tests/testthat/test_read_trees.R

context("Test reading in trees.")

# the last tree is bad (due to ms segfault)
suppressWarnings( expect_warning( trees <- trees_from_ms("bad_trees.txt"), "skipping 1 bad trees") )

expected <- list(structure(list(edge = structure(c(271L, 272L, 273L, 274L, 
274L, 275L, 275L, 273L, 276L, 276L, 277L, 278L, 278L, 279L, 279L, 
277L, 280L, 281L, 281L, 280L, 282L, 283L, 283L, 284L, 284L, 285L, 
285L, 282L, 286L, 287L, 287L, 288L, 289L, 289L, 288L, 290L, 290L, 
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297L, 297L, 296L, 298L, 298L, 299L, 299L, 292L, 300L, 300L, 272L, 
301L, 302L, 302L, 303L, 303L, 301L, 304L, 305L, 305L, 304L, 306L, 
307L, 307L, 306L, 308L, 308L, 309L, 309L, 271L, 310L, 311L, 311L, 
312L, 313L, 314L, 314L, 315L, 316L, 316L, 317L, 317L, 318L, 318L, 
315L, 319L, 319L, 313L, 320L, 321L, 322L, 322L, 323L, 323L, 321L, 
324L, 325L, 325L, 324L, 326L, 326L, 327L, 327L, 328L, 328L, 320L, 
329L, 329L, 330L, 330L, 331L, 331L, 312L, 332L, 333L, 334L, 334L, 
333L, 335L, 335L, 332L, 336L, 336L, 337L, 337L, 338L, 339L, 339L, 
340L, 341L, 341L, 342L, 342L, 343L, 344L, 344L, 345L, 345L, 343L, 
346L, 346L, 340L, 347L, 347L, 338L, 348L, 348L, 349L, 350L, 351L, 
351L, 350L, 352L, 352L, 349L, 353L, 354L, 354L, 355L, 355L, 356L, 
356L, 357L, 357L, 353L, 358L, 358L, 359L, 359L, 360L, 360L, 310L, 
361L, 362L, 363L, 364L, 365L, 365L, 366L, 367L, 367L, 366L, 368L, 
368L, 369L, 369L, 364L, 370L, 370L, 371L, 372L, 372L, 373L, 373L, 
374L, 375L, 375L, 374L, 376L, 376L, 377L, 378L, 379L, 379L, 380L, 
380L, 378L, 381L, 381L, 377L, 382L, 382L, 371L, 383L, 383L, 384L, 
385L, 385L, 386L, 386L, 384L, 387L, 387L, 363L, 388L, 389L, 390L, 
391L, 391L, 390L, 392L, 392L, 393L, 393L, 389L, 394L, 394L, 388L, 
395L, 396L, 396L, 397L, 397L, 395L, 398L, 398L, 399L, 400L, 400L, 
401L, 402L, 402L, 403L, 403L, 404L, 404L, 401L, 405L, 406L, 406L, 
407L, 407L, 405L, 408L, 409L, 409L, 408L, 410L, 411L, 411L, 412L, 
412L, 410L, 413L, 413L, 414L, 414L, 399L, 415L, 415L, 362L, 416L, 
417L, 417L, 416L, 418L, 419L, 420L, 420L, 419L, 421L, 421L, 422L, 
423L, 423L, 424L, 424L, 425L, 425L, 426L, 426L, 427L, 427L, 428L, 
428L, 429L, 430L, 431L, 432L, 432L, 431L, 433L, 433L, 434L, 434L, 
430L, 435L, 436L, 436L, 437L, 438L, 438L, 439L, 439L, 437L, 440L, 
441L, 442L, 442L, 443L, 443L, 444L, 444L, 441L, 445L, 446L, 446L, 
447L, 447L, 445L, 448L, 449L, 449L, 448L, 450L, 450L, 440L, 451L, 
451L, 452L, 453L, 453L, 452L, 454L, 454L, 455L, 455L, 456L, 456L, 
435L, 457L, 458L, 459L, 459L, 460L, 460L, 458L, 461L, 461L, 457L, 
462L, 462L, 463L, 464L, 464L, 465L, 465L, 463L, 466L, 466L, 429L, 
467L, 467L, 468L, 468L, 469L, 469L, 422L, 470L, 470L, 418L, 471L, 
472L, 473L, 473L, 474L, 475L, 476L, 476L, 475L, 477L, 478L, 478L, 
477L, 479L, 479L, 480L, 480L, 481L, 481L, 482L, 482L, 474L, 483L, 
483L, 484L, 484L, 472L, 485L, 486L, 486L, 487L, 487L, 485L, 488L, 
489L, 489L, 488L, 490L, 490L, 471L, 491L, 491L, 361L, 492L, 492L, 
493L, 494L, 494L, 495L, 496L, 496L, 497L, 497L, 495L, 498L, 498L, 
499L, 500L, 500L, 499L, 501L, 502L, 503L, 503L, 504L, 504L, 502L, 
505L, 505L, 506L, 506L, 501L, 507L, 508L, 509L, 509L, 508L, 510L, 
510L, 507L, 511L, 511L, 512L, 512L, 513L, 513L, 493L, 514L, 515L, 
515L, 516L, 517L, 517L, 518L, 518L, 516L, 519L, 519L, 520L, 521L, 
521L, 522L, 522L, 520L, 523L, 523L, 514L, 524L, 525L, 525L, 524L, 
526L, 526L, 527L, 527L, 528L, 529L, 530L, 530L, 531L, 531L, 529L, 
532L, 532L, 533L, 533L, 528L, 534L, 535L, 535L, 534L, 536L, 536L, 
537L, 537L, 538L, 538L, 539L, 539L, 272L, 273L, 274L, 1L, 275L, 
2L, 3L, 276L, 4L, 277L, 278L, 5L, 279L, 6L, 7L, 280L, 281L, 8L, 
9L, 282L, 283L, 10L, 284L, 11L, 285L, 12L, 13L, 286L, 287L, 14L, 
288L, 289L, 15L, 16L, 290L, 17L, 291L, 18L, 19L, 292L, 293L, 
20L, 294L, 21L, 295L, 22L, 296L, 297L, 23L, 24L, 298L, 25L, 299L, 
26L, 27L, 300L, 28L, 29L, 301L, 302L, 30L, 303L, 31L, 32L, 304L, 
305L, 33L, 34L, 306L, 307L, 35L, 36L, 308L, 37L, 309L, 38L, 39L, 
310L, 311L, 40L, 312L, 313L, 314L, 41L, 315L, 316L, 42L, 317L, 
43L, 318L, 44L, 45L, 319L, 46L, 47L, 320L, 321L, 322L, 48L, 323L, 
49L, 50L, 324L, 325L, 51L, 52L, 326L, 53L, 327L, 54L, 328L, 55L, 
56L, 329L, 57L, 330L, 58L, 331L, 59L, 60L, 332L, 333L, 334L, 
61L, 62L, 335L, 63L, 64L, 336L, 65L, 337L, 66L, 338L, 339L, 67L, 
340L, 341L, 68L, 342L, 69L, 343L, 344L, 70L, 345L, 71L, 72L, 
346L, 73L, 74L, 347L, 75L, 76L, 348L, 77L, 349L, 350L, 351L, 
78L, 79L, 352L, 80L, 81L, 353L, 354L, 82L, 355L, 83L, 356L, 84L, 
357L, 85L, 86L, 358L, 87L, 359L, 88L, 360L, 89L, 90L, 361L, 362L, 
363L, 364L, 365L, 91L, 366L, 367L, 92L, 93L, 368L, 94L, 369L, 
95L, 96L, 370L, 97L, 371L, 372L, 98L, 373L, 99L, 374L, 375L, 
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123L, 397L, 124L, 125L, 398L, 126L, 399L, 400L, 127L, 401L, 402L, 
128L, 403L, 129L, 404L, 130L, 131L, 405L, 406L, 132L, 407L, 133L, 
134L, 408L, 409L, 135L, 136L, 410L, 411L, 137L, 412L, 138L, 139L, 
413L, 140L, 414L, 141L, 142L, 415L, 143L, 144L, 416L, 417L, 145L, 
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424L, 151L, 425L, 152L, 426L, 153L, 427L, 154L, 428L, 155L, 429L, 
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436L, 161L, 437L, 438L, 162L, 439L, 163L, 164L, 440L, 441L, 442L, 
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463L, 464L, 189L, 465L, 190L, 191L, 466L, 192L, 193L, 467L, 194L, 
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211L, 212L, 485L, 486L, 213L, 487L, 214L, 215L, 488L, 489L, 216L, 
217L, 490L, 218L, 219L, 491L, 220L, 221L, 492L, 222L, 493L, 494L, 
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506L, 234L, 235L, 507L, 508L, 509L, 236L, 237L, 510L, 238L, 239L, 
511L, 240L, 512L, 241L, 513L, 242L, 243L, 514L, 515L, 244L, 516L, 
517L, 245L, 518L, 246L, 247L, 519L, 248L, 520L, 521L, 249L, 522L, 
250L, 251L, 523L, 252L, 253L, 524L, 525L, 254L, 255L, 526L, 256L, 
527L, 257L, 528L, 529L, 530L, 258L, 531L, 259L, 260L, 532L, 261L, 
533L, 262L, 263L, 534L, 535L, 264L, 265L, 536L, 266L, 537L, 267L, 
538L, 268L, 539L, 269L, 270L), .Dim = c(538L, 2L)), Nnode = 269L, 
    tip.label = c("180", "72", "262", "223", "206", "26", "219", 
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    "152", "88", "195", "161", "228", "142", "187", "202", "211", 
    "45", "266", "35", "218", "48", "83", "68", "143", "43", 
    "184", "15", "159", "197", "114", "171", "29", "57", "145", 
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    "245", "108", "112", "31", "109", "169", "118", "189", "244", 
    "246", "132", "172", "89", "167", "102", "104", "10", "14", 
    "22", "97", "259", "33", "74", "32", "176", "46", "4", "66", 
    "28", "69", "242", "141", "250", "251", "124", "225", "181", 
    "254", "3", "154", "7", "151", "155", "203", "213", "42", 
    "265", "125", "240", "263", "221", "216", "253", "212", "179", 
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    "186", "117", "70", "111", "191", "79", "38", "85", "131", 
    "164", "227", "243", "268", "120", "264", "12", "237", "258", 
    "27", "82", "107", "207", "96", "200", "5", "76", "173"), 
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    176553.906, 91296.828, 85257.078, 3852.359, 81404.719, 81404.719, 
    628.594, 266669.781, 113786.188, 432.664, 64246.988, 49106.535, 
    49106.535, 90.656, 113262.867, 82379.891, 30882.977, 30882.977, 
    127156.453, 197832.719, 55466.793, 700.785, 54766.008, 395.402, 
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    311643.031, 96768.93, 103962.352, 389.141, 103573.211, 103573.211, 
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    23381.631, 2828.205, 20553.426, 1373.762, 19179.664, 19179.664, 
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    0.03, 0.026, 4000.435, 4000.435, 0.003, 4000.458, 0.02, 4000.438, 
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    4000.43, 4000.43, 114857.75, 1226157.625, 709838.25, 43469.938, 
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    171191.375, 1746967.625, 17836.908, 17836.908, 1004130.188, 
    760674.312, 22358.438, 738315.875, 54804.062, 395246.312, 
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    220282.625, 28852.906, 191429.719, 191429.719, 313455.344, 
    326116.156, 43940.32, 43940.32, 12.094, 370044.375, 140323.656, 
    229720.719, 16931.047, 212789.672, 171659.656, 41130.02, 
    41130.02)), .Names = c("edge", "Nnode", "tip.label", "edge.length"
), class = "phylo", order = "cladewise"), structure(list(edge = structure(c(271L, 
272L, 273L, 274L, 274L, 275L, 275L, 273L, 276L, 276L, 277L, 277L, 
272L, 278L, 278L, 279L, 279L, 280L, 281L, 282L, 282L, 281L, 283L, 
284L, 285L, 285L, 284L, 286L, 286L, 287L, 288L, 288L, 287L, 289L, 
289L, 290L, 290L, 283L, 291L, 292L, 292L, 291L, 293L, 293L, 280L, 
294L, 295L, 296L, 296L, 295L, 297L, 297L, 298L, 298L, 299L, 299L, 
294L, 300L, 300L, 301L, 302L, 302L, 303L, 303L, 304L, 304L, 305L, 
306L, 306L, 307L, 307L, 308L, 308L, 305L, 309L, 310L, 310L, 311L, 
311L, 309L, 312L, 312L, 313L, 313L, 314L, 314L, 301L, 315L, 316L, 
316L, 315L, 317L, 317L, 318L, 318L, 271L, 319L, 320L, 321L, 322L, 
323L, 323L, 322L, 324L, 325L, 326L, 326L, 325L, 327L, 327L, 328L, 
329L, 329L, 328L, 330L, 330L, 324L, 331L, 331L, 321L, 332L, 333L, 
333L, 332L, 334L, 335L, 335L, 336L, 337L, 337L, 336L, 338L, 338L, 
334L, 339L, 340L, 341L, 342L, 342L, 341L, 343L, 344L, 344L, 343L, 
345L, 346L, 346L, 347L, 348L, 348L, 347L, 349L, 349L, 350L, 350L, 
351L, 351L, 345L, 352L, 353L, 354L, 354L, 353L, 355L, 355L, 352L, 
356L, 357L, 357L, 358L, 358L, 356L, 359L, 359L, 340L, 360L, 360L, 
361L, 361L, 339L, 362L, 363L, 364L, 364L, 365L, 365L, 366L, 366L, 
363L, 367L, 367L, 368L, 368L, 362L, 369L, 369L, 370L, 370L, 371L, 
371L, 320L, 372L, 373L, 373L, 372L, 374L, 375L, 376L, 376L, 377L, 
377L, 375L, 378L, 378L, 374L, 379L, 380L, 381L, 381L, 382L, 382L, 
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expect_equal( trees, expected )
petrelharp/msarg documentation built on May 25, 2019, 2:54 a.m.