R Under development (unstable) (2025-07-18 r88431 ucrt) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(BGmisc) > > test_check("BGmisc") Your scale might be reverse coded because you have negative correlations. Please check your data. Standardizing column names... TRUE0NULL0000FALSENULLNULLNULL Standardizing column names... FALSE210000FALSENULLNULLNULL Removed duplicates Standardizing column names... Step 1: Checking for single parents... No missing single parents found. All parents are listed in the pedigree. Step 2: Determining the if moms are the same sex and dads are same sex Role: momID 1 unique sex codes found: 0 Modal sex code: 0 All parents consistently coded. Role: dadID 1 unique sex codes found: 1 Modal sex code: 1 All parents consistently coded. Validation Results: FALSEFALSE0101numeric(0)numeric(0)TRUETRUE REPAIR IN EARLY ALPHA Step 1: Checking for single parents... Missing single parents found. All parents are listed in the pedigree. Step 2: Determining the if moms are the same sex and dads are same sex Role: momID 1 unique sex codes found: F Modal sex code: F All parents consistently coded. Role: dadID 1 unique sex codes found: M Modal sex code: M All parents consistently coded. Validation Results: c(431, 432, 433, 434, 435, 436, 437)c(8, 9, 10, 33, 48, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 157, 178, 184, 185, 186, 189, 191, 192, 193, 194, 197, 233, 250, 251, 264, 266, 267, 268, 269, 273, 275, 286, 296, 297, 311, 320, 332, 358, 360, 361, 362, 371, 372, 376, 382, 389, 394, 395, 396, 397, 406, 408, 410, 412, 415, 416, 417, 419, 421, 422, 423, 425, 427, 438, 440, 441, 442, 444, 445, 446, 447, 452, 453, 470, 479, 481, 483, 484, 485, 486, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 501, 503, 524, 532, 549, 554, 561, 595, 669)TRUEFALSEFMFMnumeric(0)numeric(0)TRUETRUE Step 3: Attempting to repair missing parents... REPAIR IN EARLY ALPHA Corrected sex of moms for: 566, 2, 2, 2, 6, 11, 13, 15, 15, 17, 17, 17, 22, 24, 24, 24, 584, 28, 28, 28, 28, 33, 33, 36, 36, 39, 39, 39, 2, 43, 43, 43, 49, 49, 52, 52, 55, 55, 54, 54, 61, 61, 61, 61, 61, 61, 61, 69, 71, 71, 71, 71, 63, 63, 78, 81, 81, 81, 86, 86, 86, 86, 92, 92, 95, 95, 95, 95, 95, 95, 95, 103, 103, 103, 103, 103, 109, 109, 109, 109, 114, 114, 114, 118, 118, 583, 107, 107, 107, 126, 126, 126, 126, 126, 132, 132, 135, 135, 135, 135, 135, 135, 583, 583, 585, 584, 584, 584, 584, 586, 163, 163, 163, 188, 165, 165, 165, 171, 171, 171, 171, 176, 585, 585, 585, 586, 199, 479, 189, 188, 188, 197, 517, 516, 517, 518, 518, 203, 203, 203, 257, 207, 207, 468, 210, 571, 468, 468, 468, 223, 216, 216, 216, 216, 216, 570, 223, 223, 538, 224, 538, 538, 231, 234, 231, 237, 231, 231, 231, 231, 231, 231, 231, 247, 251, 251, 251, 570, 505, 505, 257, 257, 257, 257, 264, 264, 264, 264, 276, 276, 276, 517, 517, 291, 516, 600, 516, 516, 516, 516, 303, 567, 291, 291, 291, 589, 589, 600, 600, 502, 502, 303, 339, 502, 322, 563, 591, 308, 560, 560, 560, 560, 560, 560, 560, 339, 535, 322, 322, 323, 323, 323, 323, 323, 520, 322, 322, 620, 323, 323, 341, 506, 515, 341, 341, 541, 344, 344, 344, 344, 351, 510, 510, 354, 359, 359, 359, 355, 590, 370, 590, 590, 372, 370, 372, 376, 382, 376, 376, 376, 614, 614, 614, 614, 382, 382, 387, 387, 387, 398, 398, 398, 402, 402, 448, 412, 615, 430, 430, 430, 430, 430, 432, 432, 448, 448, 189, 189, 450, 450, 450, 450, 450, 410, 467, 576, 574, 572, 467, 469, 469, 469, 471, 479, 479, 615, 627, 351, 362, 362, 675, 527, 510, 510, 351, 512, 351, 517, 520, 514, 534, 527, 617, 531, 531, 534, 506, 351, 543, 541, 543, 514, 545, 545, 339, 339, 339, 339, 554, 348, 348, 348, 546, 560, 566, 567, 576, 608, 576, 576, 576, 576, 576, 572, 587, 591, 591, 303, 510, 510, 510, 510, 596, 596, 605, 605, 609, 612, 648, 617, 620, 620, 624, 624, 627, 627, 627, 627, 627, 627, 627, 627, 228, 131, 641, 641, 642, 642, 642, 642, 648, 650, 650, 650, 655, 655, 655, 655, 674, 661, 661, 665, 665, 665, 674, 671, 675, 675, 675 Corrected sex of dads for: 564, 1, 1, 1, 3, 7, 7, 7, 8, 10, 3, 3, 18, 18, 18, 3, 23, 23, 23, 158, 4, 4, 4, 4, 679, 29, 29, 5, 5, 38, 38, 38, 1, 44, 44, 44, 45, 1, 1, 50, 50, 53, 53, 58, 58, 1, 1, 1, 1, 1, 1, 1, 62, 70, 70, 70, 70, 76, 76, 79, 64, 64, 64, 66, 66, 66, 66, 67, 67, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 104, 104, 104, 104, 105, 105, 105, 106, 106, 153, 121, 121, 121, 1, 1, 1, 1, 1, 128, 128, 1, 1, 1, 1, 1, 1, 144, 1, 1, 1, 1, 1, 1, 1, 144, 151, 156, 153, 153, 156, 179, 158, 158, 158, 158, 182, 159, 159, 159, 187, 164, 164, 164, 160, 160, 160, 160, 161, 162, 179, 179, 179, 182, 183, 183, 183, 499, 476, 447, 167, 167, 167, 167, 167, 187, 187, 440, 195, 200, 282, 200, 201, 201, 202, 202, 202, 258, 204, 204, 212, 204, 464, 212, 212, 212, 222, 214, 214, 214, 214, 214, 255, 222, 222, 230, 226, 230, 230, 249, 233, 235, 233, 238, 233, 233, 233, 233, 233, 233, 233, 232, 249, 250, 636, 636, 636, 255, 504, 504, 258, 258, 258, 258, 273, 263, 263, 263, 263, 263, 263, 263, 263, 274, 274, 260, 260, 260, 200, 200, 290, 282, 283, 282, 285, 282, 282, 282, 302, 568, 290, 290, 290, 295, 295, 292, 292, 298, 298, 306, 306, 302, 536, 306, 321, 302, 302, 302, 302, 312, 312, 312, 312, 312, 312, 312, 317, 536, 529, 321, 321, 528, 325, 325, 325, 325, 331, 522, 321, 321, 619, 333, 333, 340, 537, 503, 340, 340, 539, 340, 340, 340, 340, 350, 352, 352, 353, 358, 358, 358, 353, 364, 167, 358, 363, 365, 368, 365, 365, 371, 368, 371, 373, 373, 375, 380, 406, 375, 375, 375, 393, 439, 393, 393, 393, 380, 380, 438, 389, 389, 389, 383, 384, 383, 384, 395, 395, 395, 399, 399, 425, 444, 406, 406, 406, 413, 406, 406, 406, 406, 406, 406, 488, 426, 426, 429, 439, 443, 440, 440, 443, 443, 443, 443, 444, 444, 447, 447, 454, 454, 457, 457, 457, 457, 457, 411, 465, 575, 465, 573, 465, 613, 470, 470, 470, 474, 476, 476, 480, 482, 482, 482, 482, 483, 429, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 500, 500, 625, 519, 350, 361, 361, 508, 526, 509, 509, 350, 513, 350, 200, 522, 523, 524, 525, 526, 616, 532, 532, 533, 524, 537, 350, 542, 539, 542, 523, 536, 536, 536, 553, 549, 549, 549, 553, 346, 345, 345, 345, 333, 316, 312, 564, 568, 575, 607, 575, 575, 575, 575, 575, 573, 182, 302, 302, 302, 639, 352, 352, 352, 352, 597, 597, 606, 606, 610, 611, 647, 616, 619, 619, 623, 623, 625, 625, 625, 625, 625, 625, 625, 625, 226, 225, 640, 640, 610, 610, 610, 610, 647, 649, 649, 649, 654, 654, 654, 654, 673, 660, 660, 660, 660, 660, 670, 673, 660, 508, 508, 508 Added 113 phantom parents. Added phantom dads for: 680, 681, 682, 683, 684, 685, 686 Added phantom moms for: 687, 688, 689, 690, 691, 692, 693, 694, 695, 696, 697, 698, 699, 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711, 712, 713, 714, 715, 716, 717, 718, 719, 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731, 732, 733, 734, 735, 736, 737, 738, 739, 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750, 751, 752, 753, 754, 755, 756, 757, 758, 759, 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771, 772, 773, 774, 775, 776, 777, 778, 779, 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791, 792 Changes Made: c(566, 2, 2, 2, 6, 11, 13, 15, 15, 17, 17, 17, 22, 24, 24, 24, 584, 28, 28, 28, 28, 33, 33, 36, 36, 39, 39, 39, 2, 43, 43, 43, 49, 49, 52, 52, 55, 55, 54, 54, 61, 61, 61, 61, 61, 61, 61, 69, 71, 71, 71, 71, 63, 63, 78, 81, 81, 81, 86, 86, 86, 86, 92, 92, 95, 95, 95, 95, 95, 95, 95, 103, 103, 103, 103, 103, 109, 109, 109, 109, 114, 114, 114, 118, 118, 583, 107, 107, 107, 126, 126, 126, 126, 126, 132, 132, 135, 135, 135, 135, 135, 135, 583, 583, 585, 584, 584, 584, 584, 586, 163, 163, 163, 188, 165, 165, 165, 171, 171, 171, 171, 176, 585, 585, 585, 586, 199, 479, 189, 188, 188, 197, 517, 516, 517, 518, 518, 203, 203, 203, 257, 207, 207, 468, 210, 571, 468, 468, 468, 223, 216, 216, 216, 216, 216, 570, 223, 223, 538, 224, 538, 538, 231, 234, 231, 237, 231, 231, 231, 231, 231, 231, 231, 247, 251, 251, 251, 570, 505, 505, 257, 257, 257, 257, 264, 264, 264, 264, 276, 276, 276, 517, 517, 291, 516, 600, 516, 516, 516, 516, 303, 567, 291, 291, 291, 589, 589, 600, 600, 502, 502, 303, 339, 502, 322, 563, 591, 308, 560, 560, 560, 560, 560, 560, 560, 339, 535, 322, 322, 323, 323, 323, 323, 323, 520, 322, 322, 620, 323, 323, 341, 506, 515, 341, 341, 541, 344, 344, 344, 344, 351, 510, 510, 354, 359, 359, 359, 355, 590, 370, 590, 590, 372, 370, 372, 376, 382, 376, 376, 376, 614, 614, 614, 614, 382, 382, 387, 387, 387, 398, 398, 398, 402, 402, 448, 412, 615, 430, 430, 430, 430, 430, 432, 432, 448, 448, 189, 189, 450, 450, 450, 450, 450, 410, 467, 576, 574, 572, 467, 469, 469, 469, 471, 479, 479, 615, 627, 351, 362, 362, 675, 527, 510, 510, 351, 512, 351, 517, 520, 514, 534, 527, 617, 531, 531, 534, 506, 351, 543, 541, 543, 514, 545, 545, 339, 339, 339, 339, 554, 348, 348, 348, 546, 560, 566, 567, 576, 608, 576, 576, 576, 576, 576, 572, 587, 591, 591, 303, 510, 510, 510, 510, 596, 596, 605, 605, 609, 612, 648, 617, 620, 620, 624, 624, 627, 627, 627, 627, 627, 627, 627, 627, 228, 131, 641, 641, 642, 642, 642, 642, 648, 650, 650, 650, 655, 655, 655, 655, 674, 661, 661, 665, 665, 665, 674, 671, 675, 675, 675)c(564, 1, 1, 1, 3, 7, 7, 7, 8, 10, 3, 3, 18, 18, 18, 3, 23, 23, 23, 158, 4, 4, 4, 4, 679, 29, 29, 5, 5, 38, 38, 38, 1, 44, 44, 44, 45, 1, 1, 50, 50, 53, 53, 58, 58, 1, 1, 1, 1, 1, 1, 1, 62, 70, 70, 70, 70, 76, 76, 79, 64, 64, 64, 66, 66, 66, 66, 67, 67, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 104, 104, 104, 104, 105, 105, 105, 106, 106, 153, 121, 121, 121, 1, 1, 1, 1, 1, 128, 128, 1, 1, 1, 1, 1, 1, 144, 1, 1, 1, 1, 1, 1, 1, 144, 151, 156, 153, 153, 156, 179, 158, 158, 158, 158, 182, 159, 159, 159, 187, 164, 164, 164, 160, 160, 160, 160, 161, 162, 179, 179, 179, 182, 183, 183, 183, 499, 476, 447, 167, 167, 167, 167, 167, 187, 187, 440, 195, 200, 282, 200, 201, 201, 202, 202, 202, 258, 204, 204, 212, 204, 464, 212, 212, 212, 222, 214, 214, 214, 214, 214, 255, 222, 222, 230, 226, 230, 230, 249, 233, 235, 233, 238, 233, 233, 233, 233, 233, 233, 233, 232, 249, 250, 636, 636, 636, 255, 504, 504, 258, 258, 258, 258, 273, 263, 263, 263, 263, 263, 263, 263, 263, 274, 274, 260, 260, 260, 200, 200, 290, 282, 283, 282, 285, 282, 282, 282, 302, 568, 290, 290, 290, 295, 295, 292, 292, 298, 298, 306, 306, 302, 536, 306, 321, 302, 302, 302, 302, 312, 312, 312, 312, 312, 312, 312, 317, 536, 529, 321, 321, 528, 325, 325, 325, 325, 331, 522, 321, 321, 619, 333, 333, 340, 537, 503, 340, 340, 539, 340, 340, 340, 340, 350, 352, 352, 353, 358, 358, 358, 353, 364, 167, 358, 363, 365, 368, 365, 365, 371, 368, 371, 373, 373, 375, 380, 406, 375, 375, 375, 393, 439, 393, 393, 393, 380, 380, 438, 389, 389, 389, 383, 384, 383, 384, 395, 395, 395, 399, 399, 425, 444, 406, 406, 406, 413, 406, 406, 406, 406, 406, 406, 488, 426, 426, 429, 439, 443, 440, 440, 443, 443, 443, 443, 444, 444, 447, 447, 454, 454, 457, 457, 457, 457, 457, 411, 465, 575, 465, 573, 465, 613, 470, 470, 470, 474, 476, 476, 480, 482, 482, 482, 482, 483, 429, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 500, 500, 625, 519, 350, 361, 361, 508, 526, 509, 509, 350, 513, 350, 200, 522, 523, 524, 525, 526, 616, 532, 532, 533, 524, 537, 350, 542, 539, 542, 523, 536, 536, 536, 553, 549, 549, 549, 553, 346, 345, 345, 345, 333, 316, 312, 564, 568, 575, 607, 575, 575, 575, 575, 575, 573, 182, 302, 302, 302, 639, 352, 352, 352, 352, 597, 597, 606, 606, 610, 611, 647, 616, 619, 619, 623, 623, 625, 625, 625, 625, 625, 625, 625, 625, 226, 225, 640, 640, 610, 610, 610, 610, 647, 649, 649, 649, 654, 654, 654, 654, 673, 660, 660, 660, 660, 660, 670, 673, 660, 508, 508, 508)c(680, 681, 682, 683, 684, 685, 686)c(687, 688, 689, 690, 691, 692, 693, 694, 695, 696, 697, 698, 699, 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711, 712, 713, 714, 715, 716, 717, 718, 719, 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731, 732, 733, 734, 735, 736, 737, 738, 739, 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750, 751, 752, 753, 754, 755, 756, 757, 758, 759, 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771, 772, 773, 774, 775, 776, 777, 778, 779, 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791, 792) Step 1: Checking for single parents... Missing single parents found. All parents are listed in the pedigree. Step 2: Determining the if moms are the same sex and dads are same sex Role: momID 1 unique sex codes found: F Modal sex code: F All parents consistently coded. Role: dadID 1 unique sex codes found: M Modal sex code: M All parents consistently coded. Validation Results: c(431, 432, 433, 434, 435, 436, 437)c(8, 9, 10, 33, 48, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 157, 178, 184, 185, 186, 189, 191, 192, 193, 194, 197, 233, 250, 251, 264, 266, 267, 268, 269, 273, 275, 286, 296, 297, 311, 320, 332, 358, 360, 361, 362, 371, 372, 376, 382, 389, 394, 395, 396, 397, 406, 408, 410, 412, 415, 416, 417, 419, 421, 422, 423, 425, 427, 438, 440, 441, 442, 444, 445, 446, 447, 452, 453, 470, 479, 481, 483, 484, 485, 486, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 501, 503, 524, 532, 549, 554, 561, 595, 669)TRUEFALSEFMFMnumeric(0)numeric(0)TRUETRUE Step 3: Attempting to repair missing parents... REPAIR IN EARLY ALPHA Corrected sex of moms for: 566, 2, 2, 2, 6, 11, 13, 15, 15, 17, 17, 17, 22, 24, 24, 24, 584, 28, 28, 28, 28, 33, 33, 36, 36, 39, 39, 39, 2, 43, 43, 43, 49, 49, 52, 52, 55, 55, 54, 54, 61, 61, 61, 61, 61, 61, 61, 69, 71, 71, 71, 71, 63, 63, 78, 81, 81, 81, 86, 86, 86, 86, 92, 92, 95, 95, 95, 95, 95, 95, 95, 103, 103, 103, 103, 103, 109, 109, 109, 109, 114, 114, 114, 118, 118, 583, 107, 107, 107, 126, 126, 126, 126, 126, 132, 132, 135, 135, 135, 135, 135, 135, 583, 583, 585, 584, 584, 584, 584, 586, 163, 163, 163, 188, 165, 165, 165, 171, 171, 171, 171, 176, 585, 585, 585, 586, 199, 479, 189, 188, 188, 197, 517, 516, 517, 518, 518, 203, 203, 203, 257, 207, 207, 468, 210, 571, 468, 468, 468, 223, 216, 216, 216, 216, 216, 570, 223, 223, 538, 224, 538, 538, 231, 234, 231, 237, 231, 231, 231, 231, 231, 231, 231, 247, 251, 251, 251, 570, 505, 505, 257, 257, 257, 257, 264, 264, 264, 264, 276, 276, 276, 517, 517, 291, 516, 600, 516, 516, 516, 516, 303, 567, 291, 291, 291, 589, 589, 600, 600, 502, 502, 303, 339, 502, 322, 563, 591, 308, 560, 560, 560, 560, 560, 560, 560, 339, 535, 322, 322, 323, 323, 323, 323, 323, 520, 322, 322, 620, 323, 323, 341, 506, 515, 341, 341, 541, 344, 344, 344, 344, 351, 510, 510, 354, 359, 359, 359, 355, 590, 370, 590, 590, 372, 370, 372, 376, 382, 376, 376, 376, 614, 614, 614, 614, 382, 382, 387, 387, 387, 398, 398, 398, 402, 402, 448, 412, 615, 430, 430, 430, 430, 430, 432, 432, 448, 448, 189, 189, 450, 450, 450, 450, 450, 410, 467, 576, 574, 572, 467, 469, 469, 469, 471, 479, 479, 615, 627, 351, 362, 362, 675, 527, 510, 510, 351, 512, 351, 517, 520, 514, 534, 527, 617, 531, 531, 534, 506, 351, 543, 541, 543, 514, 545, 545, 339, 339, 339, 339, 554, 348, 348, 348, 546, 560, 566, 567, 576, 608, 576, 576, 576, 576, 576, 572, 587, 591, 591, 303, 510, 510, 510, 510, 596, 596, 605, 605, 609, 612, 648, 617, 620, 620, 624, 624, 627, 627, 627, 627, 627, 627, 627, 627, 228, 131, 641, 641, 642, 642, 642, 642, 648, 650, 650, 650, 655, 655, 655, 655, 674, 661, 661, 665, 665, 665, 674, 671, 675, 675, 675 Corrected sex of dads for: 564, 1, 1, 1, 3, 7, 7, 7, 8, 10, 3, 3, 18, 18, 18, 3, 23, 23, 23, 158, 4, 4, 4, 4, 679, 29, 29, 5, 5, 38, 38, 38, 1, 44, 44, 44, 45, 1, 1, 50, 50, 53, 53, 58, 58, 1, 1, 1, 1, 1, 1, 1, 62, 70, 70, 70, 70, 76, 76, 79, 64, 64, 64, 66, 66, 66, 66, 67, 67, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 104, 104, 104, 104, 105, 105, 105, 106, 106, 153, 121, 121, 121, 1, 1, 1, 1, 1, 128, 128, 1, 1, 1, 1, 1, 1, 144, 1, 1, 1, 1, 1, 1, 1, 144, 151, 156, 153, 153, 156, 179, 158, 158, 158, 158, 182, 159, 159, 159, 187, 164, 164, 164, 160, 160, 160, 160, 161, 162, 179, 179, 179, 182, 183, 183, 183, 499, 476, 447, 167, 167, 167, 167, 167, 187, 187, 440, 195, 200, 282, 200, 201, 201, 202, 202, 202, 258, 204, 204, 212, 204, 464, 212, 212, 212, 222, 214, 214, 214, 214, 214, 255, 222, 222, 230, 226, 230, 230, 249, 233, 235, 233, 238, 233, 233, 233, 233, 233, 233, 233, 232, 249, 250, 636, 636, 636, 255, 504, 504, 258, 258, 258, 258, 273, 263, 263, 263, 263, 263, 263, 263, 263, 274, 274, 260, 260, 260, 200, 200, 290, 282, 283, 282, 285, 282, 282, 282, 302, 568, 290, 290, 290, 295, 295, 292, 292, 298, 298, 306, 306, 302, 536, 306, 321, 302, 302, 302, 302, 312, 312, 312, 312, 312, 312, 312, 317, 536, 529, 321, 321, 528, 325, 325, 325, 325, 331, 522, 321, 321, 619, 333, 333, 340, 537, 503, 340, 340, 539, 340, 340, 340, 340, 350, 352, 352, 353, 358, 358, 358, 353, 364, 167, 358, 363, 365, 368, 365, 365, 371, 368, 371, 373, 373, 375, 380, 406, 375, 375, 375, 393, 439, 393, 393, 393, 380, 380, 438, 389, 389, 389, 383, 384, 383, 384, 395, 395, 395, 399, 399, 425, 444, 406, 406, 406, 413, 406, 406, 406, 406, 406, 406, 488, 426, 426, 429, 439, 443, 440, 440, 443, 443, 443, 443, 444, 444, 447, 447, 454, 454, 457, 457, 457, 457, 457, 411, 465, 575, 465, 573, 465, 613, 470, 470, 470, 474, 476, 476, 480, 482, 482, 482, 482, 483, 429, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 500, 500, 625, 519, 350, 361, 361, 508, 526, 509, 509, 350, 513, 350, 200, 522, 523, 524, 525, 526, 616, 532, 532, 533, 524, 537, 350, 542, 539, 542, 523, 536, 536, 536, 553, 549, 549, 549, 553, 346, 345, 345, 345, 333, 316, 312, 564, 568, 575, 607, 575, 575, 575, 575, 575, 573, 182, 302, 302, 302, 639, 352, 352, 352, 352, 597, 597, 606, 606, 610, 611, 647, 616, 619, 619, 623, 623, 625, 625, 625, 625, 625, 625, 625, 625, 226, 225, 640, 640, 610, 610, 610, 610, 647, 649, 649, 649, 654, 654, 654, 654, 673, 660, 660, 660, 660, 660, 670, 673, 660, 508, 508, 508 Added 113 phantom parents. Added phantom dads for: 680, 681, 682, 683, 684, 685, 686 Added phantom moms for: 687, 688, 689, 690, 691, 692, 693, 694, 695, 696, 697, 698, 699, 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711, 712, 713, 714, 715, 716, 717, 718, 719, 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731, 732, 733, 734, 735, 736, 737, 738, 739, 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750, 751, 752, 753, 754, 755, 756, 757, 758, 759, 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771, 772, 773, 774, 775, 776, 777, 778, 779, 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791, 792 Changes Made: c(566, 2, 2, 2, 6, 11, 13, 15, 15, 17, 17, 17, 22, 24, 24, 24, 584, 28, 28, 28, 28, 33, 33, 36, 36, 39, 39, 39, 2, 43, 43, 43, 49, 49, 52, 52, 55, 55, 54, 54, 61, 61, 61, 61, 61, 61, 61, 69, 71, 71, 71, 71, 63, 63, 78, 81, 81, 81, 86, 86, 86, 86, 92, 92, 95, 95, 95, 95, 95, 95, 95, 103, 103, 103, 103, 103, 109, 109, 109, 109, 114, 114, 114, 118, 118, 583, 107, 107, 107, 126, 126, 126, 126, 126, 132, 132, 135, 135, 135, 135, 135, 135, 583, 583, 585, 584, 584, 584, 584, 586, 163, 163, 163, 188, 165, 165, 165, 171, 171, 171, 171, 176, 585, 585, 585, 586, 199, 479, 189, 188, 188, 197, 517, 516, 517, 518, 518, 203, 203, 203, 257, 207, 207, 468, 210, 571, 468, 468, 468, 223, 216, 216, 216, 216, 216, 570, 223, 223, 538, 224, 538, 538, 231, 234, 231, 237, 231, 231, 231, 231, 231, 231, 231, 247, 251, 251, 251, 570, 505, 505, 257, 257, 257, 257, 264, 264, 264, 264, 276, 276, 276, 517, 517, 291, 516, 600, 516, 516, 516, 516, 303, 567, 291, 291, 291, 589, 589, 600, 600, 502, 502, 303, 339, 502, 322, 563, 591, 308, 560, 560, 560, 560, 560, 560, 560, 339, 535, 322, 322, 323, 323, 323, 323, 323, 520, 322, 322, 620, 323, 323, 341, 506, 515, 341, 341, 541, 344, 344, 344, 344, 351, 510, 510, 354, 359, 359, 359, 355, 590, 370, 590, 590, 372, 370, 372, 376, 382, 376, 376, 376, 614, 614, 614, 614, 382, 382, 387, 387, 387, 398, 398, 398, 402, 402, 448, 412, 615, 430, 430, 430, 430, 430, 432, 432, 448, 448, 189, 189, 450, 450, 450, 450, 450, 410, 467, 576, 574, 572, 467, 469, 469, 469, 471, 479, 479, 615, 627, 351, 362, 362, 675, 527, 510, 510, 351, 512, 351, 517, 520, 514, 534, 527, 617, 531, 531, 534, 506, 351, 543, 541, 543, 514, 545, 545, 339, 339, 339, 339, 554, 348, 348, 348, 546, 560, 566, 567, 576, 608, 576, 576, 576, 576, 576, 572, 587, 591, 591, 303, 510, 510, 510, 510, 596, 596, 605, 605, 609, 612, 648, 617, 620, 620, 624, 624, 627, 627, 627, 627, 627, 627, 627, 627, 228, 131, 641, 641, 642, 642, 642, 642, 648, 650, 650, 650, 655, 655, 655, 655, 674, 661, 661, 665, 665, 665, 674, 671, 675, 675, 675)c(564, 1, 1, 1, 3, 7, 7, 7, 8, 10, 3, 3, 18, 18, 18, 3, 23, 23, 23, 158, 4, 4, 4, 4, 679, 29, 29, 5, 5, 38, 38, 38, 1, 44, 44, 44, 45, 1, 1, 50, 50, 53, 53, 58, 58, 1, 1, 1, 1, 1, 1, 1, 62, 70, 70, 70, 70, 76, 76, 79, 64, 64, 64, 66, 66, 66, 66, 67, 67, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 104, 104, 104, 104, 105, 105, 105, 106, 106, 153, 121, 121, 121, 1, 1, 1, 1, 1, 128, 128, 1, 1, 1, 1, 1, 1, 144, 1, 1, 1, 1, 1, 1, 1, 144, 151, 156, 153, 153, 156, 179, 158, 158, 158, 158, 182, 159, 159, 159, 187, 164, 164, 164, 160, 160, 160, 160, 161, 162, 179, 179, 179, 182, 183, 183, 183, 499, 476, 447, 167, 167, 167, 167, 167, 187, 187, 440, 195, 200, 282, 200, 201, 201, 202, 202, 202, 258, 204, 204, 212, 204, 464, 212, 212, 212, 222, 214, 214, 214, 214, 214, 255, 222, 222, 230, 226, 230, 230, 249, 233, 235, 233, 238, 233, 233, 233, 233, 233, 233, 233, 232, 249, 250, 636, 636, 636, 255, 504, 504, 258, 258, 258, 258, 273, 263, 263, 263, 263, 263, 263, 263, 263, 274, 274, 260, 260, 260, 200, 200, 290, 282, 283, 282, 285, 282, 282, 282, 302, 568, 290, 290, 290, 295, 295, 292, 292, 298, 298, 306, 306, 302, 536, 306, 321, 302, 302, 302, 302, 312, 312, 312, 312, 312, 312, 312, 317, 536, 529, 321, 321, 528, 325, 325, 325, 325, 331, 522, 321, 321, 619, 333, 333, 340, 537, 503, 340, 340, 539, 340, 340, 340, 340, 350, 352, 352, 353, 358, 358, 358, 353, 364, 167, 358, 363, 365, 368, 365, 365, 371, 368, 371, 373, 373, 375, 380, 406, 375, 375, 375, 393, 439, 393, 393, 393, 380, 380, 438, 389, 389, 389, 383, 384, 383, 384, 395, 395, 395, 399, 399, 425, 444, 406, 406, 406, 413, 406, 406, 406, 406, 406, 406, 488, 426, 426, 429, 439, 443, 440, 440, 443, 443, 443, 443, 444, 444, 447, 447, 454, 454, 457, 457, 457, 457, 457, 411, 465, 575, 465, 573, 465, 613, 470, 470, 470, 474, 476, 476, 480, 482, 482, 482, 482, 483, 429, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 500, 500, 625, 519, 350, 361, 361, 508, 526, 509, 509, 350, 513, 350, 200, 522, 523, 524, 525, 526, 616, 532, 532, 533, 524, 537, 350, 542, 539, 542, 523, 536, 536, 536, 553, 549, 549, 549, 553, 346, 345, 345, 345, 333, 316, 312, 564, 568, 575, 607, 575, 575, 575, 575, 575, 573, 182, 302, 302, 302, 639, 352, 352, 352, 352, 597, 597, 606, 606, 610, 611, 647, 616, 619, 619, 623, 623, 625, 625, 625, 625, 625, 625, 625, 625, 226, 225, 640, 640, 610, 610, 610, 610, 647, 649, 649, 649, 654, 654, 654, 654, 673, 660, 660, 660, 660, 660, 670, 673, 660, 508, 508, 508)c(680, 681, 682, 683, 684, 685, 686)c(687, 688, 689, 690, 691, 692, 693, 694, 695, 696, 697, 698, 699, 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711, 712, 713, 714, 715, 716, 717, 718, 719, 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731, 732, 733, 734, 735, 736, 737, 738, 739, 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750, 751, 752, 753, 754, 755, 756, 757, 758, 759, 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771, 772, 773, 774, 775, 776, 777, 778, 779, 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791, 792) Step 1: Checking for single parents... Missing single parents found. All parents are listed in the pedigree. Step 2: Determining the if moms are the same sex and dads are same sex Role: momID 1 unique sex codes found: F Modal sex code: F All parents consistently coded. Role: dadID 1 unique sex codes found: M Modal sex code: M All parents consistently coded. Validation Results: c(431, 432, 433, 434, 435, 436, 437)c(8, 9, 10, 33, 48, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 157, 178, 184, 185, 186, 189, 191, 192, 193, 194, 197, 233, 250, 251, 264, 266, 267, 268, 269, 273, 275, 286, 296, 297, 311, 320, 332, 358, 360, 361, 362, 371, 372, 376, 382, 389, 394, 395, 396, 397, 406, 408, 410, 412, 415, 416, 417, 419, 421, 422, 423, 425, 427, 438, 440, 441, 442, 444, 445, 446, 447, 452, 453, 470, 479, 481, 483, 484, 485, 486, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 501, 503, 524, 532, 549, 554, 561, 595, 669)TRUEFALSEFMFMnumeric(0)numeric(0)TRUETRUE No individuals with more than two parents detected. No duplicate edges detected. No cyclic relationships detected. No individuals with more than two parents detected. No duplicate edges detected. Cyclic relationships detected: 57 Individuals with more than two parents detected: 7 Duplicate edges detected: 47 No cyclic relationships detected. Individuals with more than two parents detected: 1 Duplicate edges detected: 10110211 No cyclic relationships detected. Standardizing column names... Step 1: Checking how many sexes/genders... 2 unique sex codes found: 1, 0 Role: dadID 1 unique sex codes found: 1 Modal sex code: 1 All parents consistently coded. Role: momID 1 unique sex codes found: 0 Modal sex code: 0 All parents consistently coded. Checks Made: c(1, 0)21010numeric(0)numeric(0)numeric(0)numeric(0) Standardizing column names... Step 1: Checking how many sexes/genders... 3 unique sex codes found: 5, 0, 1 Role: dadID 2 unique sex codes found: 5, 1 Modal sex code: 1 1 parents have inconsistent sex coding. Role: momID 1 unique sex codes found: 0 Modal sex code: 0 All parents consistently coded. Checks Made: c(5, 0, 1)3c(5, 1)01016numeric(0)numeric(0) Standardizing column names... Step 1: Checking how many sexes/genders... 3 unique sex codes found: 5, 0, 1 Role: dadID 2 unique sex codes found: 5, 1 Modal sex code: 1 1 parents have inconsistent sex coding. Role: momID 1 unique sex codes found: 0 Modal sex code: 0 All parents consistently coded. Step 2: Attempting to repair sex coding... Changes Made: Standardizing column names... Step 1: Checking how many sexes/genders... 3 unique sex codes found: 1, 0, 5 Role: dadID 1 unique sex codes found: 1 Modal sex code: 1 All parents consistently coded. Role: momID 2 unique sex codes found: 5, 0 Modal sex code: 0 1 parents have inconsistent sex coding. Checks Made: c(1, 0, 5)31c(5, 0)10numeric(0)numeric(0)36 Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Standardizing column names... Computing parent-child adjacency matrix... Constructed sparse matrix Component model is identified. Component model is not identified. Non-identified parameters are A, C Component model is not identified. Non-identified parameters are Comp1, Comp2 456 [1] "cn" Reading file: D:\temp\2025_07_19_04_15_16_29117\RtmpOGxSmn\filed304cde62dc.ged File is 19 lines long Found 2 individual blocks File has 2 people Post-processing data frame Processing parents Combining Duplicate Columns Removing empty columns Reading file: D:\temp\2025_07_19_04_15_16_29117\RtmpOGxSmn\filed304f89108a.ged File is 8 lines long Found 2 individual blocks File has 2 people Post-processing data frame Processing parents Combining Duplicate Columns Removing empty columns Reading file: D:\temp\2025_07_19_04_15_16_29117\RtmpOGxSmn\filed3047e2e302.ged File is 3 lines long Found 1 individual blocks File has 1 people Post-processing data frame Processing parents Combining Duplicate Columns Removing empty columns Reading file: D:\temp\2025_07_19_04_15_16_29117\RtmpOGxSmn\filed30464946d86.ged File is 5 lines long Found 1 individual blocks File has 1 people Post-processing data frame Processing parents Combining Duplicate Columns Removing empty columns Slimming down the data frame Reading file: D:\temp\2025_07_19_04_15_16_29117\RtmpOGxSmn\filed3041097675b.ged File is 9 lines long Found 1 individual blocks File has 1 people Post-processing data frame Processing parents Combining Duplicate Columns Removing empty columns Reading file: D:\temp\2025_07_19_04_15_16_29117\RtmpOGxSmn\filed3041097675b.ged File is 9 lines long Parsing GEDCOM file File has 1 people Post-processing data frame Processing parents Combining Duplicate Columns Removing empty columns Reading file: D:\temp\2025_07_19_04_15_16_29117\RtmpOGxSmn\filed3047cfe2c47.ged File is 2 lines long Found 1 individual blocks File has 1 people Post-processing data frame Processing parents Combining Duplicate Columns Removing empty columns Reading file: D:\temp\2025_07_19_04_15_16_29117\RtmpOGxSmn\filed30447a118dd.ged File is 9 lines long Found 1 individual blocks File has 1 people Post-processing data frame Processing parents Combining Duplicate Columns Removing empty columns Reading file: D:\temp\2025_07_19_04_15_16_29117\RtmpOGxSmn\filed30447a118dd.ged File is 9 lines long Parsing GEDCOM file File has 1 people Post-processing data frame Processing parents Combining Duplicate Columns Removing empty columns Step 2: Let's try to build connection between each two generations Step 2.1: mark a group of potential sons and daughters in the i th generation Step 2.2: mark a group of potential parents in the i-1 th generation Step 2.3: connect the i and i-1 th generation Step 2.1: mark a group of potential sons and daughters in the i th generation Step 2.2: mark a group of potential parents in the i-1 th generation Step 2.3: connect the i and i-1 th generation Step 2.1: mark a group of potential sons and daughters in the i th generation Step 2.2: mark a group of potential parents in the i-1 th generation Step 2.3: connect the i and i-1 th generation Output folder: testout/data/links_10/ Input file: dataRelatedPairs.csv testout/data/links_10/df_mt1_r0.9-r1.1.csv testout/data/links_10/df_mt1_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.45-r0.55.csv testout/data/links_10/df_mt1_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.225-r0.275.csv 2 Processed 30 rows from lines 2 to 31 32 testout/data/links_10/df_mt1_r0.9-r1.1.csv testout/data/links_10/df_mt1_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.45-r0.55.csv testout/data/links_10/df_mt1_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.1125-r0.1375.csv 32 Processed 30 rows from lines 32 to 31 62 testout/data/links_10/df_mt1_r0.9-r1.1.csv testout/data/links_10/df_mt1_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.45-r0.55.csv testout/data/links_10/df_mt1_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.1125-r0.1375.csv testout/data/links_10/df_mt0_r0.05625-r0.06875.csv 62 Processed 30 rows from lines 62 to 61 92 testout/data/links_10/df_mt1_r0.9-r1.1.csv testout/data/links_10/df_mt1_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.45-r0.55.csv testout/data/links_10/df_mt1_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.1125-r0.1375.csv testout/data/links_10/df_mt0_r0.05625-r0.06875.csv 92 Processed 30 rows from lines 92 to 91 122 testout/data/links_10/df_mt1_r0.9-r1.1.csv testout/data/links_10/df_mt1_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.1125-r0.1375.csv 122 Processed 30 rows from lines 122 to 121 152 testout/data/links_10/df_mt1_r0.9-r1.1.csv testout/data/links_10/df_mt1_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.45-r0.55.csv testout/data/links_10/df_mt1_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.1125-r0.1375.csv 152 Processed 30 rows from lines 152 to 151 182 testout/data/links_10/df_mt1_r0.9-r1.1.csv testout/data/links_10/df_mt1_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.45-r0.55.csv testout/data/links_10/df_mt1_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.1125-r0.1375.csv 182 Processed 30 rows from lines 182 to 181 212 testout/data/links_10/df_mt1_r0.9-r1.1.csv testout/data/links_10/df_mt1_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.1125-r0.1375.csv 212 Processed 30 rows from lines 212 to 211 242 testout/data/links_10/df_mt1_r0.9-r1.1.csv testout/data/links_10/df_mt1_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.1125-r0.1375.csv testout/data/links_10/df_mt0_r0.05625-r0.06875.csv 242 Processed 30 rows from lines 242 to 241 272 testout/data/links_10/df_mt1_r0.9-r1.1.csv testout/data/links_10/df_mt1_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.45-r0.55.csv testout/data/links_10/df_mt1_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.225-r0.275.csv testout/data/links_10/df_mt1_r0.1125-r0.1375.csv testout/data/links_10/df_mt0_r0.1125-r0.1375.csv testout/data/links_10/df_mt0_r0.05625-r0.06875.csv 272 Processed 30 rows from lines 272 to 271 302 testout/data/links_10/df_mt1_r0.9-r1.1.csv testout/data/links_10/df_mt1_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.45-r0.55.csv testout/data/links_10/df_mt1_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.225-r0.275.csv testout/data/links_10/df_mt1_r0.1125-r0.1375.csv testout/data/links_10/df_mt0_r0.1125-r0.1375.csv testout/data/links_10/df_mt0_r0.05625-r0.06875.csv 302 Processed 30 rows from lines 302 to 301 332 testout/data/links_10/df_mt1_r0.9-r1.1.csv testout/data/links_10/df_mt1_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.1125-r0.1375.csv testout/data/links_10/df_mt0_r0.05625-r0.06875.csv 332 Processed 30 rows from lines 332 to 331 362 testout/data/links_10/df_mt1_r0.9-r1.1.csv testout/data/links_10/df_mt1_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.45-r0.55.csv testout/data/links_10/df_mt0_r0.225-r0.275.csv testout/data/links_10/df_mt0_r0.1125-r0.1375.csv testout/data/links_10/df_mt0_r0.05625-r0.06875.csv 362 Processed 14 rows from lines 362 to 361 Counting mothers... Summarizing maternal lines... Summarized 11 maternal lines. Counting mothers... Summarizing maternal lines... Summarized 11 maternal lines. Summarizing paternal lines... Summarized 11 paternal lines. Counting mothers... Counting fathers... Summarizing families... Summarized 2 families. Summarizing maternal lines... Summarized 2 maternal lines. Summarizing paternal lines... Summarized 4 paternal lines. Counting mothers... Counting fathers... Summarizing families... Summarized 1 families. Summarizing maternal lines... Summarized 1 maternal lines. Summarizing paternal lines... Summarized 1 paternal lines. Finding oldest families... Finding oldest maternal lines... Finding oldest paternal lines... Summarized 1 families. Summarizing maternal lines... Summarized 11 maternal lines. Summarizing paternal lines... Summarized 11 paternal lines. No individuals with more than two parents detected. No duplicate edges detected. No cyclic relationships detected. Summarizing families... Summarized 1 families. No individuals with more than two parents detected. No duplicate edges detected. No cyclic relationships detected. No individuals with more than two parents detected. No duplicate edges detected. No cyclic relationships detected. Standardizing column names... The input pedigree is not in the same format as the output of simulatePedigree twin1 1 twin2 2 Standardizing column names... The input pedigree is not in the same format as the output of simulatePedigree twin1 1 twin2 2 Standardizing column names... The input pedigree is not in the same format as the output of simulatePedigree twin1 1 twin2 2 Standardizing column names... The input pedigree is not in the same format as the output of simulatePedigree Standardizing column names... The input pedigree is not in the same format as the output of simulatePedigree [ FAIL 0 | WARN 0 | SKIP 0 | PASS 673 ] > > proc.time() user system elapsed 11.98 1.92 15.42