Remove problematic rows (NA values, consecutive duplicates, infinite values) and warn about potential issues.
Arguments
- x
A matrix (nx2), list of matrices, or tibble with coo columns.
- ...
Additional arguments (reserved for future use).
- .cols
Column name(s) to process when
xis a tibble. IfNULL, automatically detects columns containing coo objects.- .ldk_col
Character. Name of landmark column. If
NULL, usescolname_ldk.- remove_na
Logical. Remove rows with NA values. Default TRUE.
- remove_duplicates
Logical. Remove consecutive duplicate points. Default TRUE.
- remove_infinite
Logical. Remove rows with Inf/-Inf values. Default TRUE.
- min_points
Integer. Warn if fewer than this many points remain. Default 3.
- warn_collinear
Logical. Warn if all points are collinear. Default TRUE.
Value
If
xis a single matrix: returns the cleaned matrixIf
xis a list: returns a list of cleaned matricesIf
xis a tibble: returns the tibble with cleaned coo column(s)
Details
Performs the following checks and cleaning operations:
Remove NA rows: Rows containing NA in either coordinate
Remove consecutive duplicates: Identical adjacent points
Remove infinite values: Rows containing Inf or -Inf
Warn if too few points: Less than
min_pointsremainWarn if collinear: All points lie on a line
Messages indicate which shapes were affected and what was removed. Landmarks are synced - if a point is removed, its landmark is also removed.
See also
coo_sample() for resampling
Examples
# Clean a single shape
coo_check(shapes$cat)
#> <xy [120 x 2]>
#> [,1] [,2]
#> [1,] 200 62
#> [2,] 196 56
#> [3,] 200 56
#> [4,] 206 54
#> [5,] 209 48
#> [6,] ... ...
#> [7,] 219 45
#> [8,] 213 47
#> [9,] 208 53
#> [10,] 204 59
#> [11,] 202 65
# Clean all shapes in list
coo_check(bot$coo)
#> ℹ Removed: 28 consecutive duplicates
#> ℹ Removed: 3 consecutive duplicates
#> ℹ Removed: 17 consecutive duplicates
#> ℹ Removed: 51 consecutive duplicates
#> ℹ Removed: 35 consecutive duplicates
#> ℹ Removed: 19 consecutive duplicates
#> ℹ Removed: 22 consecutive duplicates
#> ℹ Removed: 44 consecutive duplicates
#> ℹ Removed: 45 consecutive duplicates
#> ℹ Removed: 45 consecutive duplicates
#> ℹ Removed: 5 consecutive duplicates
#> ℹ Removed: 32 consecutive duplicates
#> $brahma
#> <xy [138 x 2]>
#> [,1] [,2]
#> [1,] 37 561
#> [2,] 40 540
#> [3,] 40 529
#> [4,] 43 508
#> [5,] 46 487
#> [6,] ... ...
#> [7,] 34 656
#> [8,] 33 645
#> [9,] 33 624
#> [10,] 34 603
#> [11,] 35 593
#>
#> $caney
#> <xy [168 x 2]>
#> [,1] [,2]
#> [1,] 53 535
#> [2,] 53 525
#> [3,] 54 505
#> [4,] 53 495
#> [5,] 54 485
#> [6,] ... ...
#> [7,] 76 616
#> [8,] 67 596
#> [9,] 62 585
#> [10,] 59 575
#> [11,] 55 555
#>
#> $chimay
#> <xy [189 x 2]>
#> [,1] [,2]
#> [1,] 49 333
#> [2,] 49 325
#> [3,] 49 318
#> [4,] 50 310
#> [5,] 50 302
#> [6,] ... ...
#> [7,] 59 379
#> [8,] 54 371
#> [9,] 51 364
#> [10,] 49 356
#> [11,] 48 348
#>
#> $corona
#> <xy [129 x 2]>
#> [,1] [,2]
#> [1,] 91 426
#> [2,] 91 416
#> [3,] 90 395
#> [4,] 91 385
#> [5,] 91 374
#> [6,] ... ...
#> [7,] 118 506
#> [8,] 110 486
#> [9,] 105 477
#> [10,] 101 466
#> [11,] 94 447
#>
#> $deusventrue
#> <xy [152 x 2]>
#> [,1] [,2]
#> [1,] 74 481
#> [2,] 70 472
#> [3,] 62 454
#> [4,] 59 445
#> [5,] 52 425
#> [6,] ... ...
#> [7,] 100 555
#> [8,] 97 545
#> [9,] 90 527
#> [10,] 87 518
#> [11,] 82 500
#>
#> $duvel
#> <xy [133 x 2]>
#> [,1] [,2]
#> [1,] 61 315
#> [2,] 61 304
#> [3,] 61 293
#> [4,] 61 282
#> [5,] 59 272
#> [6,] ... ...
#> [7,] 81 379
#> [8,] 74 369
#> [9,] 69 358
#> [10,] 65 348
#> [11,] 63 337
#>
#> $franziskaner
#> <xy [124 x 2]>
#> [,1] [,2]
#> [1,] 54 439
#> [2,] 54 418
#> [3,] 54 408
#> [4,] 54 389
#> [5,] 54 379
#> [6,] ... ...
#> [7,] 60 532
#> [8,] 59 511
#> [9,] 57 501
#> [10,] 54 480
#> [11,] 54 470
#>
#> $grimbergen
#> <xy [126 x 2]>
#> [,1] [,2]
#> [1,] 42 404
#> [2,] 40 394
#> [3,] 40 373
#> [4,] 40 362
#> [5,] 40 352
#> [6,] ... ...
#> [7,] 74 487
#> [8,] 60 467
#> [9,] 54 456
#> [10,] 50 446
#> [11,] 44 425
#>
#> $guiness
#> <xy [183 x 2]>
#> [,1] [,2]
#> [1,] 69 385
#> [2,] 69 377
#> [3,] 69 369
#> [4,] 69 360
#> [5,] 69 344
#> [6,] ... ...
#> [7,] 73 442
#> [8,] 71 433
#> [9,] 67 418
#> [10,] 68 410
#> [11,] 69 401
#>
#> $hoegardeen
#> <xy [190 x 2]>
#> [,1] [,2]
#> [1,] 42 544
#> [2,] 40 531
#> [3,] 40 519
#> [4,] 40 506
#> [5,] 40 493
#> [6,] ... ...
#> [7,] 58 619
#> [8,] 54 606
#> [9,] 51 594
#> [10,] 47 581
#> [11,] 46 568
#>
#> $jupiler
#> <xy [156 x 2]>
#> [,1] [,2]
#> [1,] 55 515
#> [2,] 54 501
#> [3,] 54 488
#> [4,] 54 474
#> [5,] 54 460
#> [6,] ... ...
#> [7,] 74 597
#> [8,] 69 583
#> [9,] 66 570
#> [10,] 62 556
#> [11,] 59 542
#>
#> $kingfisher
#> <xy [165 x 2]>
#> [,1] [,2]
#> [1,] 71 384
#> [2,] 71 374
#> [3,] 71 365
#> [4,] 71 355
#> [5,] 71 345
#> [6,] ... ...
#> [7,] 81 442
#> [8,] 78 433
#> [9,] 76 423
#> [10,] 73 413
#> [11,] 73 403
#>
#> $latrappe
#> <xy [136 x 2]>
#> [,1] [,2]
#> [1,] 26 389
#> [2,] 25 377
#> [3,] 25 364
#> [4,] 25 352
#> [5,] 25 339
#> [6,] ... ...
#> [7,] 28 464
#> [8,] 25 451
#> [9,] 26 439
#> [10,] 26 426
#> [11,] 26 414
#>
#> $lindemanskriek
#> <xy [176 x 2]>
#> [,1] [,2]
#> [1,] 60 427
#> [2,] 60 419
#> [3,] 55 404
#> [4,] 54 395
#> [5,] 54 387
#> [6,] ... ...
#> [7,] 77 486
#> [8,] 75 478
#> [9,] 72 469
#> [10,] 70 461
#> [11,] 65 444
#>
#> $nicechouffe
#> <xy [146 x 2]>
#> [,1] [,2]
#> [1,] 82 361
#> [2,] 81 353
#> [3,] 77 336
#> [4,] 77 327
#> [5,] 76 319
#> [6,] ... ...
#> [7,] 96 418
#> [8,] 93 410
#> [9,] 91 401
#> [10,] 89 394
#> [11,] 85 378
#>
#> $pecheresse
#> <xy [129 x 2]>
#> [,1] [,2]
#> [1,] 63 495
#> [2,] 61 476
#> [3,] 61 467
#> [4,] 60 447
#> [5,] 58 428
#> [6,] ... ...
#> [7,] 86 580
#> [8,] 83 570
#> [9,] 78 552
#> [10,] 73 533
#> [11,] 71 524
#>
#> $sierranevada
#> <xy [125 x 2]>
#> [,1] [,2]
#> [1,] 61 345
#> [2,] 61 333
#> [3,] 61 320
#> [4,] 61 308
#> [5,] 61 296
#> [6,] ... ...
#> [7,] 69 418
#> [8,] 63 407
#> [9,] 61 394
#> [10,] 59 382
#> [11,] 61 370
#>
#> $tanglefoot
#> <xy [174 x 2]>
#> [,1] [,2]
#> [1,] 48 367
#> [2,] 48 359
#> [3,] 48 351
#> [4,] 48 335
#> [5,] 49 327
#> [6,] ... ...
#> [7,] 52 423
#> [8,] 49 415
#> [9,] 48 407
#> [10,] 47 391
#> [11,] 47 383
#>
#> $tauro
#> <xy [174 x 2]>
#> [,1] [,2]
#> [1,] 56 515
#> [2,] 54 503
#> [3,] 54 491
#> [4,] 54 478
#> [5,] 54 466
#> [6,] ... ...
#> [7,] 71 587
#> [8,] 68 575
#> [9,] 63 563
#> [10,] 61 551
#> [11,] 59 538
#>
#> $westmalle
#> <xy [141 x 2]>
#> [,1] [,2]
#> [1,] 70 394
#> [2,] 70 386
#> [3,] 67 369
#> [4,] 67 361
#> [5,] 66 344
#> [6,] ... ...
#> [7,] 86 461
#> [8,] 83 452
#> [9,] 80 436
#> [10,] 76 427
#> [11,] 74 411
#>
#> $amrut
#> <xy [191 x 2]>
#> [,1] [,2]
#> [1,] 57 441
#> [2,] 57 431
#> [3,] 57 421
#> [4,] 57 411
#> [5,] 57 401
#> [6,] ... ...
#> [7,] 55 501
#> [8,] 57 491
#> [9,] 57 481
#> [10,] 57 471
#> [11,] 57 461
#>
#> $ballantines
#> <xy [146 x 2]>
#> [,1] [,2]
#> [1,] 38 357
#> [2,] 38 341
#> [3,] 38 333
#> [4,] 38 318
#> [5,] 38 310
#> [6,] ... ...
#> [7,] 38 428
#> [8,] 38 412
#> [9,] 38 404
#> [10,] 38 388
#> [11,] 38 381
#>
#> $bushmills
#> <xy [130 x 2]>
#> [,1] [,2]
#> [1,] 72 456
#> [2,] 72 441
#> [3,] 72 425
#> [4,] 72 410
#> [5,] 72 394
#> [6,] ... ...
#> [7,] 69 548
#> [8,] 70 533
#> [9,] 70 518
#> [10,] 70 502
#> [11,] 70 487
#>
#> $chivas
#> <xy [164 x 2]>
#> [,1] [,2]
#> [1,] 33 437
#> [2,] 31 429
#> [3,] 29 412
#> [4,] 29 404
#> [5,] 29 388
#> [6,] ... ...
#> [7,] 81 502
#> [8,] 73 495
#> [9,] 57 478
#> [10,] 51 470
#> [11,] 40 453
#>
#> $dalmore
#> <xy [136 x 2]>
#> [,1] [,2]
#> [1,] 52 371
#> [2,] 47 359
#> [3,] 44 346
#> [4,] 42 334
#> [5,] 42 322
#> [6,] ... ...
#> [7,] 113 442
#> [8,] 102 430
#> [9,] 89 419
#> [10,] 77 408
#> [11,] 67 396
#>
#> $famousgrouse
#> <xy [147 x 2]>
#> [,1] [,2]
#> [1,] 99 313
#> [2,] 99 303
#> [3,] 99 294
#> [4,] 99 284
#> [5,] 99 275
#> [6,] ... ...
#> [7,] 96 370
#> [8,] 97 361
#> [9,] 97 351
#> [10,] 97 342
#> [11,] 97 332
#>
#> $glendronach
#> <xy [153 x 2]>
#> [,1] [,2]
#> [1,] 73 435
#> [2,] 73 423
#> [3,] 74 411
#> [4,] 74 399
#> [5,] 74 387
#> [6,] ... ...
#> [7,] 74 507
#> [8,] 72 495
#> [9,] 72 483
#> [10,] 73 471
#> [11,] 73 459
#>
#> $glenmorangie
#> <xy [134 x 2]>
#> [,1] [,2]
#> [1,] 53 518
#> [2,] 54 501
#> [3,] 54 485
#> [4,] 55 468
#> [5,] 57 451
#> [6,] ... ...
#> [7,] 68 616
#> [8,] 62 599
#> [9,] 58 584
#> [10,] 54 567
#> [11,] 53 550
#>
#> $highlandpark
#> <xy [124 x 2]>
#> [,1] [,2]
#> [1,] 42 371
#> [2,] 42 357
#> [3,] 42 343
#> [4,] 42 329
#> [5,] 42 315
#> [6,] ... ...
#> [7,] 40 455
#> [8,] 41 441
#> [9,] 42 427
#> [10,] 42 413
#> [11,] 42 399
#>
#> $jackdaniels
#> <xy [145 x 2]>
#> [,1] [,2]
#> [1,] 63 414
#> [2,] 63 401
#> [3,] 63 388
#> [4,] 63 375
#> [5,] 63 362
#> [6,] ... ...
#> [7,] 70 493
#> [8,] 68 479
#> [9,] 65 466
#> [10,] 64 453
#> [11,] 65 440
#>
#> $jb
#> <xy [174 x 2]>
#> [,1] [,2]
#> [1,] 43 531
#> [2,] 43 520
#> [3,] 42 510
#> [4,] 42 488
#> [5,] 43 477
#> [6,] ... ...
#> [7,] 42 606
#> [8,] 40 595
#> [9,] 42 585
#> [10,] 43 563
#> [11,] 43 552
#>
#> $johnniewalker
#> <xy [168 x 2]>
#> [,1] [,2]
#> [1,] 133 175
#> [2,] 133 171
#> [3,] 133 167
#> [4,] 133 163
#> [5,] 134 155
#> [6,] ... ...
#> [7,] 133 203
#> [8,] 133 199
#> [9,] 133 191
#> [10,] 133 187
#> [11,] 133 183
#>
#> $magallan
#> <xy [141 x 2]>
#> [,1] [,2]
#> [1,] 78 397
#> [2,] 78 382
#> [3,] 80 375
#> [4,] 80 361
#> [5,] 81 346
#> [6,] ... ...
#> [7,] 75 462
#> [8,] 75 455
#> [9,] 75 441
#> [10,] 77 426
#> [11,] 77 419
#>
#> $makersmark
#> <xy [145 x 2]>
#> [,1] [,2]
#> [1,] 31 432
#> [2,] 23 420
#> [3,] 16 408
#> [4,] 13 394
#> [5,] 10 381
#> [6,] ... ...
#> [7,] 92 491
#> [8,] 79 487
#> [9,] 74 473
#> [10,] 67 464
#> [11,] 53 454
#>
#> $oban
#> <xy [179 x 2]>
#> [,1] [,2]
#> [1,] 74 457
#> [2,] 74 448
#> [3,] 74 431
#> [4,] 74 423
#> [5,] 74 414
#> [6,] ... ...
#> [7,] 72 517
#> [8,] 73 508
#> [9,] 73 500
#> [10,] 73 491
#> [11,] 73 474
#>
#> $oldpotrero
#> <xy [131 x 2]>
#> [,1] [,2]
#> [1,] 83 307
#> [2,] 77 299
#> [3,] 71 291
#> [4,] 63 274
#> [5,] 60 265
#> [6,] ... ...
#> [7,] 119 366
#> [8,] 117 358
#> [9,] 112 349
#> [10,] 101 333
#> [11,] 95 324
#>
#> $redbreast
#> <xy [177 x 2]>
#> [,1] [,2]
#> [1,] 105 233
#> [2,] 103 228
#> [3,] 101 224
#> [4,] 98 214
#> [5,] 98 210
#> [6,] ... ...
#> [7,] 137 261
#> [8,] 132 257
#> [9,] 127 253
#> [10,] 118 246
#> [11,] 113 242
#>
#> $tamdhu
#> <xy [176 x 2]>
#> [,1] [,2]
#> [1,] 49 552
#> [2,] 49 540
#> [3,] 49 527
#> [4,] 49 515
#> [5,] 49 503
#> [6,] ... ...
#> [7,] 46 625
#> [8,] 44 613
#> [9,] 45 601
#> [10,] 46 589
#> [11,] 47 577
#>
#> $wildturkey
#> <xy [185 x 2]>
#> [,1] [,2]
#> [1,] 18 569
#> [2,] 18 555
#> [3,] 18 541
#> [4,] 18 527
#> [5,] 18 513
#> [6,] ... ...
#> [7,] 20 651
#> [8,] 18 638
#> [9,] 15 625
#> [10,] 15 611
#> [11,] 15 597
#>
#> $yoichi
#> <xy [123 x 2]>
#> [,1] [,2]
#> [1,] 69 384
#> [2,] 69 369
#> [3,] 69 355
#> [4,] 69 340
#> [5,] 69 325
#> [6,] ... ...
#> [7,] 68 457
#> [8,] 68 450
#> [9,] 68 435
#> [10,] 68 421
#> [11,] 69 406
#>
#> attr(,"class")
#> [1] "out" "coo" "list"
# Clean all shapes in tibble
coo_check(bot)
#> ℹ Removed: 28 consecutive duplicates
#> ℹ Removed: 3 consecutive duplicates
#> ℹ Removed: 17 consecutive duplicates
#> ℹ Removed: 51 consecutive duplicates
#> ℹ Removed: 35 consecutive duplicates
#> ℹ Removed: 19 consecutive duplicates
#> ℹ Removed: 22 consecutive duplicates
#> ℹ Removed: 44 consecutive duplicates
#> ℹ Removed: 45 consecutive duplicates
#> ℹ Removed: 45 consecutive duplicates
#> ℹ Removed: 5 consecutive duplicates
#> ℹ Removed: 32 consecutive duplicates
#> # A tibble: 40 × 3
#> coo type dummy
#> <out> <fct> <fct>
#> 1 (138 x 2) whisky a
#> 2 (168 x 2) whisky a
#> 3 (189 x 2) whisky a
#> 4 (129 x 2) whisky a
#> 5 (152 x 2) whisky a
#> 6 (133 x 2) whisky a
#> 7 (124 x 2) whisky a
#> 8 (126 x 2) whisky a
#> 9 (183 x 2) whisky a
#> 10 (190 x 2) whisky a
#> # ℹ 30 more rows
# Disable specific checks
coo_check(bot, remove_duplicates = FALSE, warn_collinear = FALSE)
#> # A tibble: 40 × 3
#> coo type dummy
#> <out> <fct> <fct>
#> 1 (138 x 2) whisky a
#> 2 (168 x 2) whisky a
#> 3 (189 x 2) whisky a
#> 4 (129 x 2) whisky a
#> 5 (152 x 2) whisky a
#> 6 (161 x 2) whisky a
#> 7 (124 x 2) whisky a
#> 8 (126 x 2) whisky a
#> 9 (183 x 2) whisky a
#> 10 (193 x 2) whisky a
#> # ℹ 30 more rows