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tests/testthat/_snaps/allelematch_5-amAlleleFreq.md
In amregtest: Runs Allelematch Regression Tests
Loop the Loop
Code
cat(cmdstr)
Output
amAlleleFreq(amdataMini)
structure(list(multilocusMap = c(1L, 1L, 2L, 2L), loci = list(
list(name = "LOC1a-LOC1b", columnNames = c("LOC1a", "LOC1b"
), alleleFreq = c("11" = 0.125, "12" = 0.125, "13" = 0.125,
"14" = 0.125, "21" = 0.125, "22" = 0.125, "23" = 0.125, "24" = 0.125
), missingFreq = 0, numAlleles = 8L), list(name = "LOC2a-LOC2b",
columnNames = c("LOC2a", "LOC2b"), alleleFreq = c("31" = 0.142857142857143,
"32" = 0.142857142857143, "33" = 0.142857142857143, "41" = 0.142857142857143,
"42" = 0.142857142857143, "43" = 0.142857142857143, "44" = 0.142857142857143
), missingFreq = 0.125, numAlleles = 7L))), class = "amAlleleFreq")
Code
print.amAlleleFreq(af)
Output
allelematch
amAlleleFreq object
Frequencies calculated after removal of missing data
LOC1a-LOC1b (8 alleles)
Allele 11 0.125
Allele 12 0.125
Allele 13 0.125
Allele 14 0.125
Allele 21 0.125
Allele 22 0.125
Allele 23 0.125
Allele 24 0.125
LOC2a-LOC2b (7 alleles)
Allele 31 0.143
Allele 32 0.143
Allele 33 0.143
Allele 41 0.143
Allele 42 0.143
Allele 43 0.143
Allele 44 0.143
Code
cat(cmdstr)
Output
amAlleleFreq(amdataMini, multilocusMap=c(1, 1, 2, 2))
structure(list(multilocusMap = c(1L, 1L, 2L, 2L), loci = list(
list(name = "LOC1a-LOC1b", columnNames = c("LOC1a", "LOC1b"
), alleleFreq = c("11" = 0.125, "12" = 0.125, "13" = 0.125,
"14" = 0.125, "21" = 0.125, "22" = 0.125, "23" = 0.125, "24" = 0.125
), missingFreq = 0, numAlleles = 8L), list(name = "LOC2a-LOC2b",
columnNames = c("LOC2a", "LOC2b"), alleleFreq = c("31" = 0.142857142857143,
"32" = 0.142857142857143, "33" = 0.142857142857143, "41" = 0.142857142857143,
"42" = 0.142857142857143, "43" = 0.142857142857143, "44" = 0.142857142857143
), missingFreq = 0.125, numAlleles = 7L))), class = "amAlleleFreq")
Code
print.amAlleleFreq(af)
Output
allelematch
amAlleleFreq object
Frequencies calculated after removal of missing data
LOC1a-LOC1b (8 alleles)
Allele 11 0.125
Allele 12 0.125
Allele 13 0.125
Allele 14 0.125
Allele 21 0.125
Allele 22 0.125
Allele 23 0.125
Allele 24 0.125
LOC2a-LOC2b (7 alleles)
Allele 31 0.143
Allele 32 0.143
Allele 33 0.143
Allele 41 0.143
Allele 42 0.143
Allele 43 0.143
Allele 44 0.143
Code
cat(cmdstr)
Output
amAlleleFreq(amdataExample1)
structure(list(multilocusMap = c(1L, 1L, 2L, 2L, 3L, 3L, 4L,
4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L), loci = list(
list(name = "LOC1a-LOC1b", columnNames = c("LOC1a", "LOC1b"
), alleleFreq = c("109" = 0.275, "108" = 0.25, "103" = 0.15,
"120" = 0.15, "104" = 0.075, "110" = 0.05, "114" = 0.05),
missingFreq = 0, numAlleles = 7L), list(name = "LOC2a-LOC2b",
columnNames = c("LOC2a", "LOC2b"), alleleFreq = c("208" = 0.4,
"201" = 0.325, "207" = 0.1, "209" = 0.1, "203" = 0.075
), missingFreq = 0, numAlleles = 5L), list(name = "LOC3a-LOC3b",
columnNames = c("LOC3a", "LOC3b"), alleleFreq = c("306" = 0.289473684210526,
"307" = 0.236842105263158, "314" = 0.157894736842105,
"317" = 0.157894736842105, "313" = 0.0789473684210526,
"318" = 0.0789473684210526), missingFreq = 0.05, numAlleles = 6L),
list(name = "LOC4a-LOC4b", columnNames = c("LOC4a", "LOC4b"
), alleleFreq = c("417" = 0.325, "407" = 0.2, "404" = 0.175,
"413" = 0.15, "405" = 0.05, "408" = 0.05, "414" = 0.05),
missingFreq = 0, numAlleles = 7L), list(name = "LOC5a-LOC5b",
columnNames = c("LOC5a", "LOC5b"), alleleFreq = c("502" = 0.35,
"519" = 0.25, "514" = 0.125, "516" = 0.1, "505" = 0.1,
"501" = 0.075), missingFreq = 0, numAlleles = 6L), list(
name = "LOC6a-LOC6b", columnNames = c("LOC6a", "LOC6b"
), alleleFreq = c("607" = 0.325, "603" = 0.3, "618" = 0.2,
"602" = 0.1, "616" = 0.075), missingFreq = 0, numAlleles = 5L),
list(name = "LOC7a-LOC7b", columnNames = c("LOC7a", "LOC7b"
), alleleFreq = c("715" = 0.25, "709" = 0.15, "706" = 0.15,
"703" = 0.15, "719" = 0.1, "717" = 0.075, "712" = 0.075,
"713" = 0.05), missingFreq = 0, numAlleles = 8L), list(name = "LOC8a-LOC8b",
columnNames = c("LOC8a", "LOC8b"), alleleFreq = c("804" = 0.375,
"816" = 0.3, "811" = 0.175, "812" = 0.1, "805" = 0.05
), missingFreq = 0, numAlleles = 5L), list(name = "LOC9a-LOC9b",
columnNames = c("LOC9a", "LOC9b"), alleleFreq = c("914" = 0.475,
"911" = 0.35, "912" = 0.05, "918" = 0.05, "915" = 0.05,
"907" = 0.025), missingFreq = 0, numAlleles = 6L), list(
name = "LOC10a-LOC10b", columnNames = c("LOC10a", "LOC10b"
), alleleFreq = c("1015" = 0.425, "1007" = 0.225, "1006" = 0.175,
"1018" = 0.1, "1005" = 0.05, "1019" = 0.025), missingFreq = 0,
numAlleles = 6L))), class = "amAlleleFreq")
Code
print.amAlleleFreq(af)
Output
allelematch
amAlleleFreq object
Frequencies calculated after removal of missing data
LOC1a-LOC1b (7 alleles)
Allele 109 0.275
Allele 108 0.25
Allele 103 0.15
Allele 120 0.15
Allele 104 0.075
Allele 110 0.05
Allele 114 0.05
LOC2a-LOC2b (5 alleles)
Allele 208 0.4
Allele 201 0.325
Allele 207 0.1
Allele 209 0.1
Allele 203 0.075
LOC3a-LOC3b (6 alleles)
Allele 306 0.289
Allele 307 0.237
Allele 314 0.158
Allele 317 0.158
Allele 313 0.0789
Allele 318 0.0789
LOC4a-LOC4b (7 alleles)
Allele 417 0.325
Allele 407 0.2
Allele 404 0.175
Allele 413 0.15
Allele 405 0.05
Allele 408 0.05
Allele 414 0.05
LOC5a-LOC5b (6 alleles)
Allele 502 0.35
Allele 519 0.25
Allele 514 0.125
Allele 516 0.1
Allele 505 0.1
Allele 501 0.075
LOC6a-LOC6b (5 alleles)
Allele 607 0.325
Allele 603 0.3
Allele 618 0.2
Allele 602 0.1
Allele 616 0.075
LOC7a-LOC7b (8 alleles)
Allele 715 0.25
Allele 709 0.15
Allele 706 0.15
Allele 703 0.15
Allele 719 0.1
Allele 717 0.075
Allele 712 0.075
Allele 713 0.05
LOC8a-LOC8b (5 alleles)
Allele 804 0.375
Allele 816 0.3
Allele 811 0.175
Allele 812 0.1
Allele 805 0.05
LOC9a-LOC9b (6 alleles)
Allele 914 0.475
Allele 911 0.35
Allele 912 0.05
Allele 918 0.05
Allele 915 0.05
Allele 907 0.025
LOC10a-LOC10b (6 alleles)
Allele 1015 0.425
Allele 1007 0.225
Allele 1006 0.175
Allele 1018 0.1
Allele 1005 0.05
Allele 1019 0.025
Code
cat(cmdstr)
Output
amAlleleFreq(amdataExample2)
structure(list(multilocusMap = c(1L, 1L, 2L, 2L, 3L, 3L, 4L,
4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L), loci = list(
list(name = "LOC1a-LOC1b", columnNames = c("LOC1a", "LOC1b"
), alleleFreq = c("116" = 0.325, "101" = 0.225, "111" = 0.225,
"107" = 0.2, "102" = 0.025), missingFreq = 0, numAlleles = 5L),
list(name = "LOC2a-LOC2b", columnNames = c("LOC2a", "LOC2b"
), alleleFreq = c("211" = 0.375, "203" = 0.275, "216" = 0.15,
"212" = 0.075, "219" = 0.075, "214" = 0.05), missingFreq = 0,
numAlleles = 6L), list(name = "LOC3a-LOC3b", columnNames = c("LOC3a",
"LOC3b"), alleleFreq = c("305" = 0.525, "314" = 0.1, "320" = 0.1,
"315" = 0.1, "316" = 0.075, "308" = 0.05, "306" = 0.05),
missingFreq = 0, numAlleles = 7L), list(name = "LOC4a-LOC4b",
columnNames = c("LOC4a", "LOC4b"), alleleFreq = c("411" = 0.361111111111111,
"402" = 0.25, "416" = 0.222222222222222, "403" = 0.138888888888889,
"412" = 0.0277777777777778), missingFreq = 0.1, numAlleles = 5L),
list(name = "LOC5a-LOC5b", columnNames = c("LOC5a", "LOC5b"
), alleleFreq = c("514" = 0.275, "501" = 0.275, "520" = 0.25,
"515" = 0.075, "505" = 0.075, "512" = 0.05), missingFreq = 0,
numAlleles = 6L), list(name = "LOC6a-LOC6b", columnNames = c("LOC6a",
"LOC6b"), alleleFreq = c("607" = 0.3, "620" = 0.2, "601" = 0.175,
"610" = 0.1, "604" = 0.075, "617" = 0.075, "619" = 0.025,
"615" = 0.025, "616" = 0.025), missingFreq = 0, numAlleles = 9L),
list(name = "LOC7a-LOC7b", columnNames = c("LOC7a", "LOC7b"
), alleleFreq = c("711" = 0.45, "707" = 0.175, "705" = 0.125,
"713" = 0.125, "718" = 0.075, "706" = 0.025, "701" = 0.025
), missingFreq = 0, numAlleles = 7L), list(name = "LOC8a-LOC8b",
columnNames = c("LOC8a", "LOC8b"), alleleFreq = c("808" = 0.275,
"816" = 0.225, "807" = 0.2, "820" = 0.15, "815" = 0.1,
"819" = 0.05), missingFreq = 0, numAlleles = 6L), list(
name = "LOC9a-LOC9b", columnNames = c("LOC9a", "LOC9b"
), alleleFreq = c("906" = 0.5, "916" = 0.210526315789474,
"919" = 0.157894736842105, "917" = 0.131578947368421),
missingFreq = 0.05, numAlleles = 4L), list(name = "LOC10a-LOC10b",
columnNames = c("LOC10a", "LOC10b"), alleleFreq = c("1002" = 0.35,
"1014" = 0.25, "1004" = 0.125, "1020" = 0.1, "1010" = 0.05,
"1016" = 0.05, "1012" = 0.025, "1005" = 0.025, "1009" = 0.025
), missingFreq = 0, numAlleles = 9L))), class = "amAlleleFreq")
Code
print.amAlleleFreq(af)
Output
allelematch
amAlleleFreq object
Frequencies calculated after removal of missing data
LOC1a-LOC1b (5 alleles)
Allele 116 0.325
Allele 101 0.225
Allele 111 0.225
Allele 107 0.2
Allele 102 0.025
LOC2a-LOC2b (6 alleles)
Allele 211 0.375
Allele 203 0.275
Allele 216 0.15
Allele 212 0.075
Allele 219 0.075
Allele 214 0.05
LOC3a-LOC3b (7 alleles)
Allele 305 0.525
Allele 314 0.1
Allele 320 0.1
Allele 315 0.1
Allele 316 0.075
Allele 308 0.05
Allele 306 0.05
LOC4a-LOC4b (5 alleles)
Allele 411 0.361
Allele 402 0.25
Allele 416 0.222
Allele 403 0.139
Allele 412 0.0278
LOC5a-LOC5b (6 alleles)
Allele 514 0.275
Allele 501 0.275
Allele 520 0.25
Allele 515 0.075
Allele 505 0.075
Allele 512 0.05
LOC6a-LOC6b (9 alleles)
Allele 607 0.3
Allele 620 0.2
Allele 601 0.175
Allele 610 0.1
Allele 604 0.075
Allele 617 0.075
Allele 619 0.025
Allele 615 0.025
Allele 616 0.025
LOC7a-LOC7b (7 alleles)
Allele 711 0.45
Allele 707 0.175
Allele 705 0.125
Allele 713 0.125
Allele 718 0.075
Allele 706 0.025
Allele 701 0.025
LOC8a-LOC8b (6 alleles)
Allele 808 0.275
Allele 816 0.225
Allele 807 0.2
Allele 820 0.15
Allele 815 0.1
Allele 819 0.05
LOC9a-LOC9b (4 alleles)
Allele 906 0.5
Allele 916 0.211
Allele 919 0.158
Allele 917 0.132
LOC10a-LOC10b (9 alleles)
Allele 1002 0.35
Allele 1014 0.25
Allele 1004 0.125
Allele 1020 0.1
Allele 1010 0.05
Allele 1016 0.05
Allele 1012 0.025
Allele 1005 0.025
Allele 1009 0.025
Code
cat(cmdstr)
Output
amAlleleFreq(amdataExample3)
structure(list(multilocusMap = c(1L, 1L, 2L, 2L, 3L, 3L, 4L,
4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L), loci = list(
list(name = "LOC1a-LOC1b", columnNames = c("LOC1a", "LOC1b"
), alleleFreq = c("103" = 0.275, "115" = 0.225, "107" = 0.2,
"117" = 0.1, "112" = 0.1, "116" = 0.1), missingFreq = 0,
numAlleles = 6L), list(name = "LOC2a-LOC2b", columnNames = c("LOC2a",
"LOC2b"), alleleFreq = c("202" = 0.5625, "219" = 0.34375,
"206" = 0.09375), missingFreq = 0.2, numAlleles = 3L), list(
name = "LOC3a-LOC3b", columnNames = c("LOC3a", "LOC3b"
), alleleFreq = c("306" = 0.236842105263158, "302" = 0.157894736842105,
"311" = 0.157894736842105, "317" = 0.131578947368421,
"313" = 0.105263157894737, "310" = 0.0789473684210526,
"316" = 0.0526315789473684, "312" = 0.0526315789473684,
"307" = 0.0263157894736842), missingFreq = 0.05, numAlleles = 9L),
list(name = "LOC4a-LOC4b", columnNames = c("LOC4a", "LOC4b"
), alleleFreq = c("411" = 0.5, "416" = 0.225, "409" = 0.2,
"412" = 0.075), missingFreq = 0, numAlleles = 4L), list(name = "LOC5a-LOC5b",
columnNames = c("LOC5a", "LOC5b"), alleleFreq = c("501" = 0.315789473684211,
"514" = 0.289473684210526, "504" = 0.184210526315789,
"510" = 0.131578947368421, "508" = 0.0789473684210526
), missingFreq = 0.05, numAlleles = 5L), list(name = "LOC6a-LOC6b",
columnNames = c("LOC6a", "LOC6b"), alleleFreq = c("604" = 0.34375,
"608" = 0.3125, "606" = 0.21875, "611" = 0.09375, "617" = 0.03125
), missingFreq = 0.2, numAlleles = 5L), list(name = "LOC7a-LOC7b",
columnNames = c("LOC7a", "LOC7b"), alleleFreq = c("718" = 0.447368421052632,
"708" = 0.421052631578947, "703" = 0.0789473684210526,
"712" = 0.0526315789473684), missingFreq = 0.05, numAlleles = 4L),
list(name = "LOC8a-LOC8b", columnNames = c("LOC8a", "LOC8b"
), alleleFreq = c("817" = 0.210526315789474, "807" = 0.184210526315789,
"819" = 0.184210526315789, "811" = 0.105263157894737, "812" = 0.105263157894737,
"809" = 0.0789473684210526, "813" = 0.0789473684210526, "802" = 0.0526315789473684
), missingFreq = 0.05, numAlleles = 8L), list(name = "LOC9a-LOC9b",
columnNames = c("LOC9a", "LOC9b"), alleleFreq = c("908" = 0.470588235294118,
"919" = 0.205882352941176, "903" = 0.147058823529412,
"910" = 0.117647058823529, "904" = 0.0588235294117647
), missingFreq = 0.15, numAlleles = 5L), list(name = "LOC10a-LOC10b",
columnNames = c("LOC10a", "LOC10b"), alleleFreq = c("1001" = 0.368421052631579,
"1008" = 0.342105263157895, "1004" = 0.131578947368421,
"1002" = 0.0789473684210526, "1020" = 0.0789473684210526
), missingFreq = 0.05, numAlleles = 5L))), class = "amAlleleFreq")
Code
print.amAlleleFreq(af)
Output
allelematch
amAlleleFreq object
Frequencies calculated after removal of missing data
LOC1a-LOC1b (6 alleles)
Allele 103 0.275
Allele 115 0.225
Allele 107 0.2
Allele 117 0.1
Allele 112 0.1
Allele 116 0.1
LOC2a-LOC2b (3 alleles)
Allele 202 0.562
Allele 219 0.344
Allele 206 0.0938
LOC3a-LOC3b (9 alleles)
Allele 306 0.237
Allele 302 0.158
Allele 311 0.158
Allele 317 0.132
Allele 313 0.105
Allele 310 0.0789
Allele 316 0.0526
Allele 312 0.0526
Allele 307 0.0263
LOC4a-LOC4b (4 alleles)
Allele 411 0.5
Allele 416 0.225
Allele 409 0.2
Allele 412 0.075
LOC5a-LOC5b (5 alleles)
Allele 501 0.316
Allele 514 0.289
Allele 504 0.184
Allele 510 0.132
Allele 508 0.0789
LOC6a-LOC6b (5 alleles)
Allele 604 0.344
Allele 608 0.312
Allele 606 0.219
Allele 611 0.0938
Allele 617 0.0312
LOC7a-LOC7b (4 alleles)
Allele 718 0.447
Allele 708 0.421
Allele 703 0.0789
Allele 712 0.0526
LOC8a-LOC8b (8 alleles)
Allele 817 0.211
Allele 807 0.184
Allele 819 0.184
Allele 811 0.105
Allele 812 0.105
Allele 809 0.0789
Allele 813 0.0789
Allele 802 0.0526
LOC9a-LOC9b (5 alleles)
Allele 908 0.471
Allele 919 0.206
Allele 903 0.147
Allele 910 0.118
Allele 904 0.0588
LOC10a-LOC10b (5 alleles)
Allele 1001 0.368
Allele 1008 0.342
Allele 1004 0.132
Allele 1002 0.0789
Allele 1020 0.0789
Code
cat(cmdstr)
Output
amAlleleFreq(amdataExample4)
structure(list(multilocusMap = c(1L, 1L, 2L, 2L, 3L, 3L, 4L,
4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L), loci = list(
list(name = "LOC1a-LOC1b", columnNames = c("LOC1a", "LOC1b"
), alleleFreq = c("104" = 0.5, "108" = 0.210526315789474,
"118" = 0.210526315789474, "111" = 0.0789473684210526), missingFreq = 0.05,
numAlleles = 4L), list(name = "LOC2a-LOC2b", columnNames = c("LOC2a",
"LOC2b"), alleleFreq = c("202" = 0.5, "208" = 0.40625, "212" = 0.09375
), missingFreq = 0.2, numAlleles = 3L), list(name = "LOC3a-LOC3b",
columnNames = c("LOC3a", "LOC3b"), alleleFreq = c("304" = 0.366666666666667,
"311" = 0.366666666666667, "307" = 0.266666666666667),
missingFreq = 0.25, numAlleles = 3L), list(name = "LOC4a-LOC4b",
columnNames = c("LOC4a", "LOC4b"), alleleFreq = c("413" = 0.411764705882353,
"408" = 0.294117647058824, "418" = 0.235294117647059,
"420" = 0.0588235294117647), missingFreq = 0.15, numAlleles = 4L),
list(name = "LOC5a-LOC5b", columnNames = c("LOC5a", "LOC5b"
), alleleFreq = c("505" = 0.566666666666667, "501" = 0.4,
"519" = 0.0333333333333333), missingFreq = 0.25, numAlleles = 3L),
list(name = "LOC6a-LOC6b", columnNames = c("LOC6a", "LOC6b"
), alleleFreq = c("608" = 0.794117647058823, "620" = 0.117647058823529,
"605" = 0.0882352941176471), missingFreq = 0.15, numAlleles = 3L),
list(name = "LOC7a-LOC7b", columnNames = c("LOC7a", "LOC7b"
), alleleFreq = c("720" = 0.382352941176471, "705" = 0.205882352941176,
"717" = 0.176470588235294, "704" = 0.117647058823529, "702" = 0.117647058823529
), missingFreq = 0.15, numAlleles = 5L), list(name = "LOC8a-LOC8b",
columnNames = c("LOC8a", "LOC8b"), alleleFreq = c("810" = 0.388888888888889,
"819" = 0.305555555555556, "801" = 0.277777777777778,
"813" = 0.0277777777777778), missingFreq = 0.1, numAlleles = 4L),
list(name = "LOC9a-LOC9b", columnNames = c("LOC9a", "LOC9b"
), alleleFreq = c("902" = 0.40625, "920" = 0.25, "904" = 0.15625,
"909" = 0.125, "906" = 0.0625), missingFreq = 0.2, numAlleles = 5L),
list(name = "LOC10a-LOC10b", columnNames = c("LOC10a", "LOC10b"
), alleleFreq = c("1007" = 0.357142857142857, "1005" = 0.321428571428571,
"1019" = 0.285714285714286, "1013" = 0.0357142857142857),
missingFreq = 0.3, numAlleles = 4L))), class = "amAlleleFreq")
Code
print.amAlleleFreq(af)
Output
allelematch
amAlleleFreq object
Frequencies calculated after removal of missing data
LOC1a-LOC1b (4 alleles)
Allele 104 0.5
Allele 108 0.211
Allele 118 0.211
Allele 111 0.0789
LOC2a-LOC2b (3 alleles)
Allele 202 0.5
Allele 208 0.406
Allele 212 0.0938
LOC3a-LOC3b (3 alleles)
Allele 304 0.367
Allele 311 0.367
Allele 307 0.267
LOC4a-LOC4b (4 alleles)
Allele 413 0.412
Allele 408 0.294
Allele 418 0.235
Allele 420 0.0588
LOC5a-LOC5b (3 alleles)
Allele 505 0.567
Allele 501 0.4
Allele 519 0.0333
LOC6a-LOC6b (3 alleles)
Allele 608 0.794
Allele 620 0.118
Allele 605 0.0882
LOC7a-LOC7b (5 alleles)
Allele 720 0.382
Allele 705 0.206
Allele 717 0.176
Allele 704 0.118
Allele 702 0.118
LOC8a-LOC8b (4 alleles)
Allele 810 0.389
Allele 819 0.306
Allele 801 0.278
Allele 813 0.0278
LOC9a-LOC9b (5 alleles)
Allele 902 0.406
Allele 920 0.25
Allele 904 0.156
Allele 909 0.125
Allele 906 0.0625
LOC10a-LOC10b (4 alleles)
Allele 1007 0.357
Allele 1005 0.321
Allele 1019 0.286
Allele 1013 0.0357
Code
cat(cmdstr)
Output
amAlleleFreq(amdataExample5)
structure(list(multilocusMap = c(1L, 1L, 2L, 2L, 3L, 3L, 4L,
4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L), loci = list(
list(name = "LOC1a-LOC1b", columnNames = c("LOC1a", "LOC1b"
), alleleFreq = c("382" = 0.575, "384" = 0.4, "388" = 0.025
), missingFreq = 0, numAlleles = 3L), list(name = "LOC2a-LOC2b",
columnNames = c("LOC2a", "LOC2b"), alleleFreq = c("224" = 0.375,
"230" = 0.3, "232" = 0.15, "236" = 0.075, "242" = 0.05,
"244" = 0.025, "238" = 0.025), missingFreq = 0, numAlleles = 7L),
list(name = "LOC3a-LOC3b", columnNames = c("LOC3a", "LOC3b"
), alleleFreq = c("159" = 0.5, "155" = 0.25, "167" = 0.25
), missingFreq = 0.9, numAlleles = 3L), list(name = "LOC4a-LOC4b",
columnNames = c("LOC4a", "LOC4b"), alleleFreq = c("193" = 0.55,
"185" = 0.225, "181" = 0.1, "191" = 0.075, "199" = 0.05
), missingFreq = 0, numAlleles = 5L), list(name = "LOC5a-LOC5b",
columnNames = c("LOC5a", "LOC5b"), alleleFreq = c("299" = 0.578947368421053,
"285" = 0.315789473684211, "301" = 0.105263157894737),
missingFreq = 0.05, numAlleles = 3L), list(name = "LOC6a-LOC6b",
columnNames = c("LOC6a", "LOC6b"), alleleFreq = c("223" = 0.8,
"213" = 0.1, "227" = 0.05, "221" = 0.05), missingFreq = 0,
numAlleles = 4L), list(name = "LOC7a-LOC7b", columnNames = c("LOC7a",
"LOC7b"), alleleFreq = c("202" = 0.35, "210" = 0.225, "192" = 0.175,
"198" = 0.075, "204" = 0.075, "216" = 0.05, "214" = 0.05),
missingFreq = 0, numAlleles = 7L), list(name = "LOC8a-LOC8b",
columnNames = c("LOC8a", "LOC8b"), alleleFreq = c("118" = 0.425,
"106" = 0.225, "102" = 0.1, "116" = 0.075, "112" = 0.075,
"114" = 0.05, "108" = 0.05), missingFreq = 0, numAlleles = 7L),
list(name = "LOC9a-LOC9b", columnNames = c("LOC9a", "LOC9b"
), alleleFreq = c("296" = 0.45, "304" = 0.225, "288" = 0.175,
"298" = 0.1, "306" = 0.05), missingFreq = 0, numAlleles = 5L),
list(name = "LOC10a-LOC10b", columnNames = c("LOC10a", "LOC10b"
), alleleFreq = c("166" = 0.775, "172" = 0.125, "174" = 0.075,
"168" = 0.025), missingFreq = 0, numAlleles = 4L))), class = "amAlleleFreq")
Code
print.amAlleleFreq(af)
Output
allelematch
amAlleleFreq object
Frequencies calculated after removal of missing data
LOC1a-LOC1b (3 alleles)
Allele 382 0.575
Allele 384 0.4
Allele 388 0.025
LOC2a-LOC2b (7 alleles)
Allele 224 0.375
Allele 230 0.3
Allele 232 0.15
Allele 236 0.075
Allele 242 0.05
Allele 244 0.025
Allele 238 0.025
LOC3a-LOC3b (3 alleles)
Allele 159 0.5
Allele 155 0.25
Allele 167 0.25
LOC4a-LOC4b (5 alleles)
Allele 193 0.55
Allele 185 0.225
Allele 181 0.1
Allele 191 0.075
Allele 199 0.05
LOC5a-LOC5b (3 alleles)
Allele 299 0.579
Allele 285 0.316
Allele 301 0.105
LOC6a-LOC6b (4 alleles)
Allele 223 0.8
Allele 213 0.1
Allele 227 0.05
Allele 221 0.05
LOC7a-LOC7b (7 alleles)
Allele 202 0.35
Allele 210 0.225
Allele 192 0.175
Allele 198 0.075
Allele 204 0.075
Allele 216 0.05
Allele 214 0.05
LOC8a-LOC8b (7 alleles)
Allele 118 0.425
Allele 106 0.225
Allele 102 0.1
Allele 116 0.075
Allele 112 0.075
Allele 114 0.05
Allele 108 0.05
LOC9a-LOC9b (5 alleles)
Allele 296 0.45
Allele 304 0.225
Allele 288 0.175
Allele 298 0.1
Allele 306 0.05
LOC10a-LOC10b (4 alleles)
Allele 166 0.775
Allele 172 0.125
Allele 174 0.075
Allele 168 0.025
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Loop the Loop
Code
cat(cmdstr)
Output
amAlleleFreq(amdataMini)
structure(list(multilocusMap = c(1L, 1L, 2L, 2L), loci = list(
list(name = "LOC1a-LOC1b", columnNames = c("LOC1a", "LOC1b"
), alleleFreq = c("11" = 0.125, "12" = 0.125, "13" = 0.125,
"14" = 0.125, "21" = 0.125, "22" = 0.125, "23" = 0.125, "24" = 0.125
), missingFreq = 0, numAlleles = 8L), list(name = "LOC2a-LOC2b",
columnNames = c("LOC2a", "LOC2b"), alleleFreq = c("31" = 0.142857142857143,
"32" = 0.142857142857143, "33" = 0.142857142857143, "41" = 0.142857142857143,
"42" = 0.142857142857143, "43" = 0.142857142857143, "44" = 0.142857142857143
), missingFreq = 0.125, numAlleles = 7L))), class = "amAlleleFreq")
Code
print.amAlleleFreq(af)
Output
allelematch
amAlleleFreq object
Frequencies calculated after removal of missing data
LOC1a-LOC1b (8 alleles)
Allele 11 0.125
Allele 12 0.125
Allele 13 0.125
Allele 14 0.125
Allele 21 0.125
Allele 22 0.125
Allele 23 0.125
Allele 24 0.125
LOC2a-LOC2b (7 alleles)
Allele 31 0.143
Allele 32 0.143
Allele 33 0.143
Allele 41 0.143
Allele 42 0.143
Allele 43 0.143
Allele 44 0.143
Code
cat(cmdstr)
Output
amAlleleFreq(amdataMini, multilocusMap=c(1, 1, 2, 2))
structure(list(multilocusMap = c(1L, 1L, 2L, 2L), loci = list(
list(name = "LOC1a-LOC1b", columnNames = c("LOC1a", "LOC1b"
), alleleFreq = c("11" = 0.125, "12" = 0.125, "13" = 0.125,
"14" = 0.125, "21" = 0.125, "22" = 0.125, "23" = 0.125, "24" = 0.125
), missingFreq = 0, numAlleles = 8L), list(name = "LOC2a-LOC2b",
columnNames = c("LOC2a", "LOC2b"), alleleFreq = c("31" = 0.142857142857143,
"32" = 0.142857142857143, "33" = 0.142857142857143, "41" = 0.142857142857143,
"42" = 0.142857142857143, "43" = 0.142857142857143, "44" = 0.142857142857143
), missingFreq = 0.125, numAlleles = 7L))), class = "amAlleleFreq")
Code
print.amAlleleFreq(af)
Output
allelematch
amAlleleFreq object
Frequencies calculated after removal of missing data
LOC1a-LOC1b (8 alleles)
Allele 11 0.125
Allele 12 0.125
Allele 13 0.125
Allele 14 0.125
Allele 21 0.125
Allele 22 0.125
Allele 23 0.125
Allele 24 0.125
LOC2a-LOC2b (7 alleles)
Allele 31 0.143
Allele 32 0.143
Allele 33 0.143
Allele 41 0.143
Allele 42 0.143
Allele 43 0.143
Allele 44 0.143
Code
cat(cmdstr)
Output
amAlleleFreq(amdataExample1)
structure(list(multilocusMap = c(1L, 1L, 2L, 2L, 3L, 3L, 4L,
4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L), loci = list(
list(name = "LOC1a-LOC1b", columnNames = c("LOC1a", "LOC1b"
), alleleFreq = c("109" = 0.275, "108" = 0.25, "103" = 0.15,
"120" = 0.15, "104" = 0.075, "110" = 0.05, "114" = 0.05),
missingFreq = 0, numAlleles = 7L), list(name = "LOC2a-LOC2b",
columnNames = c("LOC2a", "LOC2b"), alleleFreq = c("208" = 0.4,
"201" = 0.325, "207" = 0.1, "209" = 0.1, "203" = 0.075
), missingFreq = 0, numAlleles = 5L), list(name = "LOC3a-LOC3b",
columnNames = c("LOC3a", "LOC3b"), alleleFreq = c("306" = 0.289473684210526,
"307" = 0.236842105263158, "314" = 0.157894736842105,
"317" = 0.157894736842105, "313" = 0.0789473684210526,
"318" = 0.0789473684210526), missingFreq = 0.05, numAlleles = 6L),
list(name = "LOC4a-LOC4b", columnNames = c("LOC4a", "LOC4b"
), alleleFreq = c("417" = 0.325, "407" = 0.2, "404" = 0.175,
"413" = 0.15, "405" = 0.05, "408" = 0.05, "414" = 0.05),
missingFreq = 0, numAlleles = 7L), list(name = "LOC5a-LOC5b",
columnNames = c("LOC5a", "LOC5b"), alleleFreq = c("502" = 0.35,
"519" = 0.25, "514" = 0.125, "516" = 0.1, "505" = 0.1,
"501" = 0.075), missingFreq = 0, numAlleles = 6L), list(
name = "LOC6a-LOC6b", columnNames = c("LOC6a", "LOC6b"
), alleleFreq = c("607" = 0.325, "603" = 0.3, "618" = 0.2,
"602" = 0.1, "616" = 0.075), missingFreq = 0, numAlleles = 5L),
list(name = "LOC7a-LOC7b", columnNames = c("LOC7a", "LOC7b"
), alleleFreq = c("715" = 0.25, "709" = 0.15, "706" = 0.15,
"703" = 0.15, "719" = 0.1, "717" = 0.075, "712" = 0.075,
"713" = 0.05), missingFreq = 0, numAlleles = 8L), list(name = "LOC8a-LOC8b",
columnNames = c("LOC8a", "LOC8b"), alleleFreq = c("804" = 0.375,
"816" = 0.3, "811" = 0.175, "812" = 0.1, "805" = 0.05
), missingFreq = 0, numAlleles = 5L), list(name = "LOC9a-LOC9b",
columnNames = c("LOC9a", "LOC9b"), alleleFreq = c("914" = 0.475,
"911" = 0.35, "912" = 0.05, "918" = 0.05, "915" = 0.05,
"907" = 0.025), missingFreq = 0, numAlleles = 6L), list(
name = "LOC10a-LOC10b", columnNames = c("LOC10a", "LOC10b"
), alleleFreq = c("1015" = 0.425, "1007" = 0.225, "1006" = 0.175,
"1018" = 0.1, "1005" = 0.05, "1019" = 0.025), missingFreq = 0,
numAlleles = 6L))), class = "amAlleleFreq")
Code
print.amAlleleFreq(af)
Output
allelematch
amAlleleFreq object
Frequencies calculated after removal of missing data
LOC1a-LOC1b (7 alleles)
Allele 109 0.275
Allele 108 0.25
Allele 103 0.15
Allele 120 0.15
Allele 104 0.075
Allele 110 0.05
Allele 114 0.05
LOC2a-LOC2b (5 alleles)
Allele 208 0.4
Allele 201 0.325
Allele 207 0.1
Allele 209 0.1
Allele 203 0.075
LOC3a-LOC3b (6 alleles)
Allele 306 0.289
Allele 307 0.237
Allele 314 0.158
Allele 317 0.158
Allele 313 0.0789
Allele 318 0.0789
LOC4a-LOC4b (7 alleles)
Allele 417 0.325
Allele 407 0.2
Allele 404 0.175
Allele 413 0.15
Allele 405 0.05
Allele 408 0.05
Allele 414 0.05
LOC5a-LOC5b (6 alleles)
Allele 502 0.35
Allele 519 0.25
Allele 514 0.125
Allele 516 0.1
Allele 505 0.1
Allele 501 0.075
LOC6a-LOC6b (5 alleles)
Allele 607 0.325
Allele 603 0.3
Allele 618 0.2
Allele 602 0.1
Allele 616 0.075
LOC7a-LOC7b (8 alleles)
Allele 715 0.25
Allele 709 0.15
Allele 706 0.15
Allele 703 0.15
Allele 719 0.1
Allele 717 0.075
Allele 712 0.075
Allele 713 0.05
LOC8a-LOC8b (5 alleles)
Allele 804 0.375
Allele 816 0.3
Allele 811 0.175
Allele 812 0.1
Allele 805 0.05
LOC9a-LOC9b (6 alleles)
Allele 914 0.475
Allele 911 0.35
Allele 912 0.05
Allele 918 0.05
Allele 915 0.05
Allele 907 0.025
LOC10a-LOC10b (6 alleles)
Allele 1015 0.425
Allele 1007 0.225
Allele 1006 0.175
Allele 1018 0.1
Allele 1005 0.05
Allele 1019 0.025
Code
cat(cmdstr)
Output
amAlleleFreq(amdataExample2)
structure(list(multilocusMap = c(1L, 1L, 2L, 2L, 3L, 3L, 4L,
4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L), loci = list(
list(name = "LOC1a-LOC1b", columnNames = c("LOC1a", "LOC1b"
), alleleFreq = c("116" = 0.325, "101" = 0.225, "111" = 0.225,
"107" = 0.2, "102" = 0.025), missingFreq = 0, numAlleles = 5L),
list(name = "LOC2a-LOC2b", columnNames = c("LOC2a", "LOC2b"
), alleleFreq = c("211" = 0.375, "203" = 0.275, "216" = 0.15,
"212" = 0.075, "219" = 0.075, "214" = 0.05), missingFreq = 0,
numAlleles = 6L), list(name = "LOC3a-LOC3b", columnNames = c("LOC3a",
"LOC3b"), alleleFreq = c("305" = 0.525, "314" = 0.1, "320" = 0.1,
"315" = 0.1, "316" = 0.075, "308" = 0.05, "306" = 0.05),
missingFreq = 0, numAlleles = 7L), list(name = "LOC4a-LOC4b",
columnNames = c("LOC4a", "LOC4b"), alleleFreq = c("411" = 0.361111111111111,
"402" = 0.25, "416" = 0.222222222222222, "403" = 0.138888888888889,
"412" = 0.0277777777777778), missingFreq = 0.1, numAlleles = 5L),
list(name = "LOC5a-LOC5b", columnNames = c("LOC5a", "LOC5b"
), alleleFreq = c("514" = 0.275, "501" = 0.275, "520" = 0.25,
"515" = 0.075, "505" = 0.075, "512" = 0.05), missingFreq = 0,
numAlleles = 6L), list(name = "LOC6a-LOC6b", columnNames = c("LOC6a",
"LOC6b"), alleleFreq = c("607" = 0.3, "620" = 0.2, "601" = 0.175,
"610" = 0.1, "604" = 0.075, "617" = 0.075, "619" = 0.025,
"615" = 0.025, "616" = 0.025), missingFreq = 0, numAlleles = 9L),
list(name = "LOC7a-LOC7b", columnNames = c("LOC7a", "LOC7b"
), alleleFreq = c("711" = 0.45, "707" = 0.175, "705" = 0.125,
"713" = 0.125, "718" = 0.075, "706" = 0.025, "701" = 0.025
), missingFreq = 0, numAlleles = 7L), list(name = "LOC8a-LOC8b",
columnNames = c("LOC8a", "LOC8b"), alleleFreq = c("808" = 0.275,
"816" = 0.225, "807" = 0.2, "820" = 0.15, "815" = 0.1,
"819" = 0.05), missingFreq = 0, numAlleles = 6L), list(
name = "LOC9a-LOC9b", columnNames = c("LOC9a", "LOC9b"
), alleleFreq = c("906" = 0.5, "916" = 0.210526315789474,
"919" = 0.157894736842105, "917" = 0.131578947368421),
missingFreq = 0.05, numAlleles = 4L), list(name = "LOC10a-LOC10b",
columnNames = c("LOC10a", "LOC10b"), alleleFreq = c("1002" = 0.35,
"1014" = 0.25, "1004" = 0.125, "1020" = 0.1, "1010" = 0.05,
"1016" = 0.05, "1012" = 0.025, "1005" = 0.025, "1009" = 0.025
), missingFreq = 0, numAlleles = 9L))), class = "amAlleleFreq")
Code
print.amAlleleFreq(af)
Output
allelematch
amAlleleFreq object
Frequencies calculated after removal of missing data
LOC1a-LOC1b (5 alleles)
Allele 116 0.325
Allele 101 0.225
Allele 111 0.225
Allele 107 0.2
Allele 102 0.025
LOC2a-LOC2b (6 alleles)
Allele 211 0.375
Allele 203 0.275
Allele 216 0.15
Allele 212 0.075
Allele 219 0.075
Allele 214 0.05
LOC3a-LOC3b (7 alleles)
Allele 305 0.525
Allele 314 0.1
Allele 320 0.1
Allele 315 0.1
Allele 316 0.075
Allele 308 0.05
Allele 306 0.05
LOC4a-LOC4b (5 alleles)
Allele 411 0.361
Allele 402 0.25
Allele 416 0.222
Allele 403 0.139
Allele 412 0.0278
LOC5a-LOC5b (6 alleles)
Allele 514 0.275
Allele 501 0.275
Allele 520 0.25
Allele 515 0.075
Allele 505 0.075
Allele 512 0.05
LOC6a-LOC6b (9 alleles)
Allele 607 0.3
Allele 620 0.2
Allele 601 0.175
Allele 610 0.1
Allele 604 0.075
Allele 617 0.075
Allele 619 0.025
Allele 615 0.025
Allele 616 0.025
LOC7a-LOC7b (7 alleles)
Allele 711 0.45
Allele 707 0.175
Allele 705 0.125
Allele 713 0.125
Allele 718 0.075
Allele 706 0.025
Allele 701 0.025
LOC8a-LOC8b (6 alleles)
Allele 808 0.275
Allele 816 0.225
Allele 807 0.2
Allele 820 0.15
Allele 815 0.1
Allele 819 0.05
LOC9a-LOC9b (4 alleles)
Allele 906 0.5
Allele 916 0.211
Allele 919 0.158
Allele 917 0.132
LOC10a-LOC10b (9 alleles)
Allele 1002 0.35
Allele 1014 0.25
Allele 1004 0.125
Allele 1020 0.1
Allele 1010 0.05
Allele 1016 0.05
Allele 1012 0.025
Allele 1005 0.025
Allele 1009 0.025
Code
cat(cmdstr)
Output
amAlleleFreq(amdataExample3)
structure(list(multilocusMap = c(1L, 1L, 2L, 2L, 3L, 3L, 4L,
4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L), loci = list(
list(name = "LOC1a-LOC1b", columnNames = c("LOC1a", "LOC1b"
), alleleFreq = c("103" = 0.275, "115" = 0.225, "107" = 0.2,
"117" = 0.1, "112" = 0.1, "116" = 0.1), missingFreq = 0,
numAlleles = 6L), list(name = "LOC2a-LOC2b", columnNames = c("LOC2a",
"LOC2b"), alleleFreq = c("202" = 0.5625, "219" = 0.34375,
"206" = 0.09375), missingFreq = 0.2, numAlleles = 3L), list(
name = "LOC3a-LOC3b", columnNames = c("LOC3a", "LOC3b"
), alleleFreq = c("306" = 0.236842105263158, "302" = 0.157894736842105,
"311" = 0.157894736842105, "317" = 0.131578947368421,
"313" = 0.105263157894737, "310" = 0.0789473684210526,
"316" = 0.0526315789473684, "312" = 0.0526315789473684,
"307" = 0.0263157894736842), missingFreq = 0.05, numAlleles = 9L),
list(name = "LOC4a-LOC4b", columnNames = c("LOC4a", "LOC4b"
), alleleFreq = c("411" = 0.5, "416" = 0.225, "409" = 0.2,
"412" = 0.075), missingFreq = 0, numAlleles = 4L), list(name = "LOC5a-LOC5b",
columnNames = c("LOC5a", "LOC5b"), alleleFreq = c("501" = 0.315789473684211,
"514" = 0.289473684210526, "504" = 0.184210526315789,
"510" = 0.131578947368421, "508" = 0.0789473684210526
), missingFreq = 0.05, numAlleles = 5L), list(name = "LOC6a-LOC6b",
columnNames = c("LOC6a", "LOC6b"), alleleFreq = c("604" = 0.34375,
"608" = 0.3125, "606" = 0.21875, "611" = 0.09375, "617" = 0.03125
), missingFreq = 0.2, numAlleles = 5L), list(name = "LOC7a-LOC7b",
columnNames = c("LOC7a", "LOC7b"), alleleFreq = c("718" = 0.447368421052632,
"708" = 0.421052631578947, "703" = 0.0789473684210526,
"712" = 0.0526315789473684), missingFreq = 0.05, numAlleles = 4L),
list(name = "LOC8a-LOC8b", columnNames = c("LOC8a", "LOC8b"
), alleleFreq = c("817" = 0.210526315789474, "807" = 0.184210526315789,
"819" = 0.184210526315789, "811" = 0.105263157894737, "812" = 0.105263157894737,
"809" = 0.0789473684210526, "813" = 0.0789473684210526, "802" = 0.0526315789473684
), missingFreq = 0.05, numAlleles = 8L), list(name = "LOC9a-LOC9b",
columnNames = c("LOC9a", "LOC9b"), alleleFreq = c("908" = 0.470588235294118,
"919" = 0.205882352941176, "903" = 0.147058823529412,
"910" = 0.117647058823529, "904" = 0.0588235294117647
), missingFreq = 0.15, numAlleles = 5L), list(name = "LOC10a-LOC10b",
columnNames = c("LOC10a", "LOC10b"), alleleFreq = c("1001" = 0.368421052631579,
"1008" = 0.342105263157895, "1004" = 0.131578947368421,
"1002" = 0.0789473684210526, "1020" = 0.0789473684210526
), missingFreq = 0.05, numAlleles = 5L))), class = "amAlleleFreq")
Code
print.amAlleleFreq(af)
Output
allelematch
amAlleleFreq object
Frequencies calculated after removal of missing data
LOC1a-LOC1b (6 alleles)
Allele 103 0.275
Allele 115 0.225
Allele 107 0.2
Allele 117 0.1
Allele 112 0.1
Allele 116 0.1
LOC2a-LOC2b (3 alleles)
Allele 202 0.562
Allele 219 0.344
Allele 206 0.0938
LOC3a-LOC3b (9 alleles)
Allele 306 0.237
Allele 302 0.158
Allele 311 0.158
Allele 317 0.132
Allele 313 0.105
Allele 310 0.0789
Allele 316 0.0526
Allele 312 0.0526
Allele 307 0.0263
LOC4a-LOC4b (4 alleles)
Allele 411 0.5
Allele 416 0.225
Allele 409 0.2
Allele 412 0.075
LOC5a-LOC5b (5 alleles)
Allele 501 0.316
Allele 514 0.289
Allele 504 0.184
Allele 510 0.132
Allele 508 0.0789
LOC6a-LOC6b (5 alleles)
Allele 604 0.344
Allele 608 0.312
Allele 606 0.219
Allele 611 0.0938
Allele 617 0.0312
LOC7a-LOC7b (4 alleles)
Allele 718 0.447
Allele 708 0.421
Allele 703 0.0789
Allele 712 0.0526
LOC8a-LOC8b (8 alleles)
Allele 817 0.211
Allele 807 0.184
Allele 819 0.184
Allele 811 0.105
Allele 812 0.105
Allele 809 0.0789
Allele 813 0.0789
Allele 802 0.0526
LOC9a-LOC9b (5 alleles)
Allele 908 0.471
Allele 919 0.206
Allele 903 0.147
Allele 910 0.118
Allele 904 0.0588
LOC10a-LOC10b (5 alleles)
Allele 1001 0.368
Allele 1008 0.342
Allele 1004 0.132
Allele 1002 0.0789
Allele 1020 0.0789
Code
cat(cmdstr)
Output
amAlleleFreq(amdataExample4)
structure(list(multilocusMap = c(1L, 1L, 2L, 2L, 3L, 3L, 4L,
4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L), loci = list(
list(name = "LOC1a-LOC1b", columnNames = c("LOC1a", "LOC1b"
), alleleFreq = c("104" = 0.5, "108" = 0.210526315789474,
"118" = 0.210526315789474, "111" = 0.0789473684210526), missingFreq = 0.05,
numAlleles = 4L), list(name = "LOC2a-LOC2b", columnNames = c("LOC2a",
"LOC2b"), alleleFreq = c("202" = 0.5, "208" = 0.40625, "212" = 0.09375
), missingFreq = 0.2, numAlleles = 3L), list(name = "LOC3a-LOC3b",
columnNames = c("LOC3a", "LOC3b"), alleleFreq = c("304" = 0.366666666666667,
"311" = 0.366666666666667, "307" = 0.266666666666667),
missingFreq = 0.25, numAlleles = 3L), list(name = "LOC4a-LOC4b",
columnNames = c("LOC4a", "LOC4b"), alleleFreq = c("413" = 0.411764705882353,
"408" = 0.294117647058824, "418" = 0.235294117647059,
"420" = 0.0588235294117647), missingFreq = 0.15, numAlleles = 4L),
list(name = "LOC5a-LOC5b", columnNames = c("LOC5a", "LOC5b"
), alleleFreq = c("505" = 0.566666666666667, "501" = 0.4,
"519" = 0.0333333333333333), missingFreq = 0.25, numAlleles = 3L),
list(name = "LOC6a-LOC6b", columnNames = c("LOC6a", "LOC6b"
), alleleFreq = c("608" = 0.794117647058823, "620" = 0.117647058823529,
"605" = 0.0882352941176471), missingFreq = 0.15, numAlleles = 3L),
list(name = "LOC7a-LOC7b", columnNames = c("LOC7a", "LOC7b"
), alleleFreq = c("720" = 0.382352941176471, "705" = 0.205882352941176,
"717" = 0.176470588235294, "704" = 0.117647058823529, "702" = 0.117647058823529
), missingFreq = 0.15, numAlleles = 5L), list(name = "LOC8a-LOC8b",
columnNames = c("LOC8a", "LOC8b"), alleleFreq = c("810" = 0.388888888888889,
"819" = 0.305555555555556, "801" = 0.277777777777778,
"813" = 0.0277777777777778), missingFreq = 0.1, numAlleles = 4L),
list(name = "LOC9a-LOC9b", columnNames = c("LOC9a", "LOC9b"
), alleleFreq = c("902" = 0.40625, "920" = 0.25, "904" = 0.15625,
"909" = 0.125, "906" = 0.0625), missingFreq = 0.2, numAlleles = 5L),
list(name = "LOC10a-LOC10b", columnNames = c("LOC10a", "LOC10b"
), alleleFreq = c("1007" = 0.357142857142857, "1005" = 0.321428571428571,
"1019" = 0.285714285714286, "1013" = 0.0357142857142857),
missingFreq = 0.3, numAlleles = 4L))), class = "amAlleleFreq")
Code
print.amAlleleFreq(af)
Output
allelematch
amAlleleFreq object
Frequencies calculated after removal of missing data
LOC1a-LOC1b (4 alleles)
Allele 104 0.5
Allele 108 0.211
Allele 118 0.211
Allele 111 0.0789
LOC2a-LOC2b (3 alleles)
Allele 202 0.5
Allele 208 0.406
Allele 212 0.0938
LOC3a-LOC3b (3 alleles)
Allele 304 0.367
Allele 311 0.367
Allele 307 0.267
LOC4a-LOC4b (4 alleles)
Allele 413 0.412
Allele 408 0.294
Allele 418 0.235
Allele 420 0.0588
LOC5a-LOC5b (3 alleles)
Allele 505 0.567
Allele 501 0.4
Allele 519 0.0333
LOC6a-LOC6b (3 alleles)
Allele 608 0.794
Allele 620 0.118
Allele 605 0.0882
LOC7a-LOC7b (5 alleles)
Allele 720 0.382
Allele 705 0.206
Allele 717 0.176
Allele 704 0.118
Allele 702 0.118
LOC8a-LOC8b (4 alleles)
Allele 810 0.389
Allele 819 0.306
Allele 801 0.278
Allele 813 0.0278
LOC9a-LOC9b (5 alleles)
Allele 902 0.406
Allele 920 0.25
Allele 904 0.156
Allele 909 0.125
Allele 906 0.0625
LOC10a-LOC10b (4 alleles)
Allele 1007 0.357
Allele 1005 0.321
Allele 1019 0.286
Allele 1013 0.0357
Code
cat(cmdstr)
Output
amAlleleFreq(amdataExample5)
structure(list(multilocusMap = c(1L, 1L, 2L, 2L, 3L, 3L, 4L,
4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L), loci = list(
list(name = "LOC1a-LOC1b", columnNames = c("LOC1a", "LOC1b"
), alleleFreq = c("382" = 0.575, "384" = 0.4, "388" = 0.025
), missingFreq = 0, numAlleles = 3L), list(name = "LOC2a-LOC2b",
columnNames = c("LOC2a", "LOC2b"), alleleFreq = c("224" = 0.375,
"230" = 0.3, "232" = 0.15, "236" = 0.075, "242" = 0.05,
"244" = 0.025, "238" = 0.025), missingFreq = 0, numAlleles = 7L),
list(name = "LOC3a-LOC3b", columnNames = c("LOC3a", "LOC3b"
), alleleFreq = c("159" = 0.5, "155" = 0.25, "167" = 0.25
), missingFreq = 0.9, numAlleles = 3L), list(name = "LOC4a-LOC4b",
columnNames = c("LOC4a", "LOC4b"), alleleFreq = c("193" = 0.55,
"185" = 0.225, "181" = 0.1, "191" = 0.075, "199" = 0.05
), missingFreq = 0, numAlleles = 5L), list(name = "LOC5a-LOC5b",
columnNames = c("LOC5a", "LOC5b"), alleleFreq = c("299" = 0.578947368421053,
"285" = 0.315789473684211, "301" = 0.105263157894737),
missingFreq = 0.05, numAlleles = 3L), list(name = "LOC6a-LOC6b",
columnNames = c("LOC6a", "LOC6b"), alleleFreq = c("223" = 0.8,
"213" = 0.1, "227" = 0.05, "221" = 0.05), missingFreq = 0,
numAlleles = 4L), list(name = "LOC7a-LOC7b", columnNames = c("LOC7a",
"LOC7b"), alleleFreq = c("202" = 0.35, "210" = 0.225, "192" = 0.175,
"198" = 0.075, "204" = 0.075, "216" = 0.05, "214" = 0.05),
missingFreq = 0, numAlleles = 7L), list(name = "LOC8a-LOC8b",
columnNames = c("LOC8a", "LOC8b"), alleleFreq = c("118" = 0.425,
"106" = 0.225, "102" = 0.1, "116" = 0.075, "112" = 0.075,
"114" = 0.05, "108" = 0.05), missingFreq = 0, numAlleles = 7L),
list(name = "LOC9a-LOC9b", columnNames = c("LOC9a", "LOC9b"
), alleleFreq = c("296" = 0.45, "304" = 0.225, "288" = 0.175,
"298" = 0.1, "306" = 0.05), missingFreq = 0, numAlleles = 5L),
list(name = "LOC10a-LOC10b", columnNames = c("LOC10a", "LOC10b"
), alleleFreq = c("166" = 0.775, "172" = 0.125, "174" = 0.075,
"168" = 0.025), missingFreq = 0, numAlleles = 4L))), class = "amAlleleFreq")
Code
print.amAlleleFreq(af)
Output
allelematch
amAlleleFreq object
Frequencies calculated after removal of missing data
LOC1a-LOC1b (3 alleles)
Allele 382 0.575
Allele 384 0.4
Allele 388 0.025
LOC2a-LOC2b (7 alleles)
Allele 224 0.375
Allele 230 0.3
Allele 232 0.15
Allele 236 0.075
Allele 242 0.05
Allele 244 0.025
Allele 238 0.025
LOC3a-LOC3b (3 alleles)
Allele 159 0.5
Allele 155 0.25
Allele 167 0.25
LOC4a-LOC4b (5 alleles)
Allele 193 0.55
Allele 185 0.225
Allele 181 0.1
Allele 191 0.075
Allele 199 0.05
LOC5a-LOC5b (3 alleles)
Allele 299 0.579
Allele 285 0.316
Allele 301 0.105
LOC6a-LOC6b (4 alleles)
Allele 223 0.8
Allele 213 0.1
Allele 227 0.05
Allele 221 0.05
LOC7a-LOC7b (7 alleles)
Allele 202 0.35
Allele 210 0.225
Allele 192 0.175
Allele 198 0.075
Allele 204 0.075
Allele 216 0.05
Allele 214 0.05
LOC8a-LOC8b (7 alleles)
Allele 118 0.425
Allele 106 0.225
Allele 102 0.1
Allele 116 0.075
Allele 112 0.075
Allele 114 0.05
Allele 108 0.05
LOC9a-LOC9b (5 alleles)
Allele 296 0.45
Allele 304 0.225
Allele 288 0.175
Allele 298 0.1
Allele 306 0.05
LOC10a-LOC10b (4 alleles)
Allele 166 0.775
Allele 172 0.125
Allele 174 0.075
Allele 168 0.025
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