571
[22] 5.00000 12.50000 18.00000 8.00000 20.20000 5.00000 13.78571
[29] 8.25000 4.00000 5.50000 5.00000 12.40000 8.00000 125.71357
[36] 6.00000 9.50000 3.00000 11.87500 2.00000 7.00000 4.00000
[43] 18.72917 4.00000 7.50000 3.00000 9.25000 12.40000 3.00000
[50] 7.50000 14.43750 3.00000 7.50000 5.00000 32.38333 21.00000
[57] 6.00000 85.49616 18.00000 28.75000 3.00000 6.50000 9.55556
[64] 4.00000 5.00000 19.61111 2.00000 6.00000 11.00000 4.00000
[71] 15.40000 47.02381 10.00000 6.00000
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" "ac" "merge" "diss" "call"
[7] "method" "order.lab" "data"
> str(ar1)
List of 9
$ order : int [1:75] 1 2 3 5 4 6 8 7 9 10 ...
$ height : num [1:74] 11.5 9 16 26.2 10 ...
$ ac : num 0.947
$ merge : int [1:74, 1:2] -55 -27 -18 -49 -36 -33 -32 -23 -67 -59 ...
$ 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 agnes(x = ruspini, metric = "manhattan")
$ method : chr "average"
$ order.lab: chr [1:75] "1" "2" "3" "5" ...
$ data : num [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] "agnes" "twins"
>
> showProc.time()
Time (user system elapsed): 0.602 0.061 0.667
>
> summary(ar2 <- agnes(ruspini, metric="manhattan", method = "weighted"))
Object of class 'agnes' from call:
agnes(x = ruspini, metric = "manhattan", method = "weighted")
Agglomerative coefficient: 0.942387
Order of objects:
[1] 1 2 3 5 9 10 14 16 18 19 15 17 4 6 8 7 11 12 13 20 61 64 68 65 67
[26] 69 70 71 62 66 63 72 75 73 74 21 22 23 24 27 28 29 30 25 26 32 35 31 36 39
[51] 40 33 34 37 38 41 42 43 44 45 49 51 53 50 54 52 55 56 57 59 60 58 46 47 48
Merge:
[,1] [,2]
[1,] -55 -56
[2,] -27 -28
[3,] -18 -19
[4,] -49 -51
[5,] -36 -39
[6,] -33 -34
[7,] -32 -35
[8,] -23 -24
[9,] -67 -69
[10,] -59 -60
[11,] -50 -54
[12,] -29 -30
[13,] -25 -26
[14,] -16 3
[15,] -70 -71
[16,] -64 -68
[17,] -62 -66
[18,] 11 -52
[19,] -37 -38
[20,] -12 -13
[21,] -9 -10
[22,] 9 15
[23,] 1 -57
[24,] -47 -48
[25,] -42 -43
[26,] -21 -22
[27,] -15 -17
[28,] 4 -53
[29,] 2 12
[30,] 5 -40
[31,] 6 19
[32,] 13 7
[33,] -11 20
[34,] -73 -74
[35,] -72 -75
[36,] -14 14
[37,] -6 -8
[38,] -65 22
[39,] 36 27
[40,] -2 -3
[41,] 32 -31
[42,] 28 18
[43,] 26 8
[44,] -46 24
[45,] -4 37
[46,] 23 10
[47,] -1 40
[48,] 16 38
[49,] 43 29
[50,] 17 -63
[51,] 41 30
[52,] 33 -20
[53,] 35 34
[54,] 46 -58
[55,] 47 -5
[56,] 51 31
[57,] 21 39
[58,] 45 -7
[59,] -44 -45
[60,] -61 48
[61,] 42 54
[62,] 49 56
[63,] -41 25
[64,] 55 57
[65,] 60 50
[66,] 65 53
[67,] 58 52
[68,] 59 61
[69,] 64 67
[70,] 62 63
[71,] 68 44
[72,] 70 71
[73,] 69 66
[74,] 73 72
Height:
[1] 11.5000 9.0000 15.2500 21.7734 5.0000 15.8750 8.0000 4.0000
[9] 2.0000 9.0000 6.0000 32.1172 10.0000 8.0000 16.0000 27.9062
[17] 7.5000 5.0000 13.2500 97.9766 18.3125 5.0000 11.8750 8.2500
[25] 4.0000 5.5000 5.0000 22.3438 5.0000 12.5000 23.7812 8.0000
[33] 14.5000 8.0000 114.9764 6.0000 9.5000 3.0000 11.8750 2.0000
[41] 7.0000 4.0000 20.2031 4.0000 7.5000 3.0000 9.2500 12.6250
[49] 3.0000 7.5000 15.6875 3.0000 7.5000 5.0000 33.5469 21.0000
[57] 6.0000 69.4453 18.0000 28.4375 3.0000 6.5000 9.5000 4.0000
[65] 5.0000 19.1250 2.0000 6.0000 10.5000 4.0000 15.0000 41.5312
[73] 10.0000 6.0000
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" "ac" "merge" "diss" "call"
[7] "method" "order.lab" "data"
> print (ar3 <- agnes(ruspini, metric="manhattan", method = "flexible",
+ par.meth = 0.5))
Call: agnes(x = ruspini, metric = "manhattan", method = "flexible", par.method = 0.5)
Agglomerative coefficient: 0.942387
Order of objects:
[1] 1 2 3 5 9 10 14 16 18 19 15 17 4 6 8 7 11 12 13 20 61 64 68 65 67
[26] 69 70 71 62 66 63 72 75 73 74 21 22 23 24 27 28 29 30 25 26 32 35 31 36 39
[51] 40 33 34 37 38 41 42 43 44 45 49 51 53 50 54 52 55 56 57 59 60 58 46 47 48
Height (summary):
Min. 1st Qu. Median Mean 3rd Qu. Max.
2.00 5.00 8.12 14.22 15.58 114.98
Available components:
[1] "order" "height" "ac" "merge" "diss" "call"
[7] "method" "order.lab" "data"
> stopifnot(all.equal(ar2[1:4], ar3[1:4], tol=1e-12))
>
> showProc.time()
Time (user system elapsed): 0.003 0.001 0.004
>
> ## Small example, testing "flexible" vs "single"
> i8 <- -c(1:2, 9:10)
> dim(agr8 <- agriculture[i8, ])
[1] 8 2
> i5 <- -c(1:2, 8:12)
> dim(agr5 <- agriculture[i5, ])
[1] 5 2
>
> ##' Check equivalence of method "flexible" (par=...) with one
> ##' of ("single", "complete", "weighted")
> chk <- function(d, method=c("single", "complete", "weighted"),
+ trace.lev = 1,
+ iC = -(6:7), # <- not using 'call' and 'method' for comparisons
+ doplot = FALSE, tol = 1e-12)
+ {
+ if(!inherits(d, "dist")) d <- daisy(d, "manhattan")
+ method <- match.arg(method)
+ par.meth <- list("single" = c(.5, .5, 0, -.5),
+ "complete"= c(.5, .5, 0, +.5),
+ "weighted"= c(0.5))
+ a.s <- agnes(d, method=method, trace.lev=trace.lev)
+ ## From theory, this should give the same, but it does not --- why ???
+ a.f <- agnes(d, method="flex", par.method = par.meth[[method]], trace.lev=trace.lev)
+
+ if(doplot) {
+ op <- par(mfrow = c(2,2), mgp = c(1.6, 0.6, 0), mar = .1 + c(4,4,2,1))
+ on.exit(par(op))
+ plot(a.s)
+ plot(a.f)
+ }
+ structure(all.equal(a.s[iC], a.f[iC], tolerance = tol),
+ fits = list(s = a.s, f = a.f))
+ }
>
> chk(agr5, trace = 3)
C agnes(n=5, method = 2, ..): 4 merging steps
nmerge=0, j=2, d_min = D(1,4) = 3.40000; -> (-1,-4); last=4; upd(n,b);
old D(A, j), D(B, j), j=2 = (31.5,28.1); new D(A', 2) = 28.1
old D(A, j), D(B, j), j=3 = (14.7,11.3); new D(A', 3) = 11.3
old D(A, j), D(B, j), j=5 = (18.3,14.9); new D(A', 5) = 14.9
--> size(A_new)= 2
nmerge=1, j=2, d_min = D(3,5) = 3.60000; -> (-3,-5); last=5;
old D(A, j), D(B, j), j=1 = (11.3,14.9); new D(A', 1) = 11.3
old D(A, j), D(B, j), j=2 = (16.8,13.2); new D(A', 2) = 13.2
--> size(A_new)= 2
nmerge=2, j=2, d_min = D(1,3) = 11.3000; -> (1,2); last=4; upd(n,b);
old D(A, j), D(B, j), j=2 = (28.1,13.2); new D(A', 2) = 13.2
--> size(A_new)= 4
nmerge=3, j=2, d_min = D(1,2) = 13.2000; -> (3,-2); last=5;
--> size(A_new)= 5
C agnes(n=5, method = 6, ..): |par| = 4, alpha[1:4] = (0.5,0.5,0,-0.5); 4 merging steps
nmerge=0, j=2, d_min = D(1,4) = 3.40000; -> (-1,-4); last=4; upd(n,b);
old D(A, j), D(B, j), j=2 = (31.5,28.1); new D(A', 2) = 28.1
old D(A, j), D(B, j), j=3 = (14.7,11.3); new D(A', 3) = 11.3
old D(A, j), D(B, j), j=5 = (18.3,14.9); new D(A', 5) = 14.9
--> size(A_new)= 2
nmerge=1, j=2, d_min = D(3,5) = 3.60000; -> (-3,-5); last=5;
old D(A, j), D(B, j), j=1 = (11.3,14.9); new D(A', 1) = 11.3
old D(A, j), D(B, j), j=2 = (16.8,13.2); new D(A', 2) = 13.2
--> size(A_new)= 2
nmerge=2, j=2, d_min = D(1,3) = 11.3000; -> (1,2); last=4; upd(n,b);
old D(A, j), D(B, j), j=2 = (28.1,13.2); new D(A', 2) = 13.2
--> size(A_new)= 4
nmerge=3, j=2, d_min = D(1,2) = 13.2000; -> (3,-2); last=5;
--> size(A_new)= 5
[1] TRUE
attr(,"fits")
attr(,"fits")$s
Call: agnes(x = d, method = method, trace.lev = trace.lev)
Agglomerative coefficient: 0.587879
Order of objects:
[1] D F E IRL GR
Height (summary):
Min. 1st Qu. Median Mean 3rd Qu. Max.
3.40 3.55 7.45 7.88 11.78 13.20
Available components:
[1] "order" "height" "ac" "merge" "diss" "call"
[7] "method" "order.lab"
attr(,"fits")$f
Call: agnes(x = d, method = "flex", par.method = par.meth[[method]], trace.lev = trace.lev)
Agglomerative coefficient: 0.587879
Order of objects:
[1] D F E IRL GR
Height (summary):
Min. 1st Qu. Median Mean 3rd Qu. Max.
3.40 3.55 7.45 7.88 11.78 13.20
Available components:
[1] "order" "height" "ac" "merge" "diss" "call"
[7] "method" "order.lab"
>
> stopifnot(chk(agr5), chk(agr5, "complete", trace = 2), chk(agr5, "weighted"),
+ chk(agr8), chk(agr8, "complete"), chk(agr8, "weighted", trace.lev=2),
+ chk(agriculture), chk(agriculture, "complete"),
+ chk(ruspini), chk(ruspini, "complete"), chk(ruspini, "weighted"))
C agnes(n=5, method = 2, ..): 4 merging steps
C agnes(n=5, method = 6, ..): |par| = 4, alpha[1:4] = (0.5,0.5,0,-0.5); 4 merging steps
C agnes(n=5, method = 3, ..): 4 merging steps
nmerge=0, j=2, d_min = D(1,4) = 3.40000; last=4; upd(n,b); size(A_new)= 2
nmerge=1, j=2, d_min = D(3,5) = 3.60000; last=5; size(A_new)= 2
nmerge=2, j=2, d_min = D(2,3) = 16.8000; last=4; size(A_new)= 3
nmerge=3, j=2, d_min = D(1,2) = 31.5000; last=3; size(A_new)= 5
C agnes(n=5, method = 6, ..): |par| = 4, alpha[1:4] = (0.5,0.5,0,0.5); 4 merging steps
nmerge=0, j=2, d_min = D(1,4) = 3.40000; last=4; upd(n,b); size(A_new)= 2
nmerge=1, j=2, d_min = D(3,5) = 3.60000; last=5; size(A_new)= 2
nmerge=2, j=2, d_min = D(2,3) = 16.8000; last=4; size(A_new)= 3
nmerge=3, j=2, d_min = D(1,2) = 31.5000; last=3; size(A_new)= 5
C agnes(n=5, method = 5, ..): 4 merging steps
C agnes(n=5, method = 6, ..): 4 merging steps
C agnes(n=8, method = 2, ..): 7 merging steps
C agnes(n=8, method = 6, ..): |par| = 4, alpha[1:4] = (0.5,0.5,0,-0.5); 7 merging steps
C agnes(n=8, method = 3, ..): 7 merging steps
C agnes(n=8, method = 6, ..): |par| = 4, alpha[1:4] = (0.5,0.5,0,0.5); 7 merging steps
C agnes(n=8, method = 5, ..): 7 merging steps
nmerge=0, j=2, d_min = D(1,4) = 3.40000; last=4; upd(n,b); size(A_new)= 2
nmerge=1, j=2, d_min = D(3,5) = 3.60000; last=5; size(A_new)= 2
nmerge=2, j=2, d_min = D(1,6) = 5.40000; last=6; upd(n,b); size(A_new)= 3
nmerge=3, j=2, d_min = D(2,7) = 6.70000; last=7; upd(n,b); size(A_new)= 2
nmerge=4, j=2, d_min = D(1,8) = 7.75000; last=8; upd(n,b); size(A_new)= 4
nmerge=5, j=2, d_min = D(2,3) = 11.6500; last=7; size(A_new)= 4
nmerge=6, j=2, d_min = D(1,2) = 18.3750; last=5; size(A_new)= 8
C agnes(n=8, method = 6, ..): 7 merging steps
nmerge=0, j=2, d_min = D(1,4) = 3.40000; last=4; upd(n,b); size(A_new)= 2
nmerge=1, j=2, d_min = D(3,5) = 3.60000; last=5; size(A_new)= 2
nmerge=2, j=2, d_min = D(1,6) = 5.40000; last=6; upd(n,b); size(A_new)= 3
nmerge=3, j=2, d_min = D(2,7) = 6.70000; last=7; upd(n,b); size(A_new)= 2
nmerge=4, j=2, d_min = D(1,8) = 7.75000; last=8; upd(n,b); size(A_new)= 4
nmerge=5, j=2, d_min = D(2,3) = 11.6500; last=7; size(A_new)= 4
nmerge=6, j=2, d_min = D(1,2) = 18.3750; last=5; size(A_new)= 8
C agnes(n=12, method = 2, ..): 11 merging steps
C agnes(n=12, method = 6, ..): |par| = 4, alpha[1:4] = (0.5,0.5,0,-0.5); 11 merging steps
C agnes(n=12, method = 3, ..): 11 merging steps
C agnes(n=12, method = 6, ..): |par| = 4, alpha[1:4] = (0.5,0.5,0,0.5); 11 merging steps
C agnes(n=75, method = 2, ..): 74 merging steps
C agnes(n=75, method = 6, ..): |par| = 4, alpha[1:4] = (0.5,0.5,0,-0.5); 74 merging steps
C agnes(n=75, method = 3, ..): 74 merging steps
C agnes(n=75, method = 6, ..): |par| = 4, alpha[1:4] = (0.5,0.5,0,0.5); 74 merging steps
C agnes(n=75, method = 5, ..): 74 merging steps
C agnes(n=75, method = 6, ..): 74 merging steps
>
> showProc.time()
Time (user system elapsed): 0.04 0.001 0.041
>
> ## an invalid "flexible" case - now must give error early:
> x <- rbind(c( -6, -9), c( 0, 13),
+ c(-15, 6), c(-14, 0), c(12,-10))
> (dx <- daisy(x, "manhattan"))
Dissimilarities :
1 2 3 4
2 28
3 24 22
4 17 27 7
5 19 35 43 36
Metric : manhattan
Number of objects : 5
> a.x <- tryCatch(agnes(dx, method="flexible", par = -.2),
+ error = function(e)e)
> ## agnes(method=6, par.method=*) lead to invalid merge; step 4, D(.,.)=-26.1216
> if(!inherits(a.x, "error")) stop("invalid 'par' in \"flexible\" did not give error")
> if(!all(vapply(c("par[.]method", "merge"), grepl, NA, x=a.x$message)))
+ stop("error message did not contain expected words")
>
>
> proc.time()
user system elapsed
0.767 0.094 0.859
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