pwdist: Pairwise Euclidean distances between landmarks

In monogeneaGM: Geometric Morphometric Analysis of Monogenean Anchors

Description

This function computes all possible n(n-1)/2 pairwise Euclidean distances between n landmarks.

Usage

pwdist(x, average = TRUE)

Arguments

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

Details

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).

Author(s)

Tsung Fei Khang [e-mail]

References

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.

Examples

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)

Example output

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

monogeneaGM documentation built on May 29, 2017, 9:18 p.m.