kNNdist: Calculate and plot the k-Nearest Neighbor Distance

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/kNNdist.R

Description

Fast caclulation of the k-nearest neighbor distances in a matrix of points. The plot can be used to help find a suitable value for the eps neighborhood for DBSCAN. Look for the knee in the plot.

Usage

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kNNdist(x, k, ...)
kNNdistplot(x, k = 4, ...)

Arguments

x

the data set as a matrix or a dist object.

k

number of nearest neighbors used (use minPoints).

...

further arguments are passed on to kNN.

Details

See kNN for a discusion of the kd-tree related parameters.

Value

kNNdist returns a numeric vector with the distance to its k nearest neighbor.

Author(s)

Michael Hahsler

See Also

kNN.

Examples

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data(iris)
iris <- as.matrix(iris[,1:4])

kNNdist(iris, k=4, search="kd")
kNNdistplot(iris, k=4)
## the knee is around a distance of .5

cl <- dbscan(iris, eps = .5, minPts = 4)
pairs(iris, col = cl$cluster+1L)
## Note: black are noise points

Example output

               1         2         3         4
  [1,] 0.1000000 0.1414214 0.1414214 0.1414214
  [2,] 0.1414214 0.1414214 0.1414214 0.1732051
  [3,] 0.1414214 0.2449490 0.2645751 0.2645751
  [4,] 0.1414214 0.1732051 0.2236068 0.2449490
  [5,] 0.1414214 0.1414214 0.1732051 0.1732051
  [6,] 0.3316625 0.3464102 0.3605551 0.3741657
  [7,] 0.2236068 0.2645751 0.3000000 0.3162278
  [8,] 0.1000000 0.1414214 0.1732051 0.2000000
  [9,] 0.1414214 0.3000000 0.3162278 0.3464102
 [10,] 0.1000000 0.1732051 0.1732051 0.1732051
 [11,] 0.1000000 0.2828427 0.3000000 0.3316625
 [12,] 0.2236068 0.2236068 0.2828427 0.3000000
 [13,] 0.1414214 0.1732051 0.2000000 0.2000000
 [14,] 0.2449490 0.3162278 0.3464102 0.4795832
 [15,] 0.4123106 0.4690416 0.5477226 0.5567764
 [16,] 0.3605551 0.5477226 0.6164414 0.6164414
 [17,] 0.3464102 0.3605551 0.3872983 0.3872983
 [18,] 0.1000000 0.1414214 0.1732051 0.1732051
 [19,] 0.3316625 0.3872983 0.4690416 0.5099020
 [20,] 0.1414214 0.1414214 0.2449490 0.2645751
 [21,] 0.2828427 0.3000000 0.3605551 0.3605551
 [22,] 0.1414214 0.2449490 0.2449490 0.2645751
 [23,] 0.4582576 0.5099020 0.5099020 0.5196152
 [24,] 0.2000000 0.2645751 0.3741657 0.3872983
 [25,] 0.3000000 0.3741657 0.4123106 0.4242641
 [26,] 0.1732051 0.2000000 0.2236068 0.2236068
 [27,] 0.2000000 0.2236068 0.2236068 0.2449490
 [28,] 0.1414214 0.1414214 0.1414214 0.1732051
 [29,] 0.1414214 0.1414214 0.1414214 0.1732051
 [30,] 0.1414214 0.1732051 0.2236068 0.2236068
 [31,] 0.1414214 0.1414214 0.1732051 0.2236068
 [32,] 0.2828427 0.3000000 0.3000000 0.3162278
 [33,] 0.3464102 0.3464102 0.3741657 0.4242641
 [34,] 0.3464102 0.3605551 0.3872983 0.4123106
 [35,] 0.1000000 0.1414214 0.1414214 0.1732051
 [36,] 0.2236068 0.3000000 0.3162278 0.3316625
 [37,] 0.3000000 0.3162278 0.3316625 0.3464102
 [38,] 0.1414214 0.2449490 0.2645751 0.2645751
 [39,] 0.1414214 0.2000000 0.2449490 0.3000000
 [40,] 0.1000000 0.1414214 0.1414214 0.1414214
 [41,] 0.1414214 0.1732051 0.1732051 0.2449490
 [42,] 0.6244998 0.7141428 0.7681146 0.7810250
 [43,] 0.2000000 0.2236068 0.3000000 0.3000000
 [44,] 0.2236068 0.2645751 0.3162278 0.3741657
 [45,] 0.3605551 0.3741657 0.4123106 0.4123106
 [46,] 0.1414214 0.2000000 0.2000000 0.2449490
 [47,] 0.1414214 0.2449490 0.2449490 0.3000000
 [48,] 0.1414214 0.1414214 0.2236068 0.2236068
 [49,] 0.1000000 0.2236068 0.2449490 0.2449490
 [50,] 0.1414214 0.1732051 0.2236068 0.2236068
 [51,] 0.2645751 0.3316625 0.4358899 0.4582576
 [52,] 0.2645751 0.3162278 0.3464102 0.3741657
 [53,] 0.2645751 0.2828427 0.3162278 0.3464102
 [54,] 0.2000000 0.3000000 0.3162278 0.4358899
 [55,] 0.2449490 0.3162278 0.3741657 0.3741657
 [56,] 0.3000000 0.3162278 0.3162278 0.3316625
 [57,] 0.2645751 0.3741657 0.4242641 0.4582576
 [58,] 0.1414214 0.3872983 0.4582576 0.7211103
 [59,] 0.2449490 0.2449490 0.3162278 0.3162278
 [60,] 0.3872983 0.5099020 0.5196152 0.5291503
 [61,] 0.3605551 0.4582576 0.6708204 0.7141428
 [62,] 0.3000000 0.3316625 0.3605551 0.3605551
 [63,] 0.4898979 0.5196152 0.5477226 0.5830952
 [64,] 0.1414214 0.2236068 0.2449490 0.4242641
 [65,] 0.4242641 0.4472136 0.5099020 0.5196152
 [66,] 0.1414214 0.3162278 0.3162278 0.3464102
 [67,] 0.2000000 0.3000000 0.3872983 0.4123106
 [68,] 0.2449490 0.2828427 0.3316625 0.3605551
 [69,] 0.2645751 0.5099020 0.5385165 0.6782330
 [70,] 0.1732051 0.2449490 0.2645751 0.2645751
 [71,] 0.2236068 0.3000000 0.3605551 0.4242641
 [72,] 0.3316625 0.3464102 0.3741657 0.4000000
 [73,] 0.3605551 0.3605551 0.4123106 0.4242641
 [74,] 0.2236068 0.3000000 0.3872983 0.4358899
 [75,] 0.2000000 0.2645751 0.3605551 0.3872983
 [76,] 0.1414214 0.2449490 0.2645751 0.3162278
 [77,] 0.3162278 0.3464102 0.3464102 0.3741657
 [78,] 0.3162278 0.3741657 0.4123106 0.4242641
 [79,] 0.2000000 0.2449490 0.3316625 0.3464102
 [80,] 0.3464102 0.4242641 0.4358899 0.4472136
 [81,] 0.1414214 0.1732051 0.3000000 0.3000000
 [82,] 0.1414214 0.2645751 0.3464102 0.4358899
 [83,] 0.1414214 0.2645751 0.2828427 0.3000000
 [84,] 0.3316625 0.3605551 0.3605551 0.3741657
 [85,] 0.2000000 0.4123106 0.4795832 0.4898979
 [86,] 0.3741657 0.4242641 0.4582576 0.4690416
 [87,] 0.2828427 0.3162278 0.3162278 0.3316625
 [88,] 0.2645751 0.5744563 0.5916080 0.6082763
 [89,] 0.1732051 0.1732051 0.2236068 0.3162278
 [90,] 0.2000000 0.2449490 0.3000000 0.3000000
 [91,] 0.2645751 0.3162278 0.4242641 0.4242641
 [92,] 0.1414214 0.2000000 0.3000000 0.3464102
 [93,] 0.1414214 0.2449490 0.2645751 0.2645751
 [94,] 0.1414214 0.3605551 0.3872983 0.6480741
 [95,] 0.1732051 0.2236068 0.2645751 0.3000000
 [96,] 0.1414214 0.1732051 0.2449490 0.3316625
 [97,] 0.1414214 0.1414214 0.1732051 0.2236068
 [98,] 0.2000000 0.3316625 0.3464102 0.3464102
 [99,] 0.3872983 0.3872983 0.7211103 0.7937254
[100,] 0.1414214 0.1732051 0.2236068 0.2449490
[101,] 0.4242641 0.5000000 0.5099020 0.5567764
[102,] 0.0000000 0.2645751 0.3162278 0.3316625
[103,] 0.3872983 0.4000000 0.4123106 0.4582576
[104,] 0.2449490 0.2449490 0.3316625 0.3872983
[105,] 0.3000000 0.3162278 0.3605551 0.3872983
[106,] 0.2645751 0.5291503 0.5477226 0.5477226
[107,] 0.7348469 0.7615773 0.7937254 0.8774964
[108,] 0.2645751 0.4358899 0.5291503 0.5477226
[109,] 0.5567764 0.6000000 0.6164414 0.6164414
[110,] 0.6324555 0.6708204 0.7071068 0.7549834
[111,] 0.2236068 0.3741657 0.4242641 0.4242641
[112,] 0.3464102 0.3741657 0.3741657 0.3872983
[113,] 0.1732051 0.3464102 0.3605551 0.3741657
[114,] 0.2645751 0.2645751 0.3316625 0.5196152
[115,] 0.4898979 0.5099020 0.5099020 0.5196152
[116,] 0.3000000 0.3741657 0.3741657 0.3872983
[117,] 0.1414214 0.2449490 0.3605551 0.3872983
[118,] 0.4123106 0.8185353 0.8602325 1.0049876
[119,] 0.4123106 0.5477226 0.8944272 0.9273618
[120,] 0.4358899 0.5196152 0.5385165 0.5830952
[121,] 0.2236068 0.2645751 0.3000000 0.3000000
[122,] 0.3162278 0.3162278 0.3316625 0.4582576
[123,] 0.2645751 0.4123106 0.6082763 0.6782330
[124,] 0.1732051 0.2449490 0.3605551 0.3605551
[125,] 0.3000000 0.3162278 0.3741657 0.3741657
[126,] 0.3464102 0.3872983 0.4358899 0.4690416
[127,] 0.1732051 0.2449490 0.2828427 0.3872983
[128,] 0.1414214 0.2449490 0.2828427 0.3000000
[129,] 0.1000000 0.3162278 0.3316625 0.3741657
[130,] 0.3464102 0.5099020 0.5196152 0.5567764
[131,] 0.2645751 0.4582576 0.4690416 0.5099020
[132,] 0.4123106 0.8831761 0.9273618 0.9327379
[133,] 0.1000000 0.3000000 0.4242641 0.4358899
[134,] 0.3316625 0.3605551 0.3741657 0.4358899
[135,] 0.5385165 0.5567764 0.5830952 0.6633250
[136,] 0.5385165 0.5477226 0.6633250 0.6782330
[137,] 0.2449490 0.3872983 0.4242641 0.4358899
[138,] 0.1414214 0.2449490 0.3872983 0.4358899
[139,] 0.1414214 0.2236068 0.2828427 0.3162278
[140,] 0.1732051 0.3605551 0.3605551 0.3741657
[141,] 0.2449490 0.2645751 0.3464102 0.3464102
[142,] 0.2449490 0.3605551 0.4690416 0.5099020
[143,] 0.0000000 0.2645751 0.3162278 0.3316625
[144,] 0.2236068 0.3162278 0.3162278 0.3464102
[145,] 0.2449490 0.3000000 0.3162278 0.4000000
[146,] 0.2449490 0.3605551 0.3605551 0.3741657
[147,] 0.2449490 0.3741657 0.3872983 0.4123106
[148,] 0.2236068 0.3464102 0.3605551 0.3605551
[149,] 0.2449490 0.3000000 0.5567764 0.6164414
[150,] 0.2828427 0.3162278 0.3316625 0.3316625

dbscan documentation built on May 30, 2017, 5:45 a.m.

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