Description Usage Arguments Details Author(s) References Examples
This function computes all possible n(n-1)/2 pairwise Euclidean distances between n landmarks.
1 |
x |
a two-column matrix for the xy landmark coordinates |
average |
if TRUE, the pairwise distances for both left and right anchors are averaged. For data quality checks, set to FALSE |
Comparison of the pairs of pairwise Euclidean distance from the left and right form of anchors is
the basis of the quality control procedure implemented in Qscore
. In addition, pairwise Euclidean distances
provide length variables useful for the analysis of size variation (Lele & Richtsmeier, 2001).
Tsung Fei Khang tfkhang@um.edu.my
Khang TF, Soo OYM, Tan WB, Lim LHS. (2016). Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution. PeerJ 4:e1668.
Lele SR, Richtsmeier JT. 2001. An Invariant Approach to Statistical Analysis of Shape. Boca Raton: Chapman and Hall.
1 2 3 4 5 6 7 8 9 | library(cluster)
data(ligophorus_tpsdata)
#There are 11 landmarks for the ventral and dorsal anchors,
#yielding 110 pairwise Euclidean distances
#The indices for the pairwise Euclidean distances map to the upper triangle
#of the pairwise distance matrix by row
pwdist(ligophorus_tpsdata$bantingensis[[1]],average=FALSE)
|
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE
3: .onUnload failed in unloadNamespace() for 'rgl', details:
call: fun(...)
error: object 'rgl_quit' not found
[,1] [,2]
[1,] 31.906112 25.961510
[2,] 41.593269 34.713110
[3,] 43.566042 36.400549
[4,] 46.861498 40.199502
[5,] 49.335586 42.379240
[6,] 51.478151 42.011903
[7,] 38.470768 32.388269
[8,] 46.270941 35.805028
[9,] 35.510562 30.083218
[10,] 25.942244 21.470911
[11,] 17.204651 19.104973
[12,] 11.661904 10.816654
[13,] 19.235384 15.297059
[14,] 32.310989 25.806976
[15,] 48.083261 40.012498
[16,] 48.104054 43.829214
[17,] 43.185646 36.221541
[18,] 15.264338 18.248288
[19,] 16.155494 18.027756
[20,] 16.492423 17.029386
[21,] 31.016125 27.802878
[22,] 47.707442 43.462628
[23,] 65.115282 59.076222
[24,] 64.884513 60.728906
[25,] 60.307545 55.036352
[26,] 31.827661 37.336309
[27,] 33.120990 36.221541
[28,] 14.764823 10.816654
[29,] 32.557641 27.658633
[30,] 52.153619 46.690470
[31,] 56.089215 53.535035
[32,] 47.885280 43.965896
[33,] 19.313208 24.738634
[34,] 25.000000 27.459060
[35,] 18.601075 18.000000
[36,] 39.924930 39.560081
[37,] 48.041649 50.209561
[38,] 36.400549 38.078866
[39,] 12.529964 19.209373
[40,] 22.203603 25.238859
[41,] 22.360680 23.600847
[42,] 35.468296 39.357337
[43,] 20.024984 24.207437
[44,] 17.464249 12.369317
[45,] 24.186773 21.377558
[46,] 20.248457 21.023796
[47,] 5.385165 6.403124
[48,] 33.421550 22.090722
[49,] 33.837849 24.041631
[50,] 17.691806 16.278821
[51,] 37.215588 31.144823
[52,] 31.953091 26.076810
[53,] 28.844410 19.313208
[54,] 28.600699 19.104973
[55,] 9.899495 9.055385
[56,] 34.438351 34.058773
[57,] 45.398238 43.382024
[58,] 47.853944 46.861498
[59,] 78.771822 79.511006
[60,] 113.564959 101.118742
[61,] 119.016806 107.424392
[62,] 94.578010 71.063352
[63,] 112.004464 99.005050
[64,] 53.712196 49.091751
[65,] 28.231188 26.019224
[66,] 16.643317 13.341664
[67,] 13.416408 12.806248
[68,] 54.451814 59.481089
[69,] 96.254870 88.119237
[70,] 107.967588 103.324731
[71,] 97.185390 84.202138
[72,] 101.533246 94.794515
[73,] 35.171011 35.468296
[74,] 22.825424 27.294688
[75,] 15.132746 11.401754
[76,] 63.387696 67.082039
[77,] 107.079410 97.349884
[78,] 120.904921 114.586212
[79,] 113.216607 97.529483
[80,] 114.769334 106.150836
[81,] 48.764741 46.861498
[82,] 39.446166 40.607881
[83,] 48.259714 55.946403
[84,] 91.983694 86.608314
[85,] 106.230881 104.995238
[86,] 101.237345 92.227978
[87,] 100.224747 96.674712
[88,] 35.000000 38.078866
[89,] 32.388269 37.215588
[90,] 44.271887 31.890437
[91,] 61.611687 56.302753
[92,] 72.801099 72.470684
[93,] 56.727418 49.477268
[94,] 25.612497 30.594117
[95,] 50.774009 53.935146
[96,] 23.409400 29.068884
[97,] 60.166436 68.007353
[98,] 23.021729 25.632011
[99,] 62.032250 54.083269
[100,] 85.988371 75.312682
[101,] 45.343136 54.129474
[102,] 7.071068 8.602325
[103,] 72.801099 67.896981
[104,] 93.434469 83.862983
[105,] 40.224371 48.703183
[106,] 67.201190 58.137767
[107,] 76.275815 57.245087
[108,] 66.407831 59.396970
[109,] 86.579443 75.292762
[110,] 25.495098 23.345235
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