Supported by Dr. Osamu Ogasawara and  providing  . |
|
Last data update: 2014.03.03 |
Procrustes superimposition of landmark datasets with some missing valuesDescriptionThis function carries out a generalized procrustes superimposition on all fully complete specimens and produces a consensus confirguration (using "Shapes" procGPA). Each incomplete specimen is then individually rotated and aligned with the consensus configuration based on any landmarks are available (using "Shapes" procOPA). Landmarks are returned in the same shape space as the original dataset. Both 2D and 3D coordinates can be accommodated. Usagealign.missing(X, nlandmarks) Arguments
ValueReturns and n*l X 2 (or 3) matrix of aligned landmarks Author(s)J. Arbour ReferencesArbour, J. and Brown, C. 2014. Incomplete specimens in Geometric Morphometric Analyses. Methods in Ecology and Evolution 5(1):16-26. See Also
Examplesdata(dacrya) ## make some specimens incomplete dac.miss<-missing.specimens(dacrya,10,c(1,2,3,4,5,6),16) dac.miss ## align all specimens dac.aligned<-align.missing(dac.miss,16) ## compare original and aligned plot(dacrya,col="blue") points(dac.aligned,col="red") Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 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(LOST)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/LOST/align.missing.Rd_%03d_medium.png", width=480, height=480)
> ### Name: align.missing
> ### Title: Procrustes superimposition of landmark datasets with some
> ### missing values
> ### Aliases: align.missing
>
> ### ** Examples
>
>
> data(dacrya)
>
> ## make some specimens incomplete
> dac.miss<-missing.specimens(dacrya,10,c(1,2,3,4,5,6),16)
> dac.miss
V1 V2
1 507.8071 121.53779
2 640.4082 101.27195
3 637.4054 -0.00010
4 627.8968 -90.58349
5 461.3004 -113.28686
6 203.5841 -194.30992
7 -185.4216 -178.11304
8 -201.1261 -98.03457
9 -204.1590 -0.00003
10 -369.4501 -146.64459
11 -264.5717 371.61846
12 -392.6116 311.93028
13 -511.4485 230.44263
14 -607.8546 127.31723
15 -666.5654 -0.00010
16 318.5814 265.33020
17 428.7785 92.42028
18 546.5650 78.81995
19 552.9349 -0.00029
20 545.0920 -92.66716
21 404.9139 -110.33569
22 178.2401 -191.17249
23 -160.7581 -184.46480
24 -160.8918 -85.33871
25 -165.7091 -0.00009
26 -360.7268 -123.52049
27 -219.7491 303.88995
28 -332.5630 254.66210
29 -440.2240 191.64158
30 -528.5791 111.48331
31 -582.0244 -0.00031
32 285.2768 198.39702
33 760.2007 183.72314
34 948.9157 157.97696
35 930.6039 -0.03607
36 916.7256 -140.30273
37 680.8676 -146.41495
38 372.6119 -298.83230
39 -238.2889 -310.67447
40 -282.7749 -147.12355
41 -316.0868 -0.01239
42 -584.4582 -267.33851
43 -369.0453 628.99218
44 -608.1049 552.75717
45 -802.7766 408.95370
46 -939.7274 217.46024
47 -1023.0357 -0.03967
48 475.0566 420.24312
49 789.6129 204.74828
50 995.1264 159.73324
51 1006.1115 0.00126
52 1028.9559 -165.51406
53 734.2842 -200.67431
54 361.0235 -372.29854
55 -256.9534 -329.49028
56 -280.2518 -160.64213
57 -337.8385 0.00042
58 -619.4533 -273.96399
59 -414.3559 630.41779
60 -634.6936 545.40635
61 -818.6416 397.71839
62 -961.7020 206.93026
63 -1075.8356 0.00135
64 507.1354 459.81455
65 487.1917 123.73667
66 624.3497 96.67921
67 634.2273 0.00082
68 622.6315 -110.55508
69 467.9861 -125.98560
70 220.6354 -225.71352
71 -172.6371 -218.30514
72 -191.9173 -108.14383
73 -206.9631 0.00027
74 -422.9026 -172.54730
75 -238.7722 360.36419
76 -368.1971 298.40315
77 -495.9514 224.39360
78 -601.9416 123.58077
79 -672.1088 0.00086
80 327.5145 249.41597
81 477.2304 111.08258
82 610.2990 100.00472
83 615.2049 0.00000
84 613.1160 -92.99803
85 451.1934 -126.91325
86 210.4536 -208.04640
87 -158.1667 -198.85100
88 -180.4878 -93.92250
89 -203.7964 0.00000
90 -397.1504 -145.76048
91 -257.0445 337.81320
92 -381.0580 289.31450
93 -492.8580 213.79395
94 -581.4315 116.33332
95 -640.8011 0.00000
96 314.0623 222.04899
97 568.3288 143.75784
98 700.9502 112.00927
99 702.3395 -0.00012
100 702.3618 -100.04499
101 548.1953 -141.11174
102 262.0797 -274.57181
103 -207.5166 -240.74146
104 -243.6399 -117.67014
105 -252.6643 -0.00004
106 -445.9638 -183.54404
107 -294.5580 471.34766
108 -454.4407 414.20060
109 -574.2051 298.88623
110 -665.7639 154.04321
111 -728.7453 -0.00012
112 371.9168 326.59152
113 NA NA
114 815.4733 127.93218
115 811.1896 0.00000
116 NA NA
117 603.5976 -152.48496
118 272.7035 -277.49576
119 -260.5658 -259.91108
120 -273.7652 -131.18258
121 -274.8286 0.00000
122 -501.7396 -209.85714
123 -306.9438 526.99869
124 NA NA
125 -644.4911 337.35078
126 -759.8970 179.58761
127 NA NA
128 408.5117 343.23663
129 670.7912 148.72983
130 826.7234 136.60605
131 837.2716 0.00034
132 839.3772 -142.40993
133 646.5327 -187.58896
134 307.4209 -338.79946
135 -246.1398 -302.87649
136 -244.3374 -134.52626
137 -256.7226 0.00010
138 -569.7083 -215.52674
139 -354.7238 507.49973
140 -517.2175 422.44770
141 -659.4930 304.15371
142 -779.9877 157.37954
143 -874.3250 0.00036
144 390.8444 363.45950
145 705.7451 162.49231
146 872.2061 145.33495
147 891.8792 0.00025
148 892.7116 -146.08324
149 702.3427 -181.77566
150 322.8659 -340.88072
151 -288.4807 -295.36232
152 -295.8942 -143.21041
153 -306.3603 0.00009
154 -566.7402 -236.72650
155 -348.4595 587.93035
156 -552.5397 527.19271
157 -713.9590 383.72740
158 -831.8287 201.45423
159 -913.7117 0.00026
160 460.3865 384.36692
161 396.4531 105.64877
162 520.8226 87.78347
163 529.4506 -0.00027
164 519.0960 -88.34721
165 381.4359 -107.06577
166 162.5375 -184.94360
167 -152.0559 -178.98564
168 -149.5837 -84.58864
169 -158.4367 -0.00008
170 -312.5009 -144.83743
171 -203.4322 303.60544
172 -316.2467 259.11686
173 -413.2124 190.09232
174 -493.4647 100.86575
175 -553.7429 -0.00028
176 233.7912 224.00774
177 436.7125 116.53274
178 557.5051 105.01764
179 556.9626 0.00026
180 554.3286 -99.04585
181 429.1079 -110.56011
182 227.9552 -199.11664
183 -162.0433 -184.05774
184 -157.5174 -88.08032
185 -172.0555 0.00008
186 -383.7607 -150.21705
187 -216.8471 323.28681
188 -336.2997 275.30027
189 -449.3714 206.60901
190 -537.3694 110.85678
191 -608.0868 0.00028
192 265.5202 235.09939
193 617.8234 170.84220
194 794.6211 111.08085
195 790.3350 -0.02327
196 766.6704 -131.38282
197 565.1416 -134.54690
198 289.5508 -245.94482
199 -165.5340 -247.63280
200 -211.0809 -127.43196
201 -250.9495 -0.00747
202 -484.0039 -213.23532
203 -350.9684 456.58099
204 -516.6677 386.04343
205 -664.5661 284.05644
206 -772.2327 148.97705
207 -857.8591 -0.02526
208 391.3599 346.15505
209 806.0297 183.14926
210 982.5850 165.24272
211 981.6624 -0.00744
212 971.4158 -171.69233
213 729.0694 -206.42723
214 274.4446 -376.17699
215 -218.9017 -376.07929
216 -214.0423 -183.11859
217 -225.2059 -0.00171
218 -536.0076 -350.05058
219 -455.2553 708.09292
220 -697.6002 625.88206
221 -863.7190 436.64282
222 -994.3237 224.04095
223 -1113.2997 -0.00844
224 537.9148 429.88851
225 434.5095 113.23202
226 568.2954 91.39755
227 566.4388 0.00301
228 568.3853 -93.28053
229 417.7504 -124.98558
230 199.4167 -217.33121
231 -154.5515 -196.37749
232 -164.0914 -86.60806
233 -180.2781 0.00096
234 -352.9339 -139.07531
235 -213.8320 350.21236
236 -339.0940 306.25426
237 -450.5295 225.72344
238 -537.0754 123.45528
239 -601.7889 0.00320
240 269.4452 244.48606
241 606.4640 165.30836
242 777.7668 124.51754
243 765.1987 -0.00345
244 755.5611 -110.64942
245 570.3096 -130.54752
246 270.0049 -245.29264
247 -218.6957 -234.18395
248 -240.0250 -106.74573
249 -250.1477 -0.00113
250 -464.8703 -178.50127
251 -325.0290 494.84768
252 -489.7978 414.99914
253 -629.6687 299.36372
254 -741.9750 160.90336
255 -817.9926 -0.00369
256 403.9364 353.50514
257 359.5641 87.37186
258 474.1585 71.75799
259 494.0243 0.00000
260 487.8718 -70.76196
261 340.7935 -92.67742
262 169.5365 -149.99627
263 -141.8035 -140.56078
264 -150.7141 -67.60007
265 -150.2337 0.00000
266 -313.6861 -100.64700
267 -185.1340 243.36602
268 -279.5290 206.64821
269 -369.3959 155.40701
270 -450.6229 90.95930
271 -497.0073 0.00000
272 217.3069 177.58967
273 394.4954 100.84459
274 506.5922 80.99153
275 505.4153 -0.00140
276 493.3827 -79.84240
277 359.7628 -103.20075
278 173.6584 -163.01180
279 -146.0995 -150.92818
280 -158.0119 -74.55971
281 -167.0180 -0.00046
282 -303.6940 -114.84439
283 -204.8074 285.09632
284 -308.0618 242.07748
285 -406.3477 180.08567
286 -484.7991 98.79830
287 -532.5422 -0.00147
288 260.2250 203.87863
289 536.7759 118.24736
290 682.7864 107.40935
291 694.5662 0.00134
292 702.2286 -111.04473
293 527.3880 -152.18966
294 212.6490 -256.85416
295 -218.5778 -223.81295
296 -215.1949 -107.61084
297 -237.7858 0.00046
298 -437.6143 -180.27593
299 -251.6874 389.67844
300 -394.7772 332.07991
301 -530.6834 251.21151
302 -645.8532 138.39452
303 -722.6361 0.00139
304 327.3061 261.79918
305 756.7234 177.92381
306 924.5228 148.45570
307 927.5318 -0.02036
308 905.4293 -137.91644
309 NA NA
310 324.4961 -313.79793
311 -241.1324 -309.03079
312 -272.2855 -147.94923
313 -291.5155 -0.00645
314 -573.0495 -271.01686
315 NA NA
316 -608.9681 536.08430
317 -792.5654 395.41400
318 -922.8288 208.69980
319 -1009.7787 -0.02217
320 NA NA
321 416.1584 120.89188
322 NA NA
323 538.8693 -0.00017
324 522.4613 -90.30464
325 381.8599 -110.81711
326 NA NA
327 -147.9803 -173.54145
328 -159.7059 -84.22032
329 -167.6276 -0.00005
330 -311.1817 -129.87874
331 -217.0552 334.25071
332 -330.3557 283.56092
333 -428.5586 204.20510
334 -519.3397 111.43271
335 -570.6919 -0.00018
336 267.5355 225.23016
337 456.0625 102.97311
338 591.8242 85.75377
339 598.9599 0.00051
340 595.6208 -96.27534
341 428.0562 -124.15932
342 187.6072 -209.86136
343 -193.9886 -195.87346
344 -180.8471 -88.09373
345 -185.2791 0.00016
346 -351.3133 -153.88407
347 -236.5031 345.13151
348 -351.9858 288.36986
349 -458.7570 208.34523
350 -555.6493 117.73411
351 -620.5986 0.00053
352 295.4442 232.18989
353 453.2076 112.86137
354 575.7316 87.70224
355 580.3565 -0.00018
356 568.6889 -92.87293
357 NA NA
358 187.3456 -214.46574
359 -155.0586 -193.39945
360 -162.8787 -88.61788
361 -174.3426 -0.00006
362 -361.1061 -151.02321
363 -248.9819 335.91413
364 -358.8504 272.23550
365 -465.5814 201.51007
366 -554.5957 114.87840
367 -609.5260 -0.00019
368 286.0819 248.91414
369 432.9412 98.02047
370 562.8758 90.59631
371 561.3625 0.00103
372 569.5020 -99.07744
373 408.9207 -124.60355
374 202.3136 -217.82097
375 -181.3231 -186.54834
376 -180.5510 -88.92960
377 -185.9135 0.00034
378 -337.8797 -151.46790
379 -211.6167 308.96111
380 -328.1987 268.17281
381 -433.1005 195.57721
382 -526.1963 106.93041
383 -591.4500 0.00108
384 255.8646 213.09853
385 440.1754 112.87410
386 559.7937 88.00785
387 561.4146 -0.00030
388 558.3325 -95.20750
389 411.6883 -116.67632
390 195.6823 -215.73196
391 -168.5081 -195.95920
392 -156.7787 -87.92671
393 -175.6934 -0.00009
394 -356.1201 -149.16183
395 -232.6146 327.89493
396 -347.2602 273.64174
397 -450.8518 199.68127
398 -540.4195 108.36854
399 -601.9008 -0.00032
400 296.4485 231.15667
401 567.0419 141.65391
402 715.2849 110.57380
403 705.2946 -0.00169
404 690.6962 -111.82544
405 510.2238 -130.79061
406 220.9825 -235.53144
407 -192.3393 -205.63017
408 -221.7485 -102.09562
409 -223.3146 -0.00054
410 -413.0864 -173.02514
411 -326.6975 439.34738
412 -464.0219 364.13700
413 -581.8827 263.56693
414 -674.2062 140.69392
415 -729.9702 -0.00175
416 377.3526 322.25403
417 534.6428 130.84097
418 667.2057 104.01420
419 668.2315 -0.00040
420 659.3051 -102.92199
421 493.0794 -122.06861
422 228.5935 -212.39586
423 -189.0331 -190.21605
424 -205.8060 -97.69652
425 -216.8888 -0.00013
426 -387.7871 -155.27927
427 -288.1711 402.85071
428 -420.8160 331.78462
429 -540.5317 241.45642
430 -641.1865 133.38422
431 -701.3549 -0.00042
432 327.3284 290.49718
433 506.4127 126.37615
434 631.5084 102.35453
435 628.5707 -0.00197
436 632.3761 -97.94587
437 464.7137 -128.30430
438 211.1538 -205.57619
439 -169.8023 -194.58843
440 -190.7477 -95.51862
441 -215.6255 -0.00068
442 -372.7296 -158.00908
443 -258.3448 377.80524
444 -394.2535 324.21991
445 -513.2457 238.09792
446 -607.0946 129.35858
447 -668.1055 -0.00209
448 292.7469 278.09816
449 732.5332 184.44532
450 934.2192 142.18742
451 949.5477 0.00000
452 929.9735 -153.49988
453 700.7761 -215.94479
454 326.5367 -374.32679
455 -275.1209 -326.82410
456 -307.6534 -152.07175
457 -324.7770 0.00000
458 -601.8597 -245.50406
459 -386.9889 573.67857
460 -579.5964 497.15433
461 -735.0806 360.42884
462 -854.8148 189.08923
463 -950.0328 0.00000
464 456.7224 404.41400
465 638.6075 152.92923
466 804.6729 120.51087
467 793.5485 -0.00089
468 781.2082 -125.38995
469 580.3730 -145.13205
470 280.6891 -276.70961
471 -252.4788 -251.65979
472 -266.2812 -118.77010
473 -289.3403 -0.00033
474 -483.0359 -194.37959
475 -339.8823 502.35395
476 -506.3578 424.19565
477 -634.3874 301.88880
478 -745.6128 161.67536
479 -812.8338 -0.00091
480 406.4290 359.10439
481 363.3295 88.55054
482 467.3573 76.29385
483 474.8022 -0.00014
484 473.1660 -77.98919
485 354.1738 -89.25883
486 155.2663 -167.36438
487 -141.5607 -153.13163
488 -146.8808 -69.08740
489 -158.3502 -0.00005
490 -292.5322 -116.41302
491 -184.6928 272.18013
492 -281.9011 225.56871
493 -374.6774 170.57269
494 -450.8347 94.30614
495 -500.3533 -0.00014
496 238.2653 190.88608
497 487.5239 126.82297
498 608.0375 95.15760
499 595.2336 -0.00827
500 584.6102 -89.36596
501 436.1983 -98.01280
502 193.2256 -181.66536
503 -164.7880 -166.54795
504 -185.5041 -80.83606
505 -195.7956 -0.00274
506 -338.0666 -129.59173
507 -274.2059 378.21703
508 -399.5944 312.92346
509 -501.0160 223.37845
510 -589.6867 121.84045
511 -634.6971 -0.00882
512 336.6424 264.58087
513 458.0691 108.49315
514 579.3680 88.01982
515 580.0821 0.00025
516 577.3467 -106.13454
517 447.1796 -116.88530
518 195.9807 -204.73871
519 -160.3894 -182.85742
520 -167.3223 -83.91648
521 -177.0822 0.00008
522 -370.6143 -151.15106
523 -241.2937 320.50482
524 -359.0401 275.88941
525 -473.1132 206.68305
526 -560.8126 112.78408
527 -625.0867 0.00027
528 303.0256 217.62787
529 715.6760 186.77339
530 918.0215 153.15229
531 925.3260 0.00000
532 918.5448 -157.90514
533 672.1782 -170.49523
534 319.5369 -349.94823
535 -258.3962 -316.48881
536 -269.0670 -154.23509
537 -278.8942 0.00000
538 -578.0389 -237.77679
539 -368.5589 592.98675
540 -571.1113 508.24531
541 -742.9440 369.92158
542 -881.6755 196.92686
543 -977.0554 0.00000
544 457.9142 408.56738
545 541.7636 125.05431
546 704.9116 113.21300
547 700.9279 -0.00019
548 690.8878 -110.43036
549 506.4019 -135.61057
550 231.3310 -238.31629
551 -200.3185 -221.67572
552 -216.1919 -111.45995
553 -228.2417 -0.00006
554 -440.7487 -171.56351
555 -276.4527 402.75640
556 -416.0717 339.37498
557 -547.9194 245.86364
558 -655.6870 136.57170
559 -735.5257 -0.00020
560 332.5974 279.15669
561 507.3107 126.82786
562 640.7132 101.07422
563 639.7080 -0.00245
564 627.7869 -101.53604
565 463.5040 -121.78253
566 221.0617 -221.36576
567 -171.7961 -188.21239
568 -191.8511 -99.71342
569 -203.5549 -0.00078
570 -385.7717 -153.81177
571 -274.0288 388.02055
572 -404.7126 321.82668
573 -523.3067 233.68532
574 -620.7257 130.54691
575 -682.1974 -0.00261
576 334.6062 284.87433
577 402.1027 94.52723
578 524.7020 73.97693
579 527.4281 -0.00008
580 521.3021 -88.06453
581 380.9801 -106.79505
582 160.1906 -172.87517
583 NA NA
584 NA NA
585 -171.7490 -0.00003
586 -327.1009 -123.65141
587 -203.3592 280.09854
588 -307.6801 234.34614
589 -412.3091 179.19886
590 -499.4322 100.42287
591 -551.0483 -0.00009
592 NA NA
593 617.7879 151.92873
594 766.0025 113.05661
595 751.1274 -0.01852
596 730.3487 -121.31977
597 544.0393 -135.23273
598 271.3112 -242.63265
599 -207.1281 -227.82522
600 -232.2439 -110.55609
601 -267.1391 -0.00680
602 -456.2297 -202.19513
603 -349.9593 468.93917
604 -520.4480 400.60821
605 -644.2839 289.68124
606 -733.6081 151.50097
607 -784.2724 -0.01935
608 402.5944 339.73831
609 700.1970 166.27762
610 861.2263 133.18404
611 861.3304 -0.00018
612 859.6122 -149.11083
613 659.5770 -199.19049
614 295.9009 -367.24655
615 -274.3523 -337.34967
616 -278.9958 -152.13838
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