two.d.array: Convert (p x k x n) data array into 2D data matrix
In geomorph: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
Convert a three-dimensional array of landmark coordinates into a two-dimensional matrix
Usage
1
two.d.array(A, sep = ".")
Arguments
A
A 3D array (p x k x n) containing landmark coordinates for a set of specimens
sep
An optional argument for variable labeling, combining landmark labels (e.g., 1, 2, 3, ...)
and partial dimension labels (e.g., "x", "y", and "z"), much like the paste function.
The default is sep = ".", but this can be changed to any separator.
One should make sure to match separators with arrayspecs if switching between matrices and arrays.
Details
This function converts a (p x k x n) array of landmark coordinates into a two-dimensional
matrix (n x [p x k]). The latter format of the shape data is useful for performing subsequent statistical
analyses in R (e.g., PCA, MANOVA, PLS, etc.). Row labels are preserved if included in
the original array.
Value
Function returns a two-dimensional matrix of dimension (n x [p x k]), where rows
represent specimens and columns represent variables.
Author(s)
Dean Adams and Emma Sherratt
See Also
Examples
1
2
3
4
data(plethodon)
plethodon$land #original data in the form of 3D array
two.d.array(plethodon$land) # Convert to a 2D data matrix
Example output
Loading required package: rgl
Loading required package: ape
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
[,1] [,2]
[1,] 8.89372 53.77644
[2,] 9.26840 52.77072
[3,] 5.56104 54.21028
[4,] 1.87340 52.75100
[5,] 1.28180 53.18484
[6,] 1.24236 53.32288
[7,] 0.84796 54.70328
[8,] 3.35240 55.76816
[9,] 6.29068 55.70900
[10,] 8.87400 55.25544
[11,] 10.74740 55.43292
[12,] 14.39560 52.75100
, , 2
[,1] [,2]
[1,] 8.679762 54.57819
[2,] 8.935628 53.83027
[3,] 5.451914 54.65691
[4,] 1.987882 52.68871
[5,] 1.515514 53.02331
[6,] 1.338376 53.22013
[7,] 1.239966 54.44041
[8,] 3.247530 55.85752
[9,] 6.219512 55.99529
[10,] 8.758490 56.01497
[11,] 10.903828 55.83783
[12,] 14.033266 53.86963
, , 3
[,1] [,2]
[1,] 9.805328 56.06903
[2,] 10.137712 55.27961
[3,] 6.647680 55.73664
[4,] 3.448484 53.86698
[5,] 3.012230 54.34478
[6,] 2.825264 54.57330
[7,] 2.721394 55.73664
[8,] 4.549506 56.79612
[9,] 7.520188 57.35701
[10,] 9.846876 57.25314
[11,] 11.986598 57.23237
[12,] 14.749540 55.11342
, , 4
[,1] [,2]
[1,] 9.637164 58.03294
[2,] 9.952104 56.77318
[3,] 6.109836 57.94896
[4,] 2.645496 55.89135
[5,] 2.015616 56.62621
[6,] 1.721672 57.21410
[7,] 1.868644 58.51585
[8,] 3.632308 59.48167
[9,] 6.865692 59.92258
[10,] 9.763140 59.56565
[11,] 11.883736 59.46067
[12,] 15.369072 56.56322
, , 5
[,1] [,2]
[1,] 11.035692 58.75009
[2,] 11.335110 57.85184
[3,] 8.255382 58.92119
[4,] 4.555431 57.46687
[5,] 3.956595 58.08709
[6,] 3.871047 58.40790
[7,] 3.871047 59.58418
[8,] 5.795877 60.22579
[9,] 9.068088 60.24718
[10,] 11.420658 59.94776
[11,] 12.768039 59.88360
[12,] 15.847767 57.46687
, , 6
[,1] [,2]
[1,] 7.946625 55.71114
[2,] 8.476400 54.82112
[3,] 4.979885 54.90588
[4,] 2.479347 52.85035
[5,] 2.076718 53.10465
[6,] 1.737662 53.14703
[7,] 1.335033 54.20658
[8,] 2.712448 55.54161
[9,] 5.382514 56.60116
[10,] 7.861861 56.96141
[11,] 9.663096 57.49118
[12,] 13.138420 55.75352
, , 7
[,1] [,2]
[1,] 8.849841 58.66961
[2,] 9.396387 57.82877
[3,] 5.990985 58.31225
[4,] 2.501499 56.84078
[5,] 2.102100 57.28223
[6,] 1.933932 57.47141
[7,] 1.975974 58.43838
[8,] 3.741738 59.34228
[9,] 6.642636 59.72066
[10,] 8.849841 59.82577
[11,] 10.951941 59.48943
[12,] 13.579566 57.89183
, , 8
[,1] [,2]
[1,] 9.331504 56.36904
[2,] 10.154872 55.31344
[3,] 6.671392 56.62238
[4,] 2.195648 55.08121
[5,] 1.688960 55.79902
[6,] 1.520064 56.28459
[7,] 1.583400 57.34019
[8,] 3.715712 58.22690
[9,] 7.241416 58.26912
[10,] 9.774856 57.88910
[11,] 11.949392 57.59354
[12,] 15.432872 54.70119
, , 9
[,1] [,2]
[1,] 9.840795 58.49453
[2,] 10.179403 57.37289
[3,] 6.031455 58.49453
[4,] 2.624212 57.05545
[5,] 2.137463 57.35173
[6,] 1.566062 57.71150
[7,] 1.693040 58.98128
[8,] 3.745851 60.06059
[9,] 7.110768 60.14525
[10,] 10.073588 60.12408
[11,] 11.787791 59.89129
[12,] 15.131545 57.41522
, , 10
[,1] [,2]
[1,] 9.563510 56.51740
[2,] 9.900550 55.50628
[3,] 5.919265 56.36994
[4,] 1.811590 54.45303
[5,] 1.369225 55.02178
[6,] 1.221770 55.54841
[7,] 1.200705 56.87550
[8,] 3.265075 57.88662
[9,] 6.551215 58.05514
[10,] 9.437120 57.97088
[11,] 11.627880 57.52851
[12,] 15.419580 55.08498
, , 11
[,1] [,2]
[1,] 8.211782 57.04143
[2,] 8.337794 55.52929
[3,] 4.830460 59.47766
[4,] 0.336032 60.90580
[5,] 0.462044 61.68287
[6,] 0.378036 62.18692
[7,] 1.176112 63.19502
[8,] 4.053386 62.58596
[9,] 6.993666 60.56977
[10,] 9.765930 58.61658
[11,] 11.803124 57.29346
[12,] 15.016430 53.55510
, , 12
[,1] [,2]
[1,] 8.691998 54.71960
[2,] 9.660114 53.56207
[3,] 5.240454 55.43516
[4,] 1.641588 54.76169
[5,] 0.926024 55.37203
[6,] 0.610334 55.85608
[7,] 0.926024 57.09780
[8,] 3.220038 57.72918
[9,] 6.503214 57.11884
[10,] 9.533838 56.46642
[11,] 11.449024 56.48746
[12,] 15.889730 54.13031
, , 13
[,1] [,2]
[1,] 10.707338 61.44578
[2,] 11.724882 60.26636
[3,] 7.030304 61.28390
[4,] 2.890750 59.13318
[5,] 2.220096 59.78071
[6,] 2.058214 60.10447
[7,] 2.127592 61.49203
[8,] 4.393940 62.85647
[9,] 7.932218 63.11085
[10,] 11.216110 63.29586
[11,] 13.228072 63.85089
[12,] 18.500800 63.06460
, , 14
[,1] [,2]
[1,] 8.470779 53.32874
[2,] 9.155484 52.66360
[3,] 6.397101 53.21136
[4,] 4.460364 52.42884
[5,] 4.166919 52.76141
[6,] 3.990852 53.21136
[7,] 4.264734 54.07213
[8,] 5.164632 54.50252
[9,] 7.453503 54.32645
[10,] 8.842476 54.34601
[11,] 9.820626 54.26776
[12,] 12.735513 53.48524
, , 15
[,1] [,2]
[1,] 11.532672 74.42845
[2,] 12.226768 72.61312
[3,] 7.635056 75.04246
[4,] 2.776384 73.92122
[5,] 2.322552 74.32166
[6,] 1.681848 74.82889
[7,] 2.215768 76.40395
[8,] 4.965456 77.36501
[9,] 9.396992 76.99126
[10,] 12.280160 76.59082
[11,] 14.389144 76.27047
[12,] 19.488080 73.89453
, , 16
[,1] [,2]
[1,] 8.919900 55.17745
[2,] 9.675468 53.01569
[3,] 5.561820 55.57622
[4,] 0.797544 54.17003
[5,] 0.482724 54.98856
[6,] 0.272844 55.49227
[7,] 0.524700 56.81452
[8,] 3.022272 57.63305
[9,] 6.737148 57.27625
[10,] 9.864360 56.98242
[11,] 11.984148 56.45772
[12,] 16.454592 54.75769
, , 17
[,1] [,2]
[1,] 9.914553 55.94491
[2,] 10.459539 55.16935
[3,] 7.524999 55.94491
[4,] 5.009679 55.10647
[5,] 4.716225 55.48377
[6,] 4.527576 55.86107
[7,] 4.527576 56.55278
[8,] 5.743314 57.43314
[9,] 8.405361 57.34930
[10,] 10.124163 57.22353
[11,] 11.738160 57.22353
[12,] 14.484051 56.04971
, , 18
[,1] [,2]
[1,] 10.661782 62.89986
[2,] 11.616221 61.66607
[3,] 6.867305 63.76118
[4,] 2.677085 62.24805
[5,] 2.025273 62.80674
[6,] 1.489856 63.36544
[7,] 1.839041 64.78546
[8,] 4.283336 65.83301
[9,] 8.566672 65.55366
[10,] 11.616221 64.92513
[11,] 13.874284 64.76218
[12,] 18.623200 62.87658
, , 19
[,1] [,2]
[1,] 8.313908 51.34480
[2,] 9.735764 50.02168
[3,] 4.838260 51.38430
[4,] 1.303368 49.98219
[5,] 0.710928 50.57463
[6,] 0.572692 51.04858
[7,] 0.829416 52.23346
[8,] 2.784468 53.28010
[9,] 6.516840 53.35910
[10,] 9.419796 53.26036
[11,] 11.098376 53.14187
[12,] 15.818148 51.44354
, , 20
[,1] [,2]
[1,] 8.506270 57.07500
[2,] 9.813331 55.99615
[3,] 5.912895 57.30321
[4,] 1.514531 56.24512
[5,] 1.161832 56.84678
[6,] 0.871374 57.19948
[7,] 1.286314 58.36131
[8,] 3.651472 59.00447
[9,] 6.929498 59.08746
[10,] 9.979307 58.65177
[11,] 11.888031 58.77625
[12,] 16.556106 56.95052
, , 21
[,1] [,2]
[1,] 10.310018 55.68670
[2,] 11.086944 54.67879
[3,] 7.895248 55.77069
[4,] 4.388582 54.51081
[5,] 3.884630 54.80478
[6,] 3.569660 55.09875
[7,] 3.548662 56.10666
[8,] 5.291496 57.15656
[9,] 8.294210 57.40853
[10,] 10.519998 57.34554
[11,] 13.732692 57.51352
[12,] 15.958480 55.93867
, , 22
[,1] [,2]
[1,] 8.168564 57.41153
[2,] 8.189617 56.04309
[3,] 5.579045 59.41157
[4,] 0.694749 60.42211
[5,] 0.421060 61.11686
[6,] 0.336848 61.58002
[7,] 1.305286 62.52741
[8,] 3.957964 62.61162
[9,] 7.494868 60.90633
[10,] 10.084387 59.05366
[11,] 13.810768 56.90626
[12,] 15.052895 53.24304
, , 23
[,1] [,2]
[1,] 8.514847 55.94275
[2,] 9.163398 54.83394
[3,] 5.732354 55.92183
[4,] 2.238547 54.66657
[5,] 1.882890 55.00131
[6,] 1.694601 55.41973
[7,] 1.799206 56.25657
[8,] 3.640254 57.34446
[9,] 6.673799 57.59551
[10,] 9.016951 57.51183
[11,] 11.883128 57.34446
[12,] 14.100754 55.37789
, , 24
[,1] [,2]
[1,] 7.52874 58.00074
[2,] 7.90728 57.24366
[3,] 5.23647 58.12692
[4,] 1.95579 56.94924
[5,] 1.55622 57.26469
[6,] 1.36695 57.79044
[7,] 1.53519 58.73679
[8,] 3.13347 59.49387
[9,] 5.59398 59.51490
[10,] 7.90728 59.22048
[11,] 10.53603 59.17842
[12,] 12.38667 57.43293
, , 25
[,1] [,2]
[1,] 9.660255 58.00344
[2,] 10.498455 57.16524
[3,] 7.543800 58.17108
[4,] 4.253865 56.80901
[5,] 3.876675 57.27002
[6,] 3.583305 57.60530
[7,] 3.604260 58.50636
[8,] 5.196840 59.55411
[9,] 7.858125 59.70080
[10,] 10.142220 59.61698
[11,] 12.824460 59.38647
[12,] 15.108555 57.66816
, , 26
[,1] [,2]
[1,] 8.374318 56.47404
[2,] 8.837220 55.10638
[3,] 5.554824 57.02111
[4,] 1.346624 55.94802
[5,] 0.967886 56.74758
[6,] 0.799558 57.33673
[7,] 0.904763 58.51502
[8,] 3.008863 59.20937
[9,] 6.312300 58.97792
[10,] 9.110753 58.28357
[11,] 12.498354 57.84171
[12,] 15.465135 55.56928
, , 27
[,1] [,2]
[1,] 8.634288 57.98208
[2,] 9.663680 56.13338
[3,] 5.945264 58.54930
[4,] 1.491568 56.53253
[5,] 0.924352 57.41486
[6,] 0.630240 58.27619
[7,] 0.861328 59.83078
[8,] 3.361280 60.90219
[9,] 7.016672 60.86018
[10,] 9.936784 59.95683
[11,] 14.180400 59.43163
[12,] 17.016480 57.01571
, , 28
[,1] [,2]
[1,] 9.99570 57.01410
[2,] 10.63920 55.74855
[3,] 6.73530 57.70050
[4,] 1.26555 55.83435
[5,] 0.64350 56.49930
[6,] 0.49335 56.99265
[7,] 0.66495 58.25820
[8,] 3.81810 59.56665
[9,] 7.61475 59.48085
[10,] 10.85370 58.92315
[11,] 14.43585 58.53705
[12,] 17.54610 56.11320
, , 29
[,1] [,2]
[1,] 9.293050 56.80955
[2,] 9.860725 55.37985
[3,] 6.664925 57.29312
[4,] 2.733250 55.90547
[5,] 2.291725 56.15777
[6,] 2.018400 56.62032
[7,] 2.060450 57.83977
[8,] 4.205000 59.08025
[9,] 7.758225 59.01717
[10,] 10.449425 58.40745
[11,] 13.645225 57.96592
[12,] 15.831825 56.15777
, , 30
[,1] [,2]
[1,] 8.395014 57.54170
[2,] 9.238734 56.52924
[3,] 6.243528 57.96356
[4,] 2.425695 57.01438
[5,] 1.792905 57.26750
[6,] 1.455417 57.49952
[7,] 1.413231 58.51198
[8,] 3.417066 59.65100
[9,] 6.686481 59.54554
[10,] 9.133269 58.80728
[11,] 11.790987 58.51198
[12,] 14.090124 56.74017
, , 31
[,1] [,2]
[1,] 9.536103 56.41668
[2,] 10.188684 55.53254
[3,] 6.862626 56.83770
[4,] 2.778732 55.72200
[5,] 2.315610 56.16407
[6,] 1.978794 56.45878
[7,] 2.084049 57.49028
[8,] 4.189149 58.39547
[9,] 7.431003 58.62703
[10,] 10.314990 58.35337
[11,] 13.809456 57.99551
[12,] 15.935607 56.03776
, , 32
[,1] [,2]
[1,] 9.28998 57.66999
[2,] 9.43845 56.39739
[3,] 6.15090 60.06672
[4,] 0.91203 61.10601
[5,] 0.67872 61.63626
[6,] 0.57267 62.16651
[7,] 1.16655 63.16338
[8,] 4.43289 63.26943
[9,] 7.86891 61.44537
[10,] 10.90194 59.30316
[11,] 14.23191 57.26700
[12,] 15.84387 53.95824
, , 33
[,1] [,2]
[1,] 9.45411 57.01684
[2,] 10.10108 56.05682
[3,] 6.63666 57.28815
[4,] 2.69223 55.86899
[5,] 2.35831 56.36987
[6,] 2.02439 56.72466
[7,] 2.08700 57.72642
[8,] 3.88182 58.85340
[9,] 7.57581 58.89514
[10,] 10.20543 58.39426
[11,] 13.44028 58.20643
[12,] 16.13251 56.32813
, , 34
[,1] [,2]
[1,] 7.130627 56.33819
[2,] 7.546407 55.63136
[3,] 5.238828 56.50450
[4,] 1.683909 55.36111
[5,] 1.476019 55.67294
[6,] 1.247340 55.75610
[7,] 1.164184 56.75397
[8,] 2.577836 57.81421
[9,] 5.488296 57.98052
[10,] 7.691930 57.54395
[11,] 10.165821 57.39843
[12,] 12.847602 55.79768
, , 35
[,1] [,2]
[1,] 9.093168 58.07419
[2,] 9.745687 56.79020
[3,] 6.209455 58.36888
[4,] 1.852312 57.00069
[5,] 1.283989 57.48482
[6,] 1.094548 57.90580
[7,] 1.305038 59.00035
[8,] 3.388889 59.96860
[9,] 7.114562 60.32643
[10,] 9.787785 59.71601
[11,] 12.945135 59.16874
[12,] 15.239476 57.50587
, , 36
[,1] [,2]
[1,] 8.076244 58.16164
[2,] 8.837356 57.21025
[3,] 5.412352 58.26735
[4,] 1.945064 56.51257
[5,] 1.458798 56.93541
[6,] 1.205094 57.29482
[7,] 1.374230 58.20393
[8,] 3.065590 59.45130
[9,] 5.835192 59.85300
[10,] 8.625936 59.64158
[11,] 11.691526 59.76843
[12,] 14.672548 57.88680
, , 37
[,1] [,2]
[1,] 8.46210 56.89815
[2,] 9.28305 55.97195
[3,] 6.44130 56.77185
[4,] 2.31550 55.29835
[5,] 1.91555 55.57200
[6,] 1.78925 56.05615
[7,] 1.76820 57.08760
[8,] 3.17855 57.99275
[9,] 6.31500 58.45585
[10,] 8.77785 58.37165
[11,] 11.97745 58.35060
[12,] 14.46135 57.08760
, , 38
[,1] [,2]
[1,] 8.58024 57.72735
[2,] 9.65277 56.27628
[3,] 6.07767 58.31619
[4,] 1.21974 57.41190
[5,] 0.79914 58.27413
[6,] 0.65193 58.77885
[7,] 1.07253 60.12477
[8,] 3.36480 60.73464
[9,] 6.98196 60.27198
[10,] 10.01028 59.28357
[11,] 13.83774 58.88400
[12,] 16.71885 56.08701
, , 39
[,1] [,2]
[1,] 9.389055 56.73521
[2,] 10.000926 55.84905
[3,] 6.751680 56.94620
[4,] 2.869464 55.57477
[5,] 2.363088 56.06004
[6,] 2.088801 56.62972
[7,] 2.236494 57.62137
[8,] 4.198701 58.50753
[9,] 7.532343 58.38093
[10,] 9.916530 58.21214
[11,] 12.638301 58.29654
[12,] 15.338973 56.27103
, , 40
[,1] [,2]
[1,] 9.494001 56.66929
[2,] 10.125531 55.57464
[3,] 6.694218 57.25872
[4,] 1.494621 56.47983
[5,] 0.968346 56.77455
[6,] 0.842040 57.34292
[7,] 0.989397 58.33232
[8,] 3.410262 59.30067
[9,] 7.473105 58.92175
[10,] 9.957123 58.26917
[11,] 13.514742 57.72184
[12,] 15.956658 55.59569
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
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[2,] 8.679762 54.57819 8.935628 53.83027 5.451914 54.65691 1.987882 52.68871
[3,] 9.805328 56.06903 10.137712 55.27961 6.647680 55.73664 3.448484 53.86698
[4,] 9.637164 58.03294 9.952104 56.77318 6.109836 57.94896 2.645496 55.89135
[5,] 11.035692 58.75009 11.335110 57.85184 8.255382 58.92119 4.555431 57.46687
[6,] 7.946625 55.71114 8.476400 54.82112 4.979885 54.90588 2.479347 52.85035
[7,] 8.849841 58.66961 9.396387 57.82877 5.990985 58.31225 2.501499 56.84078
[8,] 9.331504 56.36904 10.154872 55.31344 6.671392 56.62238 2.195648 55.08121
[9,] 9.840795 58.49453 10.179403 57.37289 6.031455 58.49453 2.624212 57.05545
[10,] 9.563510 56.51740 9.900550 55.50628 5.919265 56.36994 1.811590 54.45303
[11,] 8.211782 57.04143 8.337794 55.52929 4.830460 59.47766 0.336032 60.90580
[12,] 8.691998 54.71960 9.660114 53.56207 5.240454 55.43516 1.641588 54.76169
[13,] 10.707338 61.44578 11.724882 60.26636 7.030304 61.28390 2.890750 59.13318
[14,] 8.470779 53.32874 9.155484 52.66360 6.397101 53.21136 4.460364 52.42884
[15,] 11.532672 74.42845 12.226768 72.61312 7.635056 75.04246 2.776384 73.92122
[16,] 8.919900 55.17745 9.675468 53.01569 5.561820 55.57622 0.797544 54.17003
[17,] 9.914553 55.94491 10.459539 55.16935 7.524999 55.94491 5.009679 55.10647
[18,] 10.661782 62.89986 11.616221 61.66607 6.867305 63.76118 2.677085 62.24805
[19,] 8.313908 51.34480 9.735764 50.02168 4.838260 51.38430 1.303368 49.98219
[20,] 8.506270 57.07500 9.813331 55.99615 5.912895 57.30321 1.514531 56.24512
[21,] 10.310018 55.68670 11.086944 54.67879 7.895248 55.77069 4.388582 54.51081
[22,] 8.168564 57.41153 8.189617 56.04309 5.579045 59.41157 0.694749 60.42211
[23,] 8.514847 55.94275 9.163398 54.83394 5.732354 55.92183 2.238547 54.66657
[24,] 7.528740 58.00074 7.907280 57.24366 5.236470 58.12692 1.955790 56.94924
[25,] 9.660255 58.00344 10.498455 57.16524 7.543800 58.17108 4.253865 56.80901
[26,] 8.374318 56.47404 8.837220 55.10638 5.554824 57.02111 1.346624 55.94802
[27,] 8.634288 57.98208 9.663680 56.13338 5.945264 58.54930 1.491568 56.53253
[28,] 9.995700 57.01410 10.639200 55.74855 6.735300 57.70050 1.265550 55.83435
[29,] 9.293050 56.80955 9.860725 55.37985 6.664925 57.29312 2.733250 55.90547
[30,] 8.395014 57.54170 9.238734 56.52924 6.243528 57.96356 2.425695 57.01438
[31,] 9.536103 56.41668 10.188684 55.53254 6.862626 56.83770 2.778732 55.72200
[32,] 9.289980 57.66999 9.438450 56.39739 6.150900 60.06672 0.912030 61.10601
[33,] 9.454110 57.01684 10.101080 56.05682 6.636660 57.28815 2.692230 55.86899
[34,] 7.130627 56.33819 7.546407 55.63136 5.238828 56.50450 1.683909 55.36111
[35,] 9.093168 58.07419 9.745687 56.79020 6.209455 58.36888 1.852312 57.00069
[36,] 8.076244 58.16164 8.837356 57.21025 5.412352 58.26735 1.945064 56.51257
[37,] 8.462100 56.89815 9.283050 55.97195 6.441300 56.77185 2.315500 55.29835
[38,] 8.580240 57.72735 9.652770 56.27628 6.077670 58.31619 1.219740 57.41190
[39,] 9.389055 56.73521 10.000926 55.84905 6.751680 56.94620 2.869464 55.57477
[40,] 9.494001 56.66929 10.125531 55.57464 6.694218 57.25872 1.494621 56.47983
[,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16]
[1,] 1.281800 53.18484 1.242360 53.32288 0.847960 54.70328 3.352400 55.76816
[2,] 1.515514 53.02331 1.338376 53.22013 1.239966 54.44041 3.247530 55.85752
[3,] 3.012230 54.34478 2.825264 54.57330 2.721394 55.73664 4.549506 56.79612
[4,] 2.015616 56.62621 1.721672 57.21410 1.868644 58.51585 3.632308 59.48167
[5,] 3.956595 58.08709 3.871047 58.40790 3.871047 59.58418 5.795877 60.22579
[6,] 2.076718 53.10465 1.737662 53.14703 1.335033 54.20658 2.712448 55.54161
[7,] 2.102100 57.28223 1.933932 57.47141 1.975974 58.43838 3.741738 59.34228
[8,] 1.688960 55.79902 1.520064 56.28459 1.583400 57.34019 3.715712 58.22690
[9,] 2.137463 57.35173 1.566062 57.71150 1.693040 58.98128 3.745851 60.06059
[10,] 1.369225 55.02178 1.221770 55.54841 1.200705 56.87550 3.265075 57.88662
[11,] 0.462044 61.68287 0.378036 62.18692 1.176112 63.19502 4.053386 62.58596
[12,] 0.926024 55.37203 0.610334 55.85608 0.926024 57.09780 3.220038 57.72918
[13,] 2.220096 59.78071 2.058214 60.10447 2.127592 61.49203 4.393940 62.85647
[14,] 4.166919 52.76141 3.990852 53.21136 4.264734 54.07213 5.164632 54.50252
[15,] 2.322552 74.32166 1.681848 74.82889 2.215768 76.40395 4.965456 77.36501
[16,] 0.482724 54.98856 0.272844 55.49227 0.524700 56.81452 3.022272 57.63305
[17,] 4.716225 55.48377 4.527576 55.86107 4.527576 56.55278 5.743314 57.43314
[18,] 2.025273 62.80674 1.489856 63.36544 1.839041 64.78546 4.283336 65.83301
[19,] 0.710928 50.57463 0.572692 51.04858 0.829416 52.23346 2.784468 53.28010
[20,] 1.161832 56.84678 0.871374 57.19948 1.286314 58.36131 3.651472 59.00447
[21,] 3.884630 54.80478 3.569660 55.09875 3.548662 56.10666 5.291496 57.15656
[22,] 0.421060 61.11686 0.336848 61.58002 1.305286 62.52741 3.957964 62.61162
[23,] 1.882890 55.00131 1.694601 55.41973 1.799206 56.25657 3.640254 57.34446
[24,] 1.556220 57.26469 1.366950 57.79044 1.535190 58.73679 3.133470 59.49387
[25,] 3.876675 57.27002 3.583305 57.60530 3.604260 58.50636 5.196840 59.55411
[26,] 0.967886 56.74758 0.799558 57.33673 0.904763 58.51502 3.008863 59.20937
[27,] 0.924352 57.41486 0.630240 58.27619 0.861328 59.83078 3.361280 60.90219
[28,] 0.643500 56.49930 0.493350 56.99265 0.664950 58.25820 3.818100 59.56665
[29,] 2.291725 56.15777 2.018400 56.62032 2.060450 57.83977 4.205000 59.08025
[30,] 1.792905 57.26750 1.455417 57.49952 1.413231 58.51198 3.417066 59.65100
[31,] 2.315610 56.16407 1.978794 56.45878 2.084049 57.49028 4.189149 58.39547
[32,] 0.678720 61.63626 0.572670 62.16651 1.166550 63.16338 4.432890 63.26943
[33,] 2.358310 56.36987 2.024390 56.72466 2.087000 57.72642 3.881820 58.85340
[34,] 1.476019 55.67294 1.247340 55.75610 1.164184 56.75397 2.577836 57.81421
[35,] 1.283989 57.48482 1.094548 57.90580 1.305038 59.00035 3.388889 59.96860
[36,] 1.458798 56.93541 1.205094 57.29482 1.374230 58.20393 3.065590 59.45130
[37,] 1.915550 55.57200 1.789250 56.05615 1.768200 57.08760 3.178550 57.99275
[38,] 0.799140 58.27413 0.651930 58.77885 1.072530 60.12477 3.364800 60.73464
[39,] 2.363088 56.06004 2.088801 56.62972 2.236494 57.62137 4.198701 58.50753
[40,] 0.968346 56.77455 0.842040 57.34292 0.989397 58.33232 3.410262 59.30067
[,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 6.290680 55.70900 8.874000 55.25544 10.747400 55.43292 14.39560 52.75100
[2,] 6.219512 55.99529 8.758490 56.01497 10.903828 55.83783 14.03327 53.86963
[3,] 7.520188 57.35701 9.846876 57.25314 11.986598 57.23237 14.74954 55.11342
[4,] 6.865692 59.92258 9.763140 59.56565 11.883736 59.46067 15.36907 56.56322
[5,] 9.068088 60.24718 11.420658 59.94776 12.768039 59.88360 15.84777 57.46687
[6,] 5.382514 56.60116 7.861861 56.96141 9.663096 57.49118 13.13842 55.75352
[7,] 6.642636 59.72066 8.849841 59.82577 10.951941 59.48943 13.57957 57.89183
[8,] 7.241416 58.26912 9.774856 57.88910 11.949392 57.59354 15.43287 54.70119
[9,] 7.110768 60.14525 10.073588 60.12408 11.787791 59.89129 15.13155 57.41522
[10,] 6.551215 58.05514 9.437120 57.97088 11.627880 57.52851 15.41958 55.08498
[11,] 6.993666 60.56977 9.765930 58.61658 11.803124 57.29346 15.01643 53.55510
[12,] 6.503214 57.11884 9.533838 56.46642 11.449024 56.48746 15.88973 54.13031
[13,] 7.932218 63.11085 11.216110 63.29586 13.228072 63.85089 18.50080 63.06460
[14,] 7.453503 54.32645 8.842476 54.34601 9.820626 54.26776 12.73551 53.48524
[15,] 9.396992 76.99126 12.280160 76.59082 14.389144 76.27047 19.48808 73.89453
[16,] 6.737148 57.27625 9.864360 56.98242 11.984148 56.45772 16.45459 54.75769
[17,] 8.405361 57.34930 10.124163 57.22353 11.738160 57.22353 14.48405 56.04971
[18,] 8.566672 65.55366 11.616221 64.92513 13.874284 64.76218 18.62320 62.87658
[19,] 6.516840 53.35910 9.419796 53.26036 11.098376 53.14187 15.81815 51.44354
[20,] 6.929498 59.08746 9.979307 58.65177 11.888031 58.77625 16.55611 56.95052
[21,] 8.294210 57.40853 10.519998 57.34554 13.732692 57.51352 15.95848 55.93867
[22,] 7.494868 60.90633 10.084387 59.05366 13.810768 56.90626 15.05289 53.24304
[23,] 6.673799 57.59551 9.016951 57.51183 11.883128 57.34446 14.10075 55.37789
[24,] 5.593980 59.51490 7.907280 59.22048 10.536030 59.17842 12.38667 57.43293
[25,] 7.858125 59.70080 10.142220 59.61698 12.824460 59.38647 15.10856 57.66816
[26,] 6.312300 58.97792 9.110753 58.28357 12.498354 57.84171 15.46514 55.56928
[27,] 7.016672 60.86018 9.936784 59.95683 14.180400 59.43163 17.01648 57.01571
[28,] 7.614750 59.48085 10.853700 58.92315 14.435850 58.53705 17.54610 56.11320
[29,] 7.758225 59.01717 10.449425 58.40745 13.645225 57.96592 15.83182 56.15777
[30,] 6.686481 59.54554 9.133269 58.80728 11.790987 58.51198 14.09012 56.74017
[31,] 7.431003 58.62703 10.314990 58.35337 13.809456 57.99551 15.93561 56.03776
[32,] 7.868910 61.44537 10.901940 59.30316 14.231910 57.26700 15.84387 53.95824
[33,] 7.575810 58.89514 10.205430 58.39426 13.440280 58.20643 16.13251 56.32813
[34,] 5.488296 57.98052 7.691930 57.54395 10.165821 57.39843 12.84760 55.79768
[35,] 7.114562 60.32643 9.787785 59.71601 12.945135 59.16874 15.23948 57.50587
[36,] 5.835192 59.85300 8.625936 59.64158 11.691526 59.76843 14.67255 57.88680
[37,] 6.315000 58.45585 8.777850 58.37165 11.977450 58.35060 14.46135 57.08760
[38,] 6.981960 60.27198 10.010280 59.28357 13.837740 58.88400 16.71885 56.08701
[39,] 7.532343 58.38093 9.916530 58.21214 12.638301 58.29654 15.33897 56.27103
[40,] 7.473105 58.92175 9.957123 58.26917 13.514742 57.72184 15.95666 55.59569
geomorph documentation built on Aug. 10, 2017, 1:11 a.m.
R Package Documentation
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
Convert a three-dimensional array of landmark coordinates into a two-dimensional matrix
Usage
1 | two.d.array(A, sep = ".")
|
Arguments
A |
A 3D array (p x k x n) containing landmark coordinates for a set of specimens |
sep |
An optional argument for variable labeling, combining landmark labels (e.g., 1, 2, 3, ...)
and partial dimension labels (e.g., "x", "y", and "z"), much like the |
Details
This function converts a (p x k x n) array of landmark coordinates into a two-dimensional matrix (n x [p x k]). The latter format of the shape data is useful for performing subsequent statistical analyses in R (e.g., PCA, MANOVA, PLS, etc.). Row labels are preserved if included in the original array.
Value
Function returns a two-dimensional matrix of dimension (n x [p x k]), where rows represent specimens and columns represent variables.
Author(s)
Dean Adams and Emma Sherratt
See Also
Examples
1 2 3 4 | data(plethodon)
plethodon$land #original data in the form of 3D array
two.d.array(plethodon$land) # Convert to a 2D data matrix
|
Example output
Loading required package: rgl
Loading required package: ape
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
[,1] [,2]
[1,] 8.89372 53.77644
[2,] 9.26840 52.77072
[3,] 5.56104 54.21028
[4,] 1.87340 52.75100
[5,] 1.28180 53.18484
[6,] 1.24236 53.32288
[7,] 0.84796 54.70328
[8,] 3.35240 55.76816
[9,] 6.29068 55.70900
[10,] 8.87400 55.25544
[11,] 10.74740 55.43292
[12,] 14.39560 52.75100
, , 2
[,1] [,2]
[1,] 8.679762 54.57819
[2,] 8.935628 53.83027
[3,] 5.451914 54.65691
[4,] 1.987882 52.68871
[5,] 1.515514 53.02331
[6,] 1.338376 53.22013
[7,] 1.239966 54.44041
[8,] 3.247530 55.85752
[9,] 6.219512 55.99529
[10,] 8.758490 56.01497
[11,] 10.903828 55.83783
[12,] 14.033266 53.86963
, , 3
[,1] [,2]
[1,] 9.805328 56.06903
[2,] 10.137712 55.27961
[3,] 6.647680 55.73664
[4,] 3.448484 53.86698
[5,] 3.012230 54.34478
[6,] 2.825264 54.57330
[7,] 2.721394 55.73664
[8,] 4.549506 56.79612
[9,] 7.520188 57.35701
[10,] 9.846876 57.25314
[11,] 11.986598 57.23237
[12,] 14.749540 55.11342
, , 4
[,1] [,2]
[1,] 9.637164 58.03294
[2,] 9.952104 56.77318
[3,] 6.109836 57.94896
[4,] 2.645496 55.89135
[5,] 2.015616 56.62621
[6,] 1.721672 57.21410
[7,] 1.868644 58.51585
[8,] 3.632308 59.48167
[9,] 6.865692 59.92258
[10,] 9.763140 59.56565
[11,] 11.883736 59.46067
[12,] 15.369072 56.56322
, , 5
[,1] [,2]
[1,] 11.035692 58.75009
[2,] 11.335110 57.85184
[3,] 8.255382 58.92119
[4,] 4.555431 57.46687
[5,] 3.956595 58.08709
[6,] 3.871047 58.40790
[7,] 3.871047 59.58418
[8,] 5.795877 60.22579
[9,] 9.068088 60.24718
[10,] 11.420658 59.94776
[11,] 12.768039 59.88360
[12,] 15.847767 57.46687
, , 6
[,1] [,2]
[1,] 7.946625 55.71114
[2,] 8.476400 54.82112
[3,] 4.979885 54.90588
[4,] 2.479347 52.85035
[5,] 2.076718 53.10465
[6,] 1.737662 53.14703
[7,] 1.335033 54.20658
[8,] 2.712448 55.54161
[9,] 5.382514 56.60116
[10,] 7.861861 56.96141
[11,] 9.663096 57.49118
[12,] 13.138420 55.75352
, , 7
[,1] [,2]
[1,] 8.849841 58.66961
[2,] 9.396387 57.82877
[3,] 5.990985 58.31225
[4,] 2.501499 56.84078
[5,] 2.102100 57.28223
[6,] 1.933932 57.47141
[7,] 1.975974 58.43838
[8,] 3.741738 59.34228
[9,] 6.642636 59.72066
[10,] 8.849841 59.82577
[11,] 10.951941 59.48943
[12,] 13.579566 57.89183
, , 8
[,1] [,2]
[1,] 9.331504 56.36904
[2,] 10.154872 55.31344
[3,] 6.671392 56.62238
[4,] 2.195648 55.08121
[5,] 1.688960 55.79902
[6,] 1.520064 56.28459
[7,] 1.583400 57.34019
[8,] 3.715712 58.22690
[9,] 7.241416 58.26912
[10,] 9.774856 57.88910
[11,] 11.949392 57.59354
[12,] 15.432872 54.70119
, , 9
[,1] [,2]
[1,] 9.840795 58.49453
[2,] 10.179403 57.37289
[3,] 6.031455 58.49453
[4,] 2.624212 57.05545
[5,] 2.137463 57.35173
[6,] 1.566062 57.71150
[7,] 1.693040 58.98128
[8,] 3.745851 60.06059
[9,] 7.110768 60.14525
[10,] 10.073588 60.12408
[11,] 11.787791 59.89129
[12,] 15.131545 57.41522
, , 10
[,1] [,2]
[1,] 9.563510 56.51740
[2,] 9.900550 55.50628
[3,] 5.919265 56.36994
[4,] 1.811590 54.45303
[5,] 1.369225 55.02178
[6,] 1.221770 55.54841
[7,] 1.200705 56.87550
[8,] 3.265075 57.88662
[9,] 6.551215 58.05514
[10,] 9.437120 57.97088
[11,] 11.627880 57.52851
[12,] 15.419580 55.08498
, , 11
[,1] [,2]
[1,] 8.211782 57.04143
[2,] 8.337794 55.52929
[3,] 4.830460 59.47766
[4,] 0.336032 60.90580
[5,] 0.462044 61.68287
[6,] 0.378036 62.18692
[7,] 1.176112 63.19502
[8,] 4.053386 62.58596
[9,] 6.993666 60.56977
[10,] 9.765930 58.61658
[11,] 11.803124 57.29346
[12,] 15.016430 53.55510
, , 12
[,1] [,2]
[1,] 8.691998 54.71960
[2,] 9.660114 53.56207
[3,] 5.240454 55.43516
[4,] 1.641588 54.76169
[5,] 0.926024 55.37203
[6,] 0.610334 55.85608
[7,] 0.926024 57.09780
[8,] 3.220038 57.72918
[9,] 6.503214 57.11884
[10,] 9.533838 56.46642
[11,] 11.449024 56.48746
[12,] 15.889730 54.13031
, , 13
[,1] [,2]
[1,] 10.707338 61.44578
[2,] 11.724882 60.26636
[3,] 7.030304 61.28390
[4,] 2.890750 59.13318
[5,] 2.220096 59.78071
[6,] 2.058214 60.10447
[7,] 2.127592 61.49203
[8,] 4.393940 62.85647
[9,] 7.932218 63.11085
[10,] 11.216110 63.29586
[11,] 13.228072 63.85089
[12,] 18.500800 63.06460
, , 14
[,1] [,2]
[1,] 8.470779 53.32874
[2,] 9.155484 52.66360
[3,] 6.397101 53.21136
[4,] 4.460364 52.42884
[5,] 4.166919 52.76141
[6,] 3.990852 53.21136
[7,] 4.264734 54.07213
[8,] 5.164632 54.50252
[9,] 7.453503 54.32645
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[35,] 1.283989 57.48482 1.094548 57.90580 1.305038 59.00035 3.388889 59.96860
[36,] 1.458798 56.93541 1.205094 57.29482 1.374230 58.20393 3.065590 59.45130
[37,] 1.915550 55.57200 1.789250 56.05615 1.768200 57.08760 3.178550 57.99275
[38,] 0.799140 58.27413 0.651930 58.77885 1.072530 60.12477 3.364800 60.73464
[39,] 2.363088 56.06004 2.088801 56.62972 2.236494 57.62137 4.198701 58.50753
[40,] 0.968346 56.77455 0.842040 57.34292 0.989397 58.33232 3.410262 59.30067
[,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24]
[1,] 6.290680 55.70900 8.874000 55.25544 10.747400 55.43292 14.39560 52.75100
[2,] 6.219512 55.99529 8.758490 56.01497 10.903828 55.83783 14.03327 53.86963
[3,] 7.520188 57.35701 9.846876 57.25314 11.986598 57.23237 14.74954 55.11342
[4,] 6.865692 59.92258 9.763140 59.56565 11.883736 59.46067 15.36907 56.56322
[5,] 9.068088 60.24718 11.420658 59.94776 12.768039 59.88360 15.84777 57.46687
[6,] 5.382514 56.60116 7.861861 56.96141 9.663096 57.49118 13.13842 55.75352
[7,] 6.642636 59.72066 8.849841 59.82577 10.951941 59.48943 13.57957 57.89183
[8,] 7.241416 58.26912 9.774856 57.88910 11.949392 57.59354 15.43287 54.70119
[9,] 7.110768 60.14525 10.073588 60.12408 11.787791 59.89129 15.13155 57.41522
[10,] 6.551215 58.05514 9.437120 57.97088 11.627880 57.52851 15.41958 55.08498
[11,] 6.993666 60.56977 9.765930 58.61658 11.803124 57.29346 15.01643 53.55510
[12,] 6.503214 57.11884 9.533838 56.46642 11.449024 56.48746 15.88973 54.13031
[13,] 7.932218 63.11085 11.216110 63.29586 13.228072 63.85089 18.50080 63.06460
[14,] 7.453503 54.32645 8.842476 54.34601 9.820626 54.26776 12.73551 53.48524
[15,] 9.396992 76.99126 12.280160 76.59082 14.389144 76.27047 19.48808 73.89453
[16,] 6.737148 57.27625 9.864360 56.98242 11.984148 56.45772 16.45459 54.75769
[17,] 8.405361 57.34930 10.124163 57.22353 11.738160 57.22353 14.48405 56.04971
[18,] 8.566672 65.55366 11.616221 64.92513 13.874284 64.76218 18.62320 62.87658
[19,] 6.516840 53.35910 9.419796 53.26036 11.098376 53.14187 15.81815 51.44354
[20,] 6.929498 59.08746 9.979307 58.65177 11.888031 58.77625 16.55611 56.95052
[21,] 8.294210 57.40853 10.519998 57.34554 13.732692 57.51352 15.95848 55.93867
[22,] 7.494868 60.90633 10.084387 59.05366 13.810768 56.90626 15.05289 53.24304
[23,] 6.673799 57.59551 9.016951 57.51183 11.883128 57.34446 14.10075 55.37789
[24,] 5.593980 59.51490 7.907280 59.22048 10.536030 59.17842 12.38667 57.43293
[25,] 7.858125 59.70080 10.142220 59.61698 12.824460 59.38647 15.10856 57.66816
[26,] 6.312300 58.97792 9.110753 58.28357 12.498354 57.84171 15.46514 55.56928
[27,] 7.016672 60.86018 9.936784 59.95683 14.180400 59.43163 17.01648 57.01571
[28,] 7.614750 59.48085 10.853700 58.92315 14.435850 58.53705 17.54610 56.11320
[29,] 7.758225 59.01717 10.449425 58.40745 13.645225 57.96592 15.83182 56.15777
[30,] 6.686481 59.54554 9.133269 58.80728 11.790987 58.51198 14.09012 56.74017
[31,] 7.431003 58.62703 10.314990 58.35337 13.809456 57.99551 15.93561 56.03776
[32,] 7.868910 61.44537 10.901940 59.30316 14.231910 57.26700 15.84387 53.95824
[33,] 7.575810 58.89514 10.205430 58.39426 13.440280 58.20643 16.13251 56.32813
[34,] 5.488296 57.98052 7.691930 57.54395 10.165821 57.39843 12.84760 55.79768
[35,] 7.114562 60.32643 9.787785 59.71601 12.945135 59.16874 15.23948 57.50587
[36,] 5.835192 59.85300 8.625936 59.64158 11.691526 59.76843 14.67255 57.88680
[37,] 6.315000 58.45585 8.777850 58.37165 11.977450 58.35060 14.46135 57.08760
[38,] 6.981960 60.27198 10.010280 59.28357 13.837740 58.88400 16.71885 56.08701
[39,] 7.532343 58.38093 9.916530 58.21214 12.638301 58.29654 15.33897 56.27103
[40,] 7.473105 58.92175 9.957123 58.26917 13.514742 57.72184 15.95666 55.59569
geomorph documentation built on Aug. 10, 2017, 1:11 a.m.
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