File: MD5

package info (click to toggle)
r-cran-qtl 1.40-8-1
  • links: PTS, VCS
  • area: main
  • in suites: stretch
  • size: 12,212 kB
  • ctags: 588
  • sloc: ansic: 13,745; cpp: 2,837; ruby: 193; sh: 184; makefile: 5
file content (607 lines) | stat: -rw-r--r-- 34,143 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
ebee197a7a268ad897417f932e0fc458 *DESCRIPTION
e51985726448c1ce67dc3b6482384c37 *NAMESPACE
be09adead3e7ef2c4a141178391fde75 *R/add.cim.covar.R
38801c883ff011aaaa32a0247cf01465 *R/add_threshold.R
65828ef5fa06d0fe23d749a29fbf2017 *R/addmarker.R
0f0acd13292fe3661a5a7293fb2b32e1 *R/addqtl.R
dd04404183a726daafc469ab56461f42 *R/argmax.geno.R
3f263a1055a2f18f02a4e4b36a83e886 *R/arithscan.R
794e3ea6145b3197fd57414a4a881916 *R/bcsft.R
91b76e69b365e126cebd77bf2572d8d9 *R/calc.genoprob.R
2ac99dcabd77e74334262d668304a279 *R/calc.pairprob.R
69e3f39b6ad6ead0037c11fc8482f1da *R/cim.R
ed3f6b1e8c227f2d9d9642baf4fb7f44 *R/compareorder.R
3e57e8fd6054f364375e721844b36ec8 *R/countXO.R
ccc0c72cb991a806f9b13d4cb5dc773e *R/discan.R
9d23f0a2de41f19c36593afa8b840c4c *R/droponemarker.R
01716718979a0f44077b0a035d14dccb *R/effectplot.R
68bf0bb09eeec5081a405d9f52daf244 *R/effectscan.R
f2a1430217d9eda781716eec5d77163b *R/errorlod.R
e3796a3ddac4248776f6a6620d365f78 *R/est.map.R
ba45e9c9c964d5e615c673b706e6ba3e *R/est.rf.R
aa38018c26e0b6aafbaecec1fb084885 *R/fitqtl.R
92d2881c85a189e66855db8845ded960 *R/fitstahl.R
b44aa39fb0dc4cbcc086446454efcb65 *R/inferFounderHap.R
80f7c7c13c5047af9d33d3d24a485af3 *R/interpPositions.R
001ee17a7897bf5326a691276840043a *R/makeqtl.R
7b44e3ca31be22450416db34e660988a *R/map_construction.R
82a8898d3887ce8d1e225955b681e96c *R/markerlrt.R
f131bea910b5191e64a482955c816395 *R/mqmaugment.R
782d37d5d5e5486a2dbca482c72bb228 *R/mqmcircleplot.R
09f530a3d237d51e8bc8cf05b651ff04 *R/mqmcofactors.R
109c416c14ba1c963e8097e160180201 *R/mqmpermutation.R
a0c753945496fea041bbf72c46e90e16 *R/mqmplots.R
d1c37f4eb2a6bd33406daa43f9bff487 *R/mqmprepare.R
d7f1f56a4c6ca1b1eda59ef571a286d6 *R/mqmscan.R
679d8f804c01da620cbe9ba4e392d233 *R/mqmscanall.R
d25399c3429a884d260c04b3b7e7205d *R/mqmsnow.R
aeec2ad4b139caf9f783b50772b30a77 *R/mqmutil.R
9cd6298ebb239929eb06c31d0d1e1d01 *R/phyloqtl_scan.R
5c8e17565630ec6c23ae9564a392138d *R/phyloqtl_sim.R
67f61afe02563d21cd324d5c7c2edb2b *R/phyloqtl_util.R
0655588ac137705ab9cf98f3d4e55590 *R/pickMarkerSubset.R
798b11fe865159d8c34fa2a8927e3073 *R/plot.R
9022533eed2cbaa648276badb891d317 *R/plot.scanone.R
c81101ec92cf9b0cf38e8dcff7603e6f *R/plot.scantwo.R
75df93c9e5d8b0180a5dd69ac75ac27e *R/plotModel.R
39e3d5edecc6762bb3dc9d537c4f62db *R/plotperm.R
64b6af87b889cf37235fe06f6bb45b70 *R/pull_stuff.R
1c48b2a8c277c668c69df2359ce6c3db *R/qtlcart_io.R
fe91b022279f80bbe7516426781cb38a *R/read.cross.R
0e0937035dd4046c79381a297f5d2cce *R/read.cross.csv.R
acb4b39b920cb4bf5b120f5a4187c458 *R/read.cross.csvs.R
9f1b47177e3fa909668086b66c122e8e *R/read.cross.gary.R
2e9c3f8b73b79b56f0704891ee359aeb *R/read.cross.karl.R
fd6828bfec4e4e0316ed2e034fcf5104 *R/read.cross.mm.R
0176ca3d36fb0101f3f44b38dd55b0ca *R/read.cross.mq.R
6974001375f68b4aab8eb1abaeb26b87 *R/read.cross.qtx.R
875074861a40ae8a94fcd0756a8c68a3 *R/read.cross.tidy.R
20fad5c707f650ebaa2206f2768696a3 *R/readMWril.R
1e97ccba8083f0130fca5a73066ccbcf *R/refineqtl.R
693630ce6da46aa475b5f6a754ac0681 *R/replacemap.R
c2effea5623aed7325f475667a6433ee *R/ril48_reorg.R
c5bfdb9bc3d20748328c27fe3600a861 *R/ripple.R
03b0a20f8902792f1bad94536a3b5165 *R/scanone.R
feca194c570efcfa3be35854df861e4b *R/scanoneboot.R
428145569bac305af214bfab29d7855e *R/scanonevar.R
0e881b83577160556a4771b9dcc08efb *R/scanonevar.meanperm.R
cd39b4e457e757f5a9b36397ec6d4ebf *R/scanonevar.varperm.R
dc4c086aacc0eaa6801f1ed578ac98e0 *R/scanqtl.R
e74bf89075f6f292b7b115e364ff7c81 *R/scantwo.R
57a366187c3ec65980ec0329c948e92c *R/scantwopermhk.R
85360bf5580d5763f979b31efee9b3a8 *R/sim.geno.R
e5da49f0318e6296ebf57282af8a7416 *R/sim_ril.R
a755fa04272d8513b40053272fd7df61 *R/simulate.R
fa1a377d08f42688219c6b1078d4c1e4 *R/stepwiseqtl.R
3168a26d35a587dca19c02b773cca757 *R/stepwiseqtlX.R
fe7de89a9f3ca4a81bdc852955ce7ce6 *R/summary.cross.R
b6511eeac7015c115804577a875a0619 *R/summary.scanone.R
16241b8b2b15eed6fe7f52dfe7d2aa78 *R/summary.scantwo.R
818d61ec95144e85fb8a94deb2ab2954 *R/summary.scantwo.old.R
c6cd187dda5782475986d51d763ded86 *R/transformPheno.R
77a6253ca5b9b85debf4f028635e5df5 *R/tryallpositions.R
cae4f232e47d2b055e6dd3ff0e498f73 *R/util.R
e64b6eaf423c13295c752de1de751fab *R/vbscan.R
7a088a393e967649514591691eb020b4 *R/viridis.R
65c83b35fc950bab6e9b5b8abd2962bf *R/write.cross.R
42130e9a1a397f9d679376014d7fed0e *R/write.cross.mq.R
4cd5c5102341ef21634a3947631cce6d *R/write.cross.qtab.R
b6203edcc91cff5d20f3cf2b7be8897d *R/xchr.R
2d5c057032f7d1853d2a3c2d59a1fc53 *build/vignette.rds
ca81356ae44df9f4ad56ab60d7e431db *data/badorder.RData
3e1ff1c1bebb8f6d01bc1ca0537bf124 *data/bristle3.RData
ff8708f3629e86efcab073db11649a7f *data/bristleX.RData
43a515f4b903ebd478ed129c1d955b55 *data/fake.4way.RData
ad9e0fa4b423ca02088d489648bf046f *data/fake.bc.RData
62d998ca504683177d2c19505a8b8749 *data/fake.f2.RData
c596d02eb0b9846c3101e8f50384562f *data/hyper.RData
9d81c813d3dcd668f323936c153918d6 *data/listeria.RData
8c7cbe5bed1eb264e812f0c9041ea12c *data/locations.RData
74752892dcdb9c3760604d64a817f185 *data/map10.RData
f42b816ec491b33fbba0ac27fa14c2c5 *data/mapthis.RData
132a988be2b0afffd0fc0e228efef7b6 *data/multitrait.RData
c1971de49f830f2912b6c4ac41f0144e *inst/BUGS.txt
0f194c0082205db7501a8fadad5653cd *inst/CITATION
017466591ffcb476c87c085674557d01 *inst/INSTALL_ME.txt
f6bc7c5215d6f1b0c94235a5ef381e25 *inst/LICENSE.txt
c8b990e307ecee343beb5a217265ffcf *inst/MQM-TODO.txt
cacc689a7a432590f3c719987bbf41fd *inst/README.md
bc8a39083d763ba22fb115632962c9f3 *inst/STATUS.txt
6bbfe0f89c64c39473a8896a290d5d8a *inst/TODO.txt
1723dec70d7b0ed3c1c99e7b7581e948 *inst/contrib/bin/CMakeLists.txt
1e10167bc08e8c501be1ac201247af7d *inst/contrib/bin/FindRLibs.cmake
a2151c53575c7e54ceef324add76f356 *inst/contrib/bin/README
f300bcbb15db0aa41bfa87e4598ca999 *inst/contrib/bin/mqmdebugout.cpp
b7f842cec0ea8e7025a4495586ba4548 *inst/contrib/bin/mqmmain.cpp
872352d722e347e7202db6d5e7208f26 *inst/contrib/bin/regressiontests.bat
72e795393b05712e52d2dfcd013853d2 *inst/contrib/bin/rtest/regression/mqm_listeria1.rtest
1fc00c7595303eb7b28b7c22552e6a32 *inst/contrib/bin/rtest/regression/scanone_mr.rtest
725982f79fa57446b0c29485db932256 *inst/contrib/bin/rtest/test_augmentation.R
200622b9e837aa6daab95d45df5f5c80 *inst/contrib/bin/rtest/test_mqm_hyper_prob.R
ff8da1695c81b1bf1fa5ae33b55f89da *inst/contrib/bin/rtest/test_mqm_listeria1.R
277edd7b8d3d18846bcd4c83d2470fda *inst/contrib/bin/rtest/test_scanone_mr.R
106fc8e130e914c8e1921dca34e3a46f *inst/contrib/bin/scripts/cleanup.sh
cf3c3279879ff2febff55923a96ba6b8 *inst/contrib/bin/scripts/create-diff.sh
973cc58b4269e7e8301bd45983a93b78 *inst/contrib/bin/scripts/profiler.sh
32d1bc0785a5d50f78ae5756d16e9f43 *inst/contrib/bin/scripts/r.sh
f6b6a330299fdb56a874a47f577ebd08 *inst/contrib/bin/scripts/regression_tests.sh
9760ebdd5b902882af0c93ea062e5e96 *inst/contrib/bin/scripts/regression_tests_windows.bat
96a589c2fd23cc2fd5d1ad8eaf425f6e *inst/contrib/bin/test/chrid.dat
cd80cecee345e6e4a8f0f4fa565131d9 *inst/contrib/bin/test/chridhyper.txt
e476e10cab390697d56bb54e9ad6b435 *inst/contrib/bin/test/cofactors.txt
0e5803c6aa09400ba7cca13fa1d2c9dd *inst/contrib/bin/test/filledgenohyper.txt
446a8d08d0deda48af4367932016e95d *inst/contrib/bin/test/geno.dat
3ba90f4528761f630956a01e28da2d02 *inst/contrib/bin/test/genohyper.txt
48aa9dfa5117e23001cdde5d75e9c681 *inst/contrib/bin/test/markerpos.txt
58e0f70e4a38f89e0ea05200b1485f4c *inst/contrib/bin/test/markerposhyper.txt
c8fcff8988bdcad867ab1d623afa53c9 *inst/contrib/bin/test/pheno.dat
c8bad11adb4ec06926194513c745d1c8 *inst/contrib/bin/test/phenohyper.txt
c73498b52f1d78efb2a60720e8b1c48c *inst/contrib/bin/test/regression/debugout_dnorm.txt
27131c5ce714adebfdd4f986662b53a6 *inst/contrib/bin/test/regression/debugout_pbeta.txt
79cdeca0abdbc0e981163e6203a294dd *inst/contrib/bin/test/regression/t11out-test0.txt
db72cd13d6a1e2f81ff68dc4886a1910 *inst/contrib/bin/test/regression/t11out.txt
12edd0259b6630dd1281baf97b2ad7cf *inst/contrib/bin/test/regression/t12out.txt
db11ebfe1d7065970b3187888bb20311 *inst/contrib/bin/test/regression/t13out.txt
4d585be836c907068dab6809184492d0 *inst/contrib/bin/test/regression/t21out.txt
93908e9b72560c748f51fc8edda09cb9 *inst/contrib/bin/test/regression/t22out.txt
ed93df5f2be805fd389820394cf61221 *inst/contrib/bin/test/regression/t23out.txt
076f23f188360ca130a7c4cf428ef4f6 *inst/contrib/bin/test/regression/t24out.txt
421333f8f1a1a217f66601fa1d2ac8a1 *inst/contrib/bin/test/regression/t25out.txt
d3c2546698c6f1a749821630abb0a4d8 *inst/contrib/bin/test/regression/t31out.txt
fa97e5f006391c4a0dbdee6f9c8025fc *inst/contrib/bin/test/regression/t32out.txt
d8acf152a44ae6e0198b2896f4174dcc *inst/contrib/bin/test/regression/t33out.txt
be52b633c566c82bffd9eca8ea0c20c5 *inst/contrib/bin/test/regression/t34out.txt
f43319ef224ad76487b64c22b01a6625 *inst/contrib/bin/test/settings.dat
e03f233c8e59be66d7f013a8db976f58 *inst/contrib/bin/test/settingshyper.txt
446a8d08d0deda48af4367932016e95d *inst/contrib/bin/test/std/genotypes1.txt
fdfed5a596dfe2cfc1c51ef4dbd06b7a *inst/contrib/bin/test/std/genotypes2.txt
3ba90f4528761f630956a01e28da2d02 *inst/contrib/bin/test/std/genotypes2m.txt
2bbf9cf9386f4a96908017107406fcd1 *inst/contrib/bin/test/std/genotypes3.txt
d9c37b331ff43e122bf6443188b3826a *inst/contrib/bin/test/std/genotypes3m.txt
48aa9dfa5117e23001cdde5d75e9c681 *inst/contrib/bin/test/std/markers1.txt
aaadb868ebb6041f45461a184900e31a *inst/contrib/bin/test/std/markers2.txt
73f35c4f2740b77be7c56adf7c33616d *inst/contrib/bin/test/std/markers3.txt
c8fcff8988bdcad867ab1d623afa53c9 *inst/contrib/bin/test/std/phenotypes1.txt
c8bad11adb4ec06926194513c745d1c8 *inst/contrib/bin/test/std/phenotypes2.txt
2411a1ba80fdd818d57ab6baad428651 *inst/contrib/bin/test/std/phenotypes3.txt
9a49e2d18c04c38baa91c18c08095c12 *inst/contrib/bin/test/std/settings1.txt
d552fec023d3136c84922f940a26d75e *inst/contrib/bin/test/std/settings2.txt
88fc63b4af80b742e159b3d2cbec8b60 *inst/contrib/bin/test/std/settings3.txt
c13ea1fd1dbd3322aa0773bb2712d6ab *inst/contrib/bin/test/t11/cofactors.txt
63810466f0b74772939995cff28dbc73 *inst/contrib/bin/test/t12/cofactors.txt
87726298c97c135ec4caaa1d77c4c3d0 *inst/contrib/bin/test/t22/cofactors.txt
9ba0cb2dbebbf849508443e305ad22f8 *inst/contrib/bin/test/t23/cofactors.txt
aa492705f6ef171b31d4b95208da2279 *inst/contrib/bin/test/t33/cofactors.txt
4b9c827a80e2681861dc2d41baa7212c *inst/contrib/bin/wincompile.bat
4b07a887cd026fadbcd9f986054f3236 *inst/contrib/biolib/CMakeLists.txt
d89ef8ce1e7a097fb859b6f0463a28ee *inst/contrib/biolib/README
73c7b09cfe6ae19cc28961e64ee7d8fd *inst/contrib/scripts/check_rqtl.sh
f605130493a82e5e91911de5b6b8b6c1 *inst/contrib/scripts/cleanup.sh
2b3f7306cdc6fb6add972d40a09d7028 *inst/contrib/scripts/install_rqtl.sh
83c1e2ea3cdf1ff0f886eb96b5c4d5e2 *inst/contrib/scripts/repl_inputs.rb
6e30a9820a443a31db0538cf07c06531 *inst/contrib/scripts/run_all_tests.sh
241ab5cd315e17513c395de2703aeec3 *inst/contrib/scripts/update_header.rb
222dabdc319e0d984f27cd86347c1402 *inst/doc/Sources/MQM/MQM-tour.Rnw
33c6a39f98c9f6ea383bb7e6120c80d6 *inst/doc/Sources/MQM/SweaveIt.R
8b9c03961a1f83a3593dd2c4f424f0ee *inst/doc/Sources/MQM/mqm/advantages_Rd.txt
9ae2c3be23d6b18713df99dea771bc74 *inst/doc/Sources/MQM/mqm/advantages_latex.txt
e5963995b8306a5709edb4a82d312737 *inst/doc/Sources/MQM/mqm/description.txt
93182cf669598c167d49a863b29e1c44 *inst/doc/Sources/MQM/mqm/limitations.txt
fe67beb7507899b848f71b812c71fd44 *inst/doc/Sources/MQM/mqm/parallelisation_references.txt
33c48149918dc1bb67bc4dc32941d1d3 *inst/doc/Sources/MQM/mqm/significance_references.txt
cbec485f87463463f5920867f8f7852b *inst/doc/Sources/MQM/mqm/standard_example.txt
00c8d3ee12a9126fd90c00fb8236d0d4 *inst/doc/Sources/MQM/mqm/standard_references.txt
f9cbb0876fe653fc8119fbfb7f35456d *inst/doc/Sources/MQM/mqm/standard_seealso.txt
dce125c0ba08d0504b05baf36296dc94 *inst/doc/Sources/MQM/sweaveit.bat
b069721f290cbd45cc9a1d4a13c93603 *inst/doc/Sources/MQM/sweaveit.sh
0242414e7ce8a4de69f373b05e7f8049 *inst/doc/Sources/geneticmaps.Rnw
380f79ca75c5ac3187513d674862dac8 *inst/doc/Sources/new_multiqtl.Rnw
7743409fb09a35b80fb22da863cbea8b *inst/doc/Sources/new_summary_scanone.Rnw
2d06706e91525e0e8f56ca2b2f025636 *inst/doc/Sources/new_summary_scantwo.Rnw
f5078ec60c48d7e3a0239c294eb05b94 *inst/doc/Sources/rqtltour.tex
c42f67bc3a255b66451f4c6053f11038 *inst/doc/Sources/rqtltour2.tex
ef706b931ed81b855a49469602f79a9f *inst/doc/bcsft.R
57abd7654f2032e9b7f6f1c133dabff6 *inst/doc/bcsft.Rnw
a4b34da18627124461d4581a3ee74b14 *inst/doc/bcsft.pdf
92b2c2c03224914617a19bc3ac02b7e4 *inst/doc/geneticmaps.R
536f8a7a96f10fc7c622a64165587051 *inst/doc/geneticmaps.pdf
40eb8179441ce7496f6c5e252c8b2b56 *inst/doc/new_multiqtl.R
2bfd394e7e6556f6f7043e9034c64234 *inst/doc/new_multiqtl.pdf
b7ee88c6b1ce5df40209c9bd58acf9b8 *inst/doc/new_summary_scanone.R
1e49e4956c20a4fb3554633734be1bbb *inst/doc/new_summary_scanone.pdf
a808a0dcf90e74a422bf3ea84f4bd55b *inst/doc/new_summary_scantwo.R
83dbe80c9f5b641b0b269be341c80df2 *inst/doc/new_summary_scantwo.pdf
5de0f099578b884016db92738d3f2dc3 *inst/doc/rqtltour.R
adda75ad8441d94dac4b49d60b6d82af *inst/doc/rqtltour.pdf
f8569d240e7f00630b002306f6af77a3 *inst/doc/rqtltour2.R
0851169416f3b84ebc829da7fd3b294e *inst/doc/rqtltour2.pdf
1b42a662f601adaa9660800eefa4e42f *inst/sampledata/README.txt
f6a9eebc3f37d26e0a5b8ed672354712 *inst/sampledata/gen.txt
9198bd35e7a221556c5e2008d00cf84c *inst/sampledata/listeria.csv
846a80e9b730dc4a5144437d1563f0a0 *inst/sampledata/listeria.qtx
e064a29e8b8199c38b094b9c8170b434 *inst/sampledata/listeria_gen.csv
2dcca54c31a1e372c6da15881636d2c4 *inst/sampledata/listeria_gen_rot.csv
01b987cb739560eafac3cf41ec0c6154 *inst/sampledata/listeria_map.txt
3bc93e86db600b2f263a1a197269e8de *inst/sampledata/listeria_maps.txt
9bc5c1daf65145ed51a7acf1c30e6146 *inst/sampledata/listeria_phe.csv
216700811ae74ee1d581d7cff9504f05 *inst/sampledata/listeria_phe_rot.csv
3efd61cac8e5cdbba21f04c0d5a56adc *inst/sampledata/listeria_qc_cro.txt
a857de8b79fd03837008a0d750dfad9c *inst/sampledata/listeria_qc_map.txt
8520b0234e8d59152126248b0cfa7566 *inst/sampledata/listeria_raw.txt
af7100ff129f117e5d3b67cd10a76f63 *inst/sampledata/listeria_rot.csv
dde45251d41488fedc3693dc67fc9429 *inst/sampledata/map.txt
ffecb0696dd5873a13e48157180271fa *inst/sampledata/phe.txt
e28aefee34bbe9f7bcab4a7a98c3bfa7 *man/MQM.Rd
13dee7325ca09ddd8e37d89a1bc18afb *man/a.starting.point.Rd
35f5486b6591f87b2d9ea77bfda5a51a *man/add.cim.covar.Rd
d2e90efd2232b98e31c1284a698726ab *man/add.threshold.Rd
4d74d20e6ae9fcd63a066859c209589a *man/addcovarint.Rd
ff2fd1f92af37e48b99a24eb718bbbc2 *man/addint.Rd
da3c0761b93d760d9c09d206242938d5 *man/addloctocross.Rd
f8bb33f845e52c9010f1e3eef17ed5bc *man/addmarker.Rd
4889660feda30faa7f9ea8aaf9ccfd1a *man/addpair.Rd
179c9aab47de193b9ce22fc9592266da *man/addqtl.Rd
52c90f99736bf48422c12f4707b09453 *man/addtoqtl.Rd
96d8b82b0ff834e4ca13e4f01bd79e01 *man/allchrsplits.Rd
f0eeacdbf7046f00d464125dadfc622a *man/argmax.geno.Rd
f8f258258899079b057d0a7fc5b0c44c *man/arithscan.Rd
823a6ccd95bf7f05212dafb54b450c0e *man/arithscanperm.Rd
30f3db3b537bbaf41f3a73bd5a04c5b8 *man/badorder.Rd
c05a603d58f71e605a2be559d7f20326 *man/bayesint.Rd
5a6bd367ecb7e3819c4371eba2b1e24c *man/bristle3.Rd
855ab1a83ad2a10c468c0da3d7672cf6 *man/bristleX.Rd
5c3ac5e812fb044fa04d6fe3be485eaf *man/c.cross.Rd
b7dbf460ff78ac5f377dbd7420e3fd28 *man/c.scanone.Rd
bf9ba0415703542965541ec32dfff26d *man/c.scanoneperm.Rd
27cbb0f6b73e0ac69662c5515192558a *man/c.scantwo.Rd
bc4e41ebc6ece9aea79e90a63c5083e5 *man/c.scantwoperm.Rd
4f5b5505a967b2d05b468eca7adec88d *man/calc.errorlod.Rd
753f7897ca580afd39d6722de7508081 *man/calc.genoprob.Rd
ae9c5060e4a3782572c32059d8d09ab1 *man/calc.penalties.Rd
d7414ce5dd7a7e1b0ab1340d8daea79a *man/cbind.scanoneperm.Rd
79ede64d1f26e0dfad7b3683e881923f *man/cbind.scantwoperm.Rd
fa7811f6e2a3ea43c2c52372537b3359 *man/checkAlleles.Rd
0b0383cdfa8aafc01f468f01df3a77af *man/chrlen.Rd
dd04999fb8c1a1492ccd255c6ca42a0b *man/chrnames.Rd
4e1da1b4b0eaa62a9e391a19bf50d472 *man/cim.Rd
965e4191289176633c68f1896a787614 *man/clean.cross.Rd
314dd49f51800915c6e03c373fd8ddf5 *man/clean.scantwo.Rd
033576e8f94473e04eb68a332a18a3ff *man/cleanGeno.Rd
2128b8f0a5de896b54ee47c78985d0c0 *man/comparecrosses.Rd
b8ec2afa6848f427bc454d4f51fa55d3 *man/comparegeno.Rd
0c7fe2e49f2d804935c5b15a07071c35 *man/compareorder.Rd
a76b0870df7f07c85c4015471be1bd6a *man/condense.scantwo.Rd
3c3e7b1ca7d08e8943318061f4eabfa8 *man/convert.map.Rd
6729d8a8a9af709664ba2ef6ca692378 *man/convert.scanone.Rd
a608c4fabf93f0c83aacdb9a647106c7 *man/convert.scantwo.Rd
88182a7fccbf7ff9bc96d1757ba58f71 *man/convert2riself.Rd
7ed7202393cdcba8ca5644f201098324 *man/convert2risib.Rd
9491ebf0f68acfe316906a5f239a0dbb *man/convert2sa.Rd
545f7dc6a54e0eeef2304068855b527e *man/countXO.Rd
f832e0b2036a5ac3e9ba4c1f929648f2 *man/drop.dupmarkers.Rd
4fa21dcb96c8e726a4bf3085561cceb1 *man/drop.markers.Rd
bec228fb22603e98b0da1c3cb6cc5b13 *man/drop.nullmarkers.Rd
49bf176801a1e2ced5bc9006dc9d39ad *man/dropfromqtl.Rd
096b6783c4f40d7a649a95f09213773a *man/droponemarker.Rd
0f95d84870702ba6ff0a267fd6e1b6a4 *man/effectplot.Rd
72ad6631eb6f7f3b49cc358d16d13e60 *man/effectscan.Rd
48b8f9155853cd335c70824b792755de *man/est.map.Rd
30426606764afdf9c6b994169ec7f818 *man/est.rf.Rd
3a51043591f7470220e36f49b71057b6 *man/fake.4way.Rd
fd1ed904f2c329da778c11a6590a7fb8 *man/fake.bc.Rd
634a140c7d495289d0b3f590d9d62a25 *man/fake.f2.Rd
c95abdbc45ccee18abdc324465f7bfaf *man/fill.geno.Rd
a63955ea854d8dcec0fa40c881663df3 *man/find.flanking.Rd
dedcc44afba05ac2793e996d60eec001 *man/find.marker.Rd
730c2da7401d6644cc4530a92e3b1da4 *man/find.markerpos.Rd
49955f3579cb744042744f6f20935dfc *man/find.pheno.Rd
d1a4fd9eb327246e8e90ba1b419b47ea *man/find.pseudomarker.Rd
ae0356bc440221337090d7d54aa46ef3 *man/findDupMarkers.Rd
611ce128c758de04eb623bc25bf5ba8f *man/findmarkerindex.Rd
529ac4ecd3ccf228a369bbd56a419c3f *man/fitqtl.Rd
302fcbaf134900dbfa2e1d43d92bb1cc *man/fitstahl.Rd
dec5b2867d3fd5270a31f678d640a36f *man/flip.order.Rd
e7ea8ff0aa2114b13d37a11360f94711 *man/formLinkageGroups.Rd
3c055c67611fff85ed39c609d11acd3f *man/formMarkerCovar.Rd
23ffb71427bbd60bd559ef5e8d7cab9a *man/geno.crosstab.Rd
90d40996ff796ed0d2b4c471494f2766 *man/geno.image.Rd
0f9e23340c941f97417f339dacf149dd *man/geno.table.Rd
8f254e0ea0ab55203f95f3dcb999c498 *man/getid.Rd
35d5419ffe33622f630090538d74b1a0 *man/groupclusteredheatmap.Rd
ec30468e804cce77bd2bb82a29724ab1 *man/hyper.Rd
4d5b3a7be2e806becb67e8ae8bd08e3a *man/inferFounderHap.Rd
db798f1159ff8a132008ebb142156a8f *man/inferredpartitions.Rd
1b0fa91082beb9a1b5e9dbd839111303 *man/interpPositions.Rd
15b866f052e23a1e6957536e5e6b18a8 *man/jittermap.Rd
591e40dfba5b2b4695aef2454b229c30 *man/listeria.Rd
d408c850a4a8575fee1fe89173659add *man/locateXO.Rd
28fcd1d0d872f90317ed511fe3cec877 *man/locations.Rd
6f87935e11c8cd26bed12e6d82a59cef *man/lodint.Rd
87981e632b4dff4ea12e05ffe6e35328 *man/makeqtl.Rd
707162a8af63aaeadd5cbeb03758bce6 *man/map10.Rd
4b5aef67ad8189ce5672437c293c3816 *man/map2table.Rd
e10ec2b321490c68a5004f06f9e772b6 *man/mapthis.Rd
7697ffd6cd4a83ae9a53a8f058b5953f *man/markerlrt.Rd
5d8d9ab636f919d2bd32f091f4a20d1e *man/markernames.Rd
fd3bcd3ed4dcfd2676f96f34c5e1c0e2 *man/max.scanPhyloQTL.Rd
40816a53472adc3b1f3defcc9e07a341 *man/max.scanone.Rd
d2a725c2fbe1a7ac50165a2bfc604afc *man/max.scantwo.Rd
e472d11285bd6ec39c2821557ebae43c *man/movemarker.Rd
1a6fda85f9931a9209ae611a4ae28898 *man/mqmaugment.Rd
fc86d572c1aae0b1382a3935d7715cce *man/mqmautocofactors.Rd
c3d19df99c7e54b9b4c757a2c9c0f05d *man/mqmextractmarkers.Rd
549262647087b0cb5aa8c366c8144739 *man/mqmfind.marker.Rd
49f5372ad8941b0e59746d4c3c64fd0b *man/mqmgetmodel.Rd
8bc5875e319e9cf8c8cd859e802f0c14 *man/mqmpermutation.Rd
edc3bf4e86c585e36f70621e5f02981b *man/mqmplotcircle.Rd
ddaf04ccfb9cea1b710822087e757ef7 *man/mqmplotcistrans.Rd
f074b74d7a22d1ad605464183c36f3e1 *man/mqmplotclusteredheatmap.Rd
15fcc6b971efe162a0d23a9c8e5f6d17 *man/mqmplotcofactors.Rd
6f88c8a538364224f624e4858a66bcdb *man/mqmplotdirectedqtl.Rd
3477b2d0fafaa11eeaa4fcdacc59b22d *man/mqmplotheatmap.Rd
4772e61d64750b1625ad6047d99c5d87 *man/mqmplotmultitrait.Rd
2e11138ccf13e2e30b2e2e71704eedc0 *man/mqmplotpermutations.Rd
f473d29e0c7b5be53966081fbd9369d6 *man/mqmplotsingletrait.Rd
a54ba4b376dc43dbe8711928f6734260 *man/mqmprocesspermutation.Rd
9e48186ffe98f298079c1485c738b5d7 *man/mqmscan.Rd
60204739e43579ae66783bbae9cb47d1 *man/mqmscanall.Rd
71e7c5a8b92a275016e5e802d455eb72 *man/mqmscanfdr.Rd
7718828d7dbb098fc6e94aef73b56835 *man/mqmsetcofactors.Rd
33a3c545e26399523fd38dd7c5ca1f65 *man/mqmtestnormal.Rd
f906cbec37e3ba36ef464499b41e8422 *man/multitrait.Rd
1250f3b4d0b959510cecaf188c0234aa *man/nchr.Rd
1f7deb0f335935f8a4903b298edf7aa1 *man/nind.Rd
d7770a39dcf5be6b3e722d0cda3d7161 *man/nmar.Rd
a3f370a50ce51354ed70049efb6b75d8 *man/nmissing.Rd
5266a15e69ebd96baaadf5395c7d90e6 *man/nphe.Rd
23dbd4ad8b077eba041896d789eec3f1 *man/nqrank.Rd
5f85b627a0743efaaedae7869528368e *man/nqtl.Rd
cea48ea2bac2ef7ae958aee4c6bbcc63 *man/ntyped.Rd
2787aad2cd5805355ce8bf536e37101c *man/nullmarkers.Rd
7e9ee9cd88a6b991c36196c34f1266d4 *man/orderMarkers.Rd
d731a816a7155e452898fe368c154cd4 *man/phenames.Rd
7d153472d3f0b39902540818fd6259d6 *man/pickMarkerSubset.Rd
cb197bdd16e3f28691fdc5c1358f9015 *man/plot.cross.Rd
994b19074d0b3929fc8ab9bc0d25b293 *man/plot.errorlod.Rd
48ab6edd2385ef8ed884901f1bd762e8 *man/plot.geno.Rd
01cc22cfff089a2a0c553d1b16a4d840 *man/plot.info.Rd
0f68a66e04a875900b55dba660fcf542 *man/plot.map.Rd
2e031824784ceca91597e58ffdfaf627 *man/plot.missing.Rd
a71480644300e56eb625814ade95a287 *man/plot.pheno.Rd
e55ab29cf8704b63eade10fd43ffac71 *man/plot.pxg.Rd
1df7291ccd09f7a0501514d8132b71aa *man/plot.qtl.Rd
ddfe34bb6d241d4f26a48b21c08b85fb *man/plot.rf.Rd
989c6b19d38a7f66a02d770c9e0e96c0 *man/plot.rfmatrix.Rd
ef07e985c0d0d52417eefc61ab65e2e3 *man/plot.scanPhyloQTL.Rd
003eb7e99701deb77ad3c3e9277baced *man/plot.scanone.Rd
514eb55d45edabe3f4a5ac9afcb70183 *man/plot.scanoneboot.Rd
eecd8b28366d39db5ed9fbf2c54afbb3 *man/plot.scanoneperm.Rd
c26b6da5bbca9e41e95f287e0f8314ce *man/plot.scantwo.Rd
b1cb100bd9c39ad14becde0129d339e7 *man/plot.scantwoperm.Rd
157c38fba72646bc68da0fb7d39f42ae *man/plotLodProfile.Rd
ae9d1e5f8089025fd2f7fff53268bc1e *man/plotModel.Rd
0543c43796b17159edb33be7b8c6f3e4 *man/pull.argmaxgeno.Rd
bc14f54020bdab5bad02784231c2f344 *man/pull.draws.Rd
692c95014f0257563bf5df5c2495a6e8 *man/pull.geno.Rd
84b743649313f13717838bc9b093013c *man/pull.genoprob.Rd
f13ad708b90326fa3c1eebc7445d72ee *man/pull.map.Rd
6048a4b528b7603475b886c7f0c49d69 *man/pull.markers.Rd
5113351810c28a3637e00e814de48c0c *man/pull.pheno.Rd
3183e45d039cc313e2cfcea1d492add8 *man/pull.rf.Rd
21490ed5a78328d20d4e1cc41c54b174 *man/qtl-internal.Rd
db0b934b4f846b2c203a6b26dd2c48f3 *man/qtlversion.Rd
ba6e4f476377b13d26f438ff0638a058 *man/read.cross.Rd
5a2497ba2057f18ba19fb1a51c15c9b2 *man/readMWril.Rd
e2ee64437825706ee747842f4bb88ffd *man/reduce2grid.Rd
a098c7308d2e957c109c4d6f3f9ae442 *man/refineqtl.Rd
51c75e5ed191274d3ed2294b194e4172 *man/reorderqtl.Rd
47b63dd66eda40e390df04405ffb2c92 *man/replace.map.Rd
36befb99381afe13818c8dd69122977b *man/replacemap.scanone.Rd
d7e3e91dd1299a6faffff29ad70031b9 *man/replacemap.scantwo.Rd
105f4d13c5aad3f9d4977507a6b7933a *man/replaceqtl.Rd
6b5b678c5d4fc417db81510d90ae37e7 *man/rescalemap.Rd
737a8328c90835ab13519d4aca2057a8 *man/ripple.Rd
7b557cde314fb3107ffa098c139db958 *man/scanPhyloQTL.Rd
0db6ac6f1177de6ea2ee30e57ccd87a3 *man/scanone.Rd
6d8a4c31fd7a4a20d2b1a570e0bd39fa *man/scanoneboot.Rd
46750e291fdd6ae237fcce3adb8114f4 *man/scanonevar.Rd
86a9e135fbce03b0ed9ffb7e2a95598d *man/scanonevar.meanperm.Rd
d4ddd7c34bcfa7ceaa0a7e6b257b3093 *man/scanonevar.varperm.Rd
95de1f7101b85b13111ca3cbc6747a08 *man/scanqtl.Rd
3484c193c9b70ee7f6f2ea4979b465ca *man/scantwo.Rd
046dc61d32ef8ab0897eff8f030b766b *man/scantwopermhk.Rd
97253b279907c72f0806d69339e3a0c9 *man/shiftmap.Rd
1c3ad4314becf31fe9b50003762f0a34 *man/sim.cross.Rd
da4f2cafb2ef00c38c72908d49f0d2ce *man/sim.geno.Rd
86d7f4dfb00c493e0e6c06f6a03e73c4 *man/sim.map.Rd
7076ca41f367f5089e8fd2043fc0afa0 *man/simFounderSnps.Rd
c0227cffd6e0f6af790c395ba923cf72 *man/simPhyloQTL.Rd
eae422e3cc12d4f01130194ed0eb1b29 *man/simulateMissingData.Rd
887b0341c2c9d9e45441d417b564288a *man/stepwiseqtl.Rd
2ea9dbf54e03ecee46765d181e0494ac *man/strip.partials.Rd
249f701db93bc27a863a1bb5996a23c8 *man/subset.cross.Rd
52d642e21fba23c3ad09347dcfb65c92 *man/subset.map.Rd
be43cfcde4af6f45c4620f3f2d1a455c *man/subset.scanone.Rd
ec249ad881ccebe98d817d7f54a7cdee *man/subset.scanoneperm.Rd
1e6227167548140d0eac6c95c5ecf52b *man/subset.scantwo.Rd
555ab94673699b4d802e19c713463dc6 *man/subset.scantwoperm.Rd
3d81a55200fee6b31f74af52b8420415 *man/summary.cross.Rd
52e1d49af936dd0c3b3921836a48f172 *man/summary.fitqtl.Rd
2a79d456338bb56e827e1cae5ecf936c *man/summary.map.Rd
d483f74ce3805574351782e4e0827e0b *man/summary.qtl.Rd
6f29cee661307bbac418766a2273bade *man/summary.ripple.Rd
62ddf80972b9b0b4124dc741b662b1b3 *man/summary.scanPhyloQTL.Rd
5f21c6807b454d1f38f5f38a73fa7bb1 *man/summary.scanone.Rd
96b033ce0694537cb0b5944483af7371 *man/summary.scanoneboot.Rd
4c9d606d678e37bfd2d70f9d581a9575 *man/summary.scanoneperm.Rd
b089553c521afdffe6213ca4f047fbd2 *man/summary.scantwo.Rd
6d59cdc921ce88fb1445bd8badf57ce7 *man/summary.scantwo.old.Rd
da4e6274538218bd293fdf66de48447f *man/summary.scantwoperm.Rd
7691ba8e775d5b4a48677009ed5afbed *man/switch.order.Rd
2e1dcf2360fc2ecbd5ecb5bf70a37a5c *man/switchAlleles.Rd
0891d4ca36eed821f72c8e03b02318eb *man/table2map.Rd
94a14cf7cd376c60681c3359ceb360d9 *man/top.errorlod.Rd
36d8f8c057c6b78499f86d463530838d *man/totmar.Rd
d5ac1ab65a99180a8d096037e6de95a7 *man/transformPheno.Rd
834347327b0a2d242a809f733ecb628b *man/tryallpositions.Rd
2f126e6ba3135e2a792085abf3d3c1c4 *man/typingGap.Rd
f88f8c6bd5ad8783a449e58704511ad9 *man/write.cross.Rd
cd3811e5bbfede40915d15ef3c55c736 *man/xaxisloc.scanone.Rd
7ab4aae0ebff42ce151372d97076416b *src/Makevars
319b18d237a724442c3334904852dfe5 *src/countXO.c
0aaed39a89c578647ff5256798d34204 *src/countXO.h
3fad63f8624d0fff754b775b69a44e62 *src/discan.c
cc1b8f0530ac6a6a2de49e5d25c47a70 *src/discan.h
64d3c7c88d2e84d8b28cc7bb7f9cb4b1 *src/discan_covar.c
7a790e059f8772ab03a69bbe2023100a *src/discan_covar.h
aca6bdc300f2b2bf8198c0a2ae5e2dca *src/effectscan.c
cec64a0383167ff081d6e5701fea37b9 *src/effectscan.h
91d0c646d29cfcdab1a35348ae688992 *src/fill_geno_nodblXO.c
5625aff805e480b0e7e5f12d7e8e35ff *src/fill_geno_nodblXO.h
1384f52a5e0fb23e3acdf59b17c416f7 *src/findDupMarkers_notexact.c
f281b01dcdce998db1e98908434e39cc *src/findDupMarkers_notexact.h
b0202319434ce7626d2d0662f072bbbc *src/fitqtl_hk.c
b3a4c6d373aac7e2cb055d56eb1befe7 *src/fitqtl_hk.h
4ad3aec8942563fd468fb3d8c0d85073 *src/fitqtl_hk_binary.c
5a5583104fb9af02041cdce3dec1dbd4 *src/fitqtl_hk_binary.h
e57fb133b5bbbf2a069e5967de5aeb7d *src/fitqtl_imp.c
6e369cbfbabd9a03d9b6c850c8368a40 *src/fitqtl_imp.h
990b602d638a54b6862e81d6db056aea *src/fitqtl_imp_binary.c
61e33070becd0b0cc34ce889250411ea *src/fitqtl_imp_binary.h
6b2f1d3bef55da72ddfe79cb3c6676fd *src/forwsel.c
aeede8a526c90a31513b03cf0b448e05 *src/forwsel.h
d3c217604a4a00a3074586ba7f3ebe40 *src/hmm_4way.c
2b0f1a76866d26663c24769e1e954208 *src/hmm_4way.h
731dbb6ac7d0ed1e9a2f4fef8047378a *src/hmm_bc.c
35305b4c312e94017d4e17a442e8ccf2 *src/hmm_bc.h
00647550d42958c47ed1cba144e51b81 *src/hmm_bci.c
9aad7974310927edb683ffc74becc216 *src/hmm_bci.h
dcb2ef85dd230d6d67252afebd9b9bb5 *src/hmm_bcsft.c
586859fd1f2bef5de18a825408d4273f *src/hmm_bcsft.h
58c6438039bfac2e332d867b92ae19e4 *src/hmm_bgmagic16.c
fc076c938068c339fe801f21fcab28f0 *src/hmm_bgmagic16.h
8607a7be83100dcd4fdd18e107721250 *src/hmm_f2.c
1221cca1b8a6a4ceefd715d7df6ce201 *src/hmm_f2.h
d5019756dc94596be218b7487983d712 *src/hmm_f2i.c
e5309233b7c5b622d44b0c50504a48c4 *src/hmm_f2i.h
6fd9b4300853f5d95a87a4bdeb71f135 *src/hmm_main.c
f1e074aad662aadca914fbc915b271c0 *src/hmm_main.h
7088a28c5d0677be0e960aa9e479af71 *src/hmm_ri4self.c
01171347006c54a49b0921bd4ea38422 *src/hmm_ri4self.h
b9981e0b11b8d4d469f4d2a2db5135c5 *src/hmm_ri4sib.c
54cdb43072337802951153e2d71e34a9 *src/hmm_ri4sib.h
b64b3dd87e24d301fe728dd0bbe5e342 *src/hmm_ri8self.c
c263e8d924b0d8b664fe565aee36df61 *src/hmm_ri8self.h
808821770dc9ac74e4a7dcc6bc1533de *src/hmm_ri8selfIRIP1.c
fe21e658eba8b9e8c491f014e89f0e2e *src/hmm_ri8selfIRIP1.h
e92ec6ea2bd7065c3dad9b75944222f5 *src/hmm_ri8sib.c
29137637a726e5a9562fcec338d8d4d9 *src/hmm_ri8sib.h
0e19aa23ea9d9ca32d3edf6df4d1c076 *src/hmm_util.c
9e5a387e330e1f4ed21df0ddbec303ef *src/hmm_util.h
b8c72e28cccd0a51e7c6675c15ae0a71 *src/inferFounderHap.c
c8febdc02d9cf116c7df6dac19943c88 *src/inferFounderHap.h
dcc492e6edf2d1029027605ddfd942e7 *src/info.c
9bf82156882dcb0303db6607335a9a17 *src/info.h
89ae76ebd36bdda1b9df5ccc17602c23 *src/lapackutil.c
37a9ebf0cdd07c045cbaeaa11f5cd428 *src/lapackutil.h
1f42b2427d1613ddbce94cf7a656b9ec *src/markerlrt.c
5f0df67e4b39c52fe4aadd5802df643a *src/markerlrt.h
9d3e63b807fb15214d57619006428f97 *src/mqm.h
b7b770c95a2af23844e6bb2d35241844 *src/mqmaugment.cpp
df157c58617019f3d9f2d4b995b8f7fb *src/mqmaugment.h
912fe0f529b5d1178eb8c3b53e776c37 *src/mqmdatatypes.cpp
f38b0f763b801a709d43ae42cb816e0e *src/mqmdatatypes.h
46cd444ada9ac8e44913a38e52b6e291 *src/mqmeliminate.cpp
2721bb3d7aeb7c5f4a0e96ca2de9530a *src/mqmeliminate.h
f491290c98972e63185b78da67b6b6dc *src/mqmmapqtl.cpp
5d6045082bf3dde6c6f5b5e5655fa3e1 *src/mqmmapqtl.h
6ff098870e76f8f7118436a7fc69a800 *src/mqmmixture.cpp
660298dff42fb7ee76552284475a7bb0 *src/mqmmixture.h
68cf7bbc09634a621b1b4f16306a6314 *src/mqmprob.cpp
70ff1060b83ff81c9327d77cb081bcc1 *src/mqmprob.h
84034b2850a15615b4b93f9960b2a068 *src/mqmregression.cpp
fef48f3073b3506c18dc44ac4e1263a7 *src/mqmregression.h
cd6d54dcec747fe0acd6c518a9a110e1 *src/mqmscan.cpp
f8565e0a549327219c4559ac3f97bf4d *src/mqmscan.h
4f3afa08828319520586ae7c0b295214 *src/pickMarkerSubset.c
b2bf753d87d65b70d88d1528421a4684 *src/pickMarkerSubset.h
9ca3c047852d2fdf009e68b56b92db95 *src/ril48_reorg.c
377509d7abdd7d9eab4b0505bb2fb72e *src/ril48_reorg.h
6da2bdf6ade8a3a6358fef0da9d7688d *src/ripple.c
22db7e365242906fe31b3667efb84016 *src/ripple.h
e380afa8990e1862f1bf1df6e0dcd6f7 *src/scanone_ehk.c
d5144ae6975330943a6ccf0d3d41319a *src/scanone_ehk.h
67796aa99da02923b7c396b59d5d98ee *src/scanone_em.c
b7dd97063f4b5163af749dad5e9937bc *src/scanone_em.h
3acaf81cf19b770b9f505677f493a545 *src/scanone_em_covar.c
677a6dbf438e2c5f43dcd4c4a4954aa4 *src/scanone_em_covar.h
0a92bf28565ff95ee34259ef29902da1 *src/scanone_hk.c
199dc17d39571c2e16074ed0d2533b0c *src/scanone_hk.h
27427ca1dda02302d9dae1f0cbbef9f5 *src/scanone_hk_binary.c
edd445fd769727396f32948cdb28394b *src/scanone_hk_binary.h
71d4db93c6c9343d2fe309f2c52e40e1 *src/scanone_imp.c
e03c1dac827d923d9ccb9e4c35a03c36 *src/scanone_imp.h
8a8e36005320aeb5798616b63d92ce39 *src/scanone_mr.c
9f53ddc3abba546032b0ec776043ecdc *src/scanone_mr.h
ef892e748503c1673ffcf9312418bc6a *src/scanone_np.c
70e4d4ddd4b464f1e8e9b4746d1ef84f *src/scanone_np.h
c35d7b106b21c37c25dc525dd1b3eff3 *src/scantwo_binary_em.c
99f75bf750810a1d9675472350e4e337 *src/scantwo_binary_em.h
fc4d6cdba8ebd23789753908dab4c65b *src/scantwo_binary_hk.c
4325c03bfc26e9ac9b44c8a80d0c752e *src/scantwo_binary_hk.h
d23daf183d219eb71572d306e89d4f32 *src/scantwo_em.c
9675a6e459347d31d8f3c2a40de897e0 *src/scantwo_em.h
b48aae5ddd42e9887f4bdc7f7efb2696 *src/scantwo_hk.c
8d8409d693d71d0eb7a137fc0148fd5b *src/scantwo_hk.h
234067e64224e57f60ff1f463dfe8d8d *src/scantwo_imp.c
df8e6d778ecd56f848f06605ae5b9bd7 *src/scantwo_imp.h
70e68462f1d7a842f6b06445fb0da5ef *src/scantwo_mr.c
e289941b41e4161284ce41dac283b403 *src/scantwo_mr.h
13273cf1c3e3847c0c2c7259d27b98a3 *src/scantwopermhk.c
e338a984de734d8b9fd86587229406b3 *src/scantwopermhk.h
63a88f1a3b95faf4a80d4215062146c9 *src/simulate.c
bb44570826471e08309fb3fa2c78ee50 *src/simulate.h
75f48d92a286467a586cd3a9944346bd *src/simulate_ril.c
7434d4c941867daffff66c223b29ca91 *src/simulate_ril.h
27ba698367ab29159e2feb19845dffe9 *src/stahl_mf.c
1c63a6419e9adb623cf0b9e8bf66e262 *src/stahl_mf.h
5a9fbf593d1289f13b8b0d3ffb1662ca *src/standalone.h
009203746e8805eb38f82fee79cd0518 *src/summary_scantwo.c
645229bb47522e6c198dd10c603c25d1 *src/summary_scantwo.h
845c5433a9eb7bbc01a92ba395fc6c32 *src/test_bcsft.c
20f614249abb950043782428b4b7ea53 *src/util.c
2f1ec5d9767dcf33686c37f27cd3a05b *src/util.h
a752e137e6514c25709667e8dc3d1af5 *src/vbscan.c
5fb15aa5b6d413aa8d80d1fdefbc86d5 *src/vbscan.h
901123a6adf78206e4f530065d0bbf7a *src/zeroin.c
f4c317d3e5c2af5405243e66b5ed354a *src/zeroin.h
f6a9eebc3f37d26e0a5b8ed672354712 *tests/gen.txt
9198bd35e7a221556c5e2008d00cf84c *tests/listeria.csv
d04dd9a92564d4c9f61dc86df6a861ca *tests/listeria.map
8520b0234e8d59152126248b0cfa7566 *tests/listeria.raw
a47368f05bf5a91580550b1d2c2f4bc5 *tests/listeria2.csv
1d9a688bc52515830ad0664ce1d4a0e5 *tests/listeria2.map
a753f49fb90ca63e0a0adce9bdb3161f *tests/map.txt
ffecb0696dd5873a13e48157180271fa *tests/phe.txt
054e7cc55d89114c4fb69d3b425c1c01 *tests/test_io.R
5b9d04dda3ed56e163694b2de7e8a4dd *tests/test_io.Rout.save
b0ecd2f5f9694a0f61d9f370ac734a61 *tests/test_mapqtl_io.R
15546ea37fca6f7b591f081af224c17e *tests/test_mapqtl_io.Rout.save
9d487b394434c61b15806926325555fd *tests/test_qtl.R
daeac5a62836a4bb905cd412989d81d7 *tests/test_scanonevar.R
d8758c0fa31de2d1248141df4366f8b0 *tests/test_scanonevar.Rout.save
566406157c3c3b9b10a97c6ddb823e3d *tests/test_tidyIO.R
81a307e45c8cf8f8d19e5fe9d0caa7fb *tests/test_tidyIO.Rout.save
3001461196cd550e16acd9df7a1d5f98 *tests/testaugmentation.R
f9001771f9c635f1e079cc830129e450 *tests/testthat.R
99e671bbe4b61dcd1225b1bdc35ce48f *tests/testthat/test-fliporder.R
c7fa1e35580f7855e1f0c375f6cc0f43 *tests/testthat/test-scantwoperm.R
3c38de5a8a7c8f6ba1e77cb4fa1a64ba *tests/testthat/test-stepwiseqtl.R
57abd7654f2032e9b7f6f1c133dabff6 *vignettes/bcsft.Rnw
8eb3984bd344d8557aad7a97941a9c8b *vignettes/fancyheadings.sty
0e3e2fcb99258ac5ca671d3cafc4ac67 *vignettes/genotypeprobabilities.pdf
36ea3b648f7f5e5ca0720876ef5a65a2 *vignettes/goldensectionsearch.pdf
af7b55dc73d4866ee50f358467df740a *vignettes/plos.bst
184292403e1f03bf2e7ceb24b5ca46b2 *vignettes/recombinationcount.pdf
42c083fe6530877a8c1af63caf3347ed *vignettes/vignette.bib
6d4070e06aad8a67922d18ef1d835f01 *vignettes/why_we_need_a_new_program.pdf