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Moved used datasets to /isnt/extdata (#25)

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This commit is contained in:
Waldir Leoncio 2023-08-09 10:54:48 +02:00
parent bb7eadd2ba
commit 687a6fb671
42 changed files with 44765 additions and 44759 deletions
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3
.Rbuildignore
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@ -4,7 +4,6 @@ PITFALLS.md
CHANGELOG.md
CITATION.cff
.travis.yml
inst/ext/ExamplesDataFormatting
inst/testdata
.github
aux

3
R/greedyMix.R
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@ -9,6 +9,9 @@
#' @references Samtools: a suite of programs for interacting
#' with high-throughput sequencing data. <http://www.htslib.org/>
#' @export
#' @examples
#' data <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS")
#' greedyMix(data)
greedyMix <- function(data, format, verbose = TRUE) {
# Parsing data format ------------------------------------------------------

2
R/load_fasta.R
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@ -9,7 +9,7 @@
#' @return A character matrix with filtered SNP data
#'
#' @examples
#' msa <- system.file("ext", "seqs.fa", package = "rBAPS")
#' msa <- system.file("extdata", "seqs.fa", package = "rBAPS")
#' snp.matrix <- load_fasta(msa)
#' @author Gerry Tonkin-Hill, Waldir Leoncio
#' @seealso rhierbaps::load_fasta

20
inst/ext/BAPS_format_clustering_diploid.txt → inst/extdata/BAPS_format_clustering_diploid.txt vendored
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@ -1,10 +1,10 @@
-9 102 56 80 100 90 118 90 88 104 1
-9 102 54 82 102 92 116 90 86 104 1
88 104 56 84 102 -9 120 90 88 100 2
86 102 56 80 102 -9 116 90 86 100 2
88 102 54 80 102 90 116 92 -9 100 3
88 102 56 80 100 90 118 90 -9 104 3
80 102 54 82 102 92 116 90 86 104 4
88 104 56 84 102 92 120 90 88 100 4
86 102 56 80 -9 90 116 90 86 100 5
88 102 54 80 -9 90 116 92 86 100 5
-9 102 56 80 100 90 118 90 88 104 1
-9 102 54 82 102 92 116 90 86 104 1
88 104 56 84 102 -9 120 90 88 100 2
86 102 56 80 102 -9 116 90 86 100 2
88 102 54 80 102 90 116 92 -9 100 3
88 102 56 80 100 90 118 90 -9 104 3
80 102 54 82 102 92 116 90 86 104 4
88 104 56 84 102 92 120 90 88 100 4
86 102 56 80 -9 90 116 90 86 100 5
88 102 54 80 -9 90 116 92 86 100 5

40
inst/ext/FASTA_clustering_haploid.fasta → inst/extdata/FASTA_clustering_haploid.fasta vendored
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@ -1,20 +1,20 @@
>1
AACGAAACGATCGCGTCACCGGAACGTTGTCCGTCTCGAATAGCACTGTGGGAACGTGTTTTACATTCGT
TAGTAACATGGTCAGCTGCTCATCCGTATT
>2
ATCAGCAAACGAGAAGTTGCAGAGGTCTTTGGTTTGAGCATTGCCCCCATACAATCGACTTCTGGCCTGG
AATGCACCACAAACATACCCCACAGGCTCG
>3
GCTTTTACTAAGGCCTATCGGATTCAACGTCACTAAGACTCGGCACTAACAGGCCGTTGTAAGCCGCTCT
GTCTGAGTATGGATGGTGGAGGCGGAGCCG
>4
ACCTGGACCTCTGTATTAACGGCTGTGATTCTGAGGGGGGTATCGCAGCGCACTTTCTAGCTATATCACG
CAAGGATAAAGTTCACCCATCACGTTGACC
>5
ACAATACGTCATCCACACCGCGCCTATGGAAGAATTTGCCCTTTCGGCGACAGCCCATGCTGTCAAGGAG
GTAACATAGCTACCAGGTCCCATTCCAGGA
>1
AACGAAACGATCGCGTCACCGGAACGTTGTCCGTCTCGAATAGCACTGTGGGAACGTGTTTTACATTCGT
TAGTAACATGGTCAGCTGCTCATCCGTATT
>2
ATCAGCAAACGAGAAGTTGCAGAGGTCTTTGGTTTGAGCATTGCCCCCATACAATCGACTTCTGGCCTGG
AATGCACCACAAACATACCCCACAGGCTCG
>3
GCTTTTACTAAGGCCTATCGGATTCAACGTCACTAAGACTCGGCACTAACAGGCCGTTGTAAGCCGCTCT
GTCTGAGTATGGATGGTGGAGGCGGAGCCG
>4
ACCTGGACCTCTGTATTAACGGCTGTGATTCTGAGGGGGGTATCGCAGCGCACTTTCTAGCTATATCACG
CAAGGATAAAGTTCACCCATCACGTTGACC
>5
ACAATACGTCATCCACACCGCGCCTATGGAAGAATTTGCCCTTTCGGCGACAGCCCATGCTGTCAAGGAG
GTAACATAGCTACCAGGTCCCATTCCAGGA

0
inst/ext/bam_example.bam → inst/extdata/bam_example.bam vendored
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0
inst/ext/sam_example.sam → inst/extdata/sam_example.sam vendored
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44290
inst/ext/seqs.fa → inst/extdata/seqs.fa vendored
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File diff suppressed because it is too large Load diff

0
inst/ext/vcf_example.vcf → inst/extdata/vcf_example.vcf vendored
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0
inst/ext/ExamplesDataFormatting/Example MLST DNA sequence data in concatenated Excel format.xls → inst/testdata/ExamplesDataFormatting/Example MLST DNA sequence data in concatenated Excel format.xls vendored
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216
inst/ext/ExamplesDataFormatting/Example baseline data in GENEPOP format for Trained clustering.txt → inst/testdata/ExamplesDataFormatting/Example baseline data in GENEPOP format for Trained clustering.txt vendored
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@ -1,108 +1,108 @@
Baseline data for trained clustering
1
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7
8
9
10
POP
Area1_1, 1717 1111 0000 0404 0505 0606 0707 1212 0707 1212
Area1_2, 0909 1010 0505 0404 0505 1010 0707 1111 0707 1212
Area1_3, 0000 1010 1414 0404 0505 0606 1111 1212 0707 1212
Area1_4, 1111 1010 1515 0404 0101 0606 1313 1111 0707 0808
Area1_5, 0101 1010 1212 0404 0505 0606 0909 1212 0707 1212
Area1_6, 1111 1010 1414 0404 0505 0606 1111 1212 0707 1010
Area1_7, 1515 1010 0707 0404 0505 0606 0707 1212 0707 1212
Area1_8, 1515 1212 0606 0404 0505 0606 1616 1212 0707 1010
Area1_9, 0909 1010 1010 0404 0505 0606 1919 1212 0707 1010
Area1_10, 0000 0000 0000 0404 0505 0606 1111 1010 0707 0000
Area1_11, 0000 0000 0000 0404 0505 0505 1919 1212 0404 1111
Area1_12, 1515 1010 0606 0404 0505 0606 1616 1212 0202 1212
Area1_13, 1515 1010 1515 0404 0505 0606 0707 0606 0707 1212
Area1_14, 0505 1010 1919 0404 0202 0606 1111 1010 0202 1212
Area1_15, 1111 1010 1414 0404 0505 0606 1616 0606 0707 1212
Area1_16, 1515 1212 0000 0404 0505 0606 1919 1212 0707 1212
Area1_17, 1515 1010 1515 0404 0505 0606 1919 1212 0707 1212
Area1_18, 1515 1010 1212 0404 0505 0606 0909 1212 0707 1010
Area1_19, 1515 1212 0606 0404 0505 0606 1515 1212 0707 1212
Area1_20, 1717 1414 1717 0404 0505 0606 0808 1212 0707 0808
Area1_21, 1515 1212 1212 0404 0505 0606 0808 1818 0707 1212
Area1_22, 1313 1111 1212 0404 0505 0606 1313 1212 0707 1212
Area1_23, 1515 1212 1212 0404 0505 0606 1313 1010 0707 1212
Area1_24, 0000 0000 0000 0404 0505 0606 1919 1212 0404 0000
Area1_25, 0000 0000 0000 0404 0202 0101 1919 1919 0707 1212
Area1_26, 1313 1010 0202 0404 0505 0606 1717 1212 0707 1212
POP
Area2_1, 1706 0505 1212 0404 0606 0808 1309 1111 0909 1413
Area2_2, 1511 0707 1209 0404 0602 0808 1111 1004 0902 1310
Area2_3, 1711 0000 1412 0402 0000 0000 1913 1002 0000 1313
Area2_4, 1715 1515 1412 0404 0505 0604 1313 1010 1007 1309
Area2_5, 1515 1515 1412 0404 0505 0606 1515 1111 0707 0908
Area2_6, 1309 0000 1212 0404 0603 0802 1311 1204 0903 1309
Area2_7, 1313 0505 1212 0404 0606 0808 1616 1414 0909 1206
Area2_8, 1307 0707 1212 0404 0606 0808 1313 1004 0909 1313
Area2_9, 0000 1212 1209 0404 0505 0606 0000 1106 0707 1208
Area2_10, 1307 0000 1212 0404 0606 0806 1313 1005 0909 1111
Area2_11, 0000 0707 1409 0505 0606 0808 1616 1110 0909 1309
Area2_12, 1807 0000 1212 0505 0606 0000 0909 0401 0909 1309
Area2_13, 1511 1212 1212 0404 0505 0604 1313 1110 0707 1210
Area2_14, 1111 1515 1412 0505 0606 0808 1414 1004 0909 1313
Area2_15, 1817 0707 1212 0505 0707 0909 1111 1004 0909 1313
Area2_16, 1913 1511 1212 0404 0606 0000 0909 1212 0909 1313
Area2_17, 1515 0000 0000 0000 0505 1006 1313 1005 0707 1212
Area2_18, 0707 0606 1408 0404 0202 0101 1313 1615 0202 1307
Area2_19, 0707 1309 0909 0502 0202 0101 2009 1510 0202 0704
POP
Area3_1, 1507 0706 1212 0202 0202 0000 0905 1409 0202 0707
Area3_2, 1507 1313 1212 0202 0202 0101 1613 1510 0202 0807
Area3_3, 1313 1414 1212 0404 0202 0101 1909 1510 0202 0704
Area3_4, 1515 0909 1212 0502 0202 0101 1409 1210 0202 0807
Area3_5, 1515 0808 1212 0502 0202 0101 1111 1510 0202 1007
Area3_6, 1306 0909 1212 0202 0202 0101 0807 1512 0202 0707
Area3_7, 0000 1009 1212 0404 0202 0101 1109 0702 0202 0808
Area3_8, 1507 0606 1212 0404 0202 0101 1908 1409 0202 0707
Area3_9, 1515 0606 1212 0202 0202 0101 0909 1510 0202 1207
Area3_10, 1307 1010 1412 0202 0202 0101 1709 1615 0202 1207
Area3_11, 1307 1005 1212 0404 0202 0101 1709 1510 0202 0703
Area3_12, 1109 0902 1212 0404 0202 0101 0909 1002 0202 1207
Area3_13, 1307 0606 1412 0404 0202 0101 0807 1515 0202 1207
Area3_14, 1717 1407 1212 0404 0202 0101 1107 1409 0202 0805
Area3_15, 1307 1007 1412 0404 0505 0101 0909 0000 0202 0807
Area3_16, 1811 0000 1212 0404 0505 0000 1515 0707 0000 1212
Area3_17, 1907 1414 1512 0402 0705 0000 0000 0000 0909 1212
POP
Area4_1, 1311 2019 1212 0404 0505 0000 1919 0707 0707 1109
Area4_2, 1309 2018 1512 0404 0505 0000 1919 0808 0707 1111
Area4_3, 1509 2118 1212 0404 0505 0000 1515 0707 0707 1107
Area4_4, 1715 2221 1512 0404 0505 0000 1919 0707 0707 1111
Area4_5, 1515 2121 1512 0404 0505 0000 1515 0707 0606 0707
Area4_6, 1717 2222 1512 0404 0505 0000 1913 0707 0707 0907
Area4_7, 1715 2221 1512 0404 0505 0000 1313 0707 0606 1111
Area4_8, 1813 2320 1512 0404 0505 0000 1515 0707 0707 1107
Area4_9, 1311 2019 1512 0404 0505 0000 1515 0707 0707 1111
Area4_10, 1311 2019 1512 0000 0505 0000 1313 0707 0707 0909
Area4_11, 1111 2625 0000 0000 0505 0606 0707 0903 0505 0505
Area4_12, 0907 2724 0000 0404 0505 0605 1914 1105 0505 0707
Area4_13, 1511 1610 1212 0404 0505 0605 1513 1105 1107 0704
Area4_14, 1513 0404 1111 0404 0505 0606 1515 1111 1207 1107
Area4_15, 1311 1616 1212 0404 0505 0606 1313 1111 0707 1107
Area4_16, 1109 0606 1212 0404 0000 0000 1515 0902 0807 0505
Area4_17, 1107 1004 1506 0404 0505 0606 1515 1212 0707 1108
Area4_18, 1107 0904 1512 0404 0505 0606 1913 1105 1107 1107
Area4_19, 1109 1313 1212 0404 0505 0606 1915 1111 1007 1107
Area4_20, 1711 1604 1212 0404 0505 0606 1915 1212 1107 1007
Area4_21, 1111 0606 1515 0404 0505 0606 1707 1009 0807 0502
Area4_22, 1311 0603 1512 0404 0505 0606 1714 0707 0807 0501
POP
Area5_1, 0711 1212 1513 0202 0707 0808 1408 0000 0909 1210
Area5_2, 1118 0101 1212 0202 0803 0901 0808 0000 1101 1211
Area5_3, 1518 0000 1512 0404 0707 0806 0909 0000 0909 1212
Area5_4, 1309 0000 1512 0202 0606 0707 1508 0000 0808 1204
Area5_5, 0718 0000 1512 0402 0707 0806 0707 0000 0909 1208
Area5_6, 1818 1414 1212 0404 0707 0000 1916 0000 0909 1208
Area5_7, 1318 1313 1212 0404 0606 0000 1908 0000 0808 1008
Area5_8, 1818 0000 1212 0404 0000 0806 1616 0000 0808 1212
Baseline data for trained clustering
1
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3
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POP
Area1_1, 1717 1111 0000 0404 0505 0606 0707 1212 0707 1212
Area1_2, 0909 1010 0505 0404 0505 1010 0707 1111 0707 1212
Area1_3, 0000 1010 1414 0404 0505 0606 1111 1212 0707 1212
Area1_4, 1111 1010 1515 0404 0101 0606 1313 1111 0707 0808
Area1_5, 0101 1010 1212 0404 0505 0606 0909 1212 0707 1212
Area1_6, 1111 1010 1414 0404 0505 0606 1111 1212 0707 1010
Area1_7, 1515 1010 0707 0404 0505 0606 0707 1212 0707 1212
Area1_8, 1515 1212 0606 0404 0505 0606 1616 1212 0707 1010
Area1_9, 0909 1010 1010 0404 0505 0606 1919 1212 0707 1010
Area1_10, 0000 0000 0000 0404 0505 0606 1111 1010 0707 0000
Area1_11, 0000 0000 0000 0404 0505 0505 1919 1212 0404 1111
Area1_12, 1515 1010 0606 0404 0505 0606 1616 1212 0202 1212
Area1_13, 1515 1010 1515 0404 0505 0606 0707 0606 0707 1212
Area1_14, 0505 1010 1919 0404 0202 0606 1111 1010 0202 1212
Area1_15, 1111 1010 1414 0404 0505 0606 1616 0606 0707 1212
Area1_16, 1515 1212 0000 0404 0505 0606 1919 1212 0707 1212
Area1_17, 1515 1010 1515 0404 0505 0606 1919 1212 0707 1212
Area1_18, 1515 1010 1212 0404 0505 0606 0909 1212 0707 1010
Area1_19, 1515 1212 0606 0404 0505 0606 1515 1212 0707 1212
Area1_20, 1717 1414 1717 0404 0505 0606 0808 1212 0707 0808
Area1_21, 1515 1212 1212 0404 0505 0606 0808 1818 0707 1212
Area1_22, 1313 1111 1212 0404 0505 0606 1313 1212 0707 1212
Area1_23, 1515 1212 1212 0404 0505 0606 1313 1010 0707 1212
Area1_24, 0000 0000 0000 0404 0505 0606 1919 1212 0404 0000
Area1_25, 0000 0000 0000 0404 0202 0101 1919 1919 0707 1212
Area1_26, 1313 1010 0202 0404 0505 0606 1717 1212 0707 1212
POP
Area2_1, 1706 0505 1212 0404 0606 0808 1309 1111 0909 1413
Area2_2, 1511 0707 1209 0404 0602 0808 1111 1004 0902 1310
Area2_3, 1711 0000 1412 0402 0000 0000 1913 1002 0000 1313
Area2_4, 1715 1515 1412 0404 0505 0604 1313 1010 1007 1309
Area2_5, 1515 1515 1412 0404 0505 0606 1515 1111 0707 0908
Area2_6, 1309 0000 1212 0404 0603 0802 1311 1204 0903 1309
Area2_7, 1313 0505 1212 0404 0606 0808 1616 1414 0909 1206
Area2_8, 1307 0707 1212 0404 0606 0808 1313 1004 0909 1313
Area2_9, 0000 1212 1209 0404 0505 0606 0000 1106 0707 1208
Area2_10, 1307 0000 1212 0404 0606 0806 1313 1005 0909 1111
Area2_11, 0000 0707 1409 0505 0606 0808 1616 1110 0909 1309
Area2_12, 1807 0000 1212 0505 0606 0000 0909 0401 0909 1309
Area2_13, 1511 1212 1212 0404 0505 0604 1313 1110 0707 1210
Area2_14, 1111 1515 1412 0505 0606 0808 1414 1004 0909 1313
Area2_15, 1817 0707 1212 0505 0707 0909 1111 1004 0909 1313
Area2_16, 1913 1511 1212 0404 0606 0000 0909 1212 0909 1313
Area2_17, 1515 0000 0000 0000 0505 1006 1313 1005 0707 1212
Area2_18, 0707 0606 1408 0404 0202 0101 1313 1615 0202 1307
Area2_19, 0707 1309 0909 0502 0202 0101 2009 1510 0202 0704
POP
Area3_1, 1507 0706 1212 0202 0202 0000 0905 1409 0202 0707
Area3_2, 1507 1313 1212 0202 0202 0101 1613 1510 0202 0807
Area3_3, 1313 1414 1212 0404 0202 0101 1909 1510 0202 0704
Area3_4, 1515 0909 1212 0502 0202 0101 1409 1210 0202 0807
Area3_5, 1515 0808 1212 0502 0202 0101 1111 1510 0202 1007
Area3_6, 1306 0909 1212 0202 0202 0101 0807 1512 0202 0707
Area3_7, 0000 1009 1212 0404 0202 0101 1109 0702 0202 0808
Area3_8, 1507 0606 1212 0404 0202 0101 1908 1409 0202 0707
Area3_9, 1515 0606 1212 0202 0202 0101 0909 1510 0202 1207
Area3_10, 1307 1010 1412 0202 0202 0101 1709 1615 0202 1207
Area3_11, 1307 1005 1212 0404 0202 0101 1709 1510 0202 0703
Area3_12, 1109 0902 1212 0404 0202 0101 0909 1002 0202 1207
Area3_13, 1307 0606 1412 0404 0202 0101 0807 1515 0202 1207
Area3_14, 1717 1407 1212 0404 0202 0101 1107 1409 0202 0805
Area3_15, 1307 1007 1412 0404 0505 0101 0909 0000 0202 0807
Area3_16, 1811 0000 1212 0404 0505 0000 1515 0707 0000 1212
Area3_17, 1907 1414 1512 0402 0705 0000 0000 0000 0909 1212
POP
Area4_1, 1311 2019 1212 0404 0505 0000 1919 0707 0707 1109
Area4_2, 1309 2018 1512 0404 0505 0000 1919 0808 0707 1111
Area4_3, 1509 2118 1212 0404 0505 0000 1515 0707 0707 1107
Area4_4, 1715 2221 1512 0404 0505 0000 1919 0707 0707 1111
Area4_5, 1515 2121 1512 0404 0505 0000 1515 0707 0606 0707
Area4_6, 1717 2222 1512 0404 0505 0000 1913 0707 0707 0907
Area4_7, 1715 2221 1512 0404 0505 0000 1313 0707 0606 1111
Area4_8, 1813 2320 1512 0404 0505 0000 1515 0707 0707 1107
Area4_9, 1311 2019 1512 0404 0505 0000 1515 0707 0707 1111
Area4_10, 1311 2019 1512 0000 0505 0000 1313 0707 0707 0909
Area4_11, 1111 2625 0000 0000 0505 0606 0707 0903 0505 0505
Area4_12, 0907 2724 0000 0404 0505 0605 1914 1105 0505 0707
Area4_13, 1511 1610 1212 0404 0505 0605 1513 1105 1107 0704
Area4_14, 1513 0404 1111 0404 0505 0606 1515 1111 1207 1107
Area4_15, 1311 1616 1212 0404 0505 0606 1313 1111 0707 1107
Area4_16, 1109 0606 1212 0404 0000 0000 1515 0902 0807 0505
Area4_17, 1107 1004 1506 0404 0505 0606 1515 1212 0707 1108
Area4_18, 1107 0904 1512 0404 0505 0606 1913 1105 1107 1107
Area4_19, 1109 1313 1212 0404 0505 0606 1915 1111 1007 1107
Area4_20, 1711 1604 1212 0404 0505 0606 1915 1212 1107 1007
Area4_21, 1111 0606 1515 0404 0505 0606 1707 1009 0807 0502
Area4_22, 1311 0603 1512 0404 0505 0606 1714 0707 0807 0501
POP
Area5_1, 0711 1212 1513 0202 0707 0808 1408 0000 0909 1210
Area5_2, 1118 0101 1212 0202 0803 0901 0808 0000 1101 1211
Area5_3, 1518 0000 1512 0404 0707 0806 0909 0000 0909 1212
Area5_4, 1309 0000 1512 0202 0606 0707 1508 0000 0808 1204
Area5_5, 0718 0000 1512 0402 0707 0806 0707 0000 0909 1208
Area5_6, 1818 1414 1212 0404 0707 0000 1916 0000 0909 1208
Area5_7, 1318 1313 1212 0404 0606 0000 1908 0000 0808 1008
Area5_8, 1818 0000 1212 0404 0000 0806 1616 0000 0808 1212

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inst/ext/ExamplesDataFormatting/Example coordinates for the spatial clustering of DNA sequences.txt → inst/testdata/ExamplesDataFormatting/Example coordinates for the spatial clustering of DNA sequences.txt vendored
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@ -1,5 +1,5 @@
3.1013610e+006 6.7104850e+006
3.1011410e+006 6.7108850e+006
3.1015790e+006 6.7101790e+006
3.1015910e+006 6.7100650e+006
3.1013610e+006 6.7104850e+006
3.1011410e+006 6.7108850e+006
3.1015790e+006 6.7101790e+006
3.1015910e+006 6.7100650e+006
3.1017660e+006 6.7104190e+006

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inst/ext/ExamplesDataFormatting/Example coordinates for the spatial clustering.txt → inst/testdata/ExamplesDataFormatting/Example coordinates for the spatial clustering.txt vendored
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@ -1,10 +1,10 @@
3.1013610e+006 6.7104850e+006
3.1016310e+006 6.7101990e+006
3.1015790e+006 6.7101790e+006
3.1015910e+006 6.7100650e+006
3.1017660e+006 6.7104190e+006
3.1017500e+006 6.7106040e+006
3.1019250e+006 6.7092640e+006
3.1017430e+006 6.7094990e+006
3.1015240e+006 6.7097430e+006
0 0
3.1013610e+006 6.7104850e+006
3.1016310e+006 6.7101990e+006
3.1015790e+006 6.7101790e+006
3.1015910e+006 6.7100650e+006
3.1017660e+006 6.7104190e+006
3.1017500e+006 6.7106040e+006
3.1019250e+006 6.7092640e+006
3.1017430e+006 6.7094990e+006
3.1015240e+006 6.7097430e+006
0 0

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inst/ext/ExamplesDataFormatting/Example data in BAPS format for clustering of diploid individuals.txt → inst/testdata/ExamplesDataFormatting/Example data in BAPS format for clustering of diploid individuals.txt vendored
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@ -1,10 +1,10 @@
-9 102 56 80 100 90 118 90 88 104 1
-9 102 54 82 102 92 116 90 86 104 1
88 104 56 84 102 -9 120 90 88 100 2
86 102 56 80 102 -9 116 90 86 100 2
88 102 54 80 102 90 116 92 -9 100 3
88 102 56 80 100 90 118 90 -9 104 3
80 102 54 82 102 92 116 90 86 104 4
88 104 56 84 102 92 120 90 88 100 4
86 102 56 80 -9 90 116 90 86 100 5
88 102 54 80 -9 90 116 92 86 100 5
-9 102 56 80 100 90 118 90 88 104 1
-9 102 54 82 102 92 116 90 86 104 1
88 104 56 84 102 -9 120 90 88 100 2
86 102 56 80 102 -9 116 90 86 100 2
88 102 54 80 102 90 116 92 -9 100 3
88 102 56 80 100 90 118 90 -9 104 3
80 102 54 82 102 92 116 90 86 104 4
88 104 56 84 102 92 120 90 88 100 4
86 102 56 80 -9 90 116 90 86 100 5
88 102 54 80 -9 90 116 92 86 100 5

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inst/ext/ExamplesDataFormatting/Example data in BAPS format for clustering of haploid individuals.txt → inst/testdata/ExamplesDataFormatting/Example data in BAPS format for clustering of haploid individuals.txt vendored
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@ -1,5 +1,5 @@
88 102 56 80 100 90 118 -9 88 104 1
80 102 54 82 102 92 116 90 86 104 2
88 104 56 84 102 -9 120 90 88 100 3
86 102 56 80 102 90 116 90 86 100 4
88 102 -9 80 102 90 116 92 86 100 5
88 102 56 80 100 90 118 -9 88 104 1
80 102 54 82 102 92 116 90 86 104 2
88 104 56 84 102 -9 120 90 88 100 3
86 102 56 80 102 90 116 90 86 100 4
88 102 -9 80 102 90 116 92 86 100 5

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inst/ext/ExamplesDataFormatting/Example data in BAPS format for clustering of tetraploid individuals.txt → inst/testdata/ExamplesDataFormatting/Example data in BAPS format for clustering of tetraploid individuals.txt vendored
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@ -1,20 +1,20 @@
88 102 56 80 100 90 118 90 88 104 1
80 102 54 82 102 92 116 90 86 104 1
88 102 56 80 100 90 118 90 88 104 1
80 102 54 82 102 92 116 90 86 104 1
88 -9 56 84 102 92 120 90 88 100 2
86 -9 56 80 102 90 116 90 86 102 2
88 -9 56 84 102 92 120 90 88 100 2
86 -9 56 80 102 90 116 90 86 100 2
88 102 54 82 102 90 116 92 86 102 3
88 102 56 80 100 90 118 90 88 104 3
88 102 54 80 102 90 116 92 86 102 3
88 102 56 80 100 90 118 90 88 104 3
80 102 54 82 102 92 116 -9 86 104 4
88 104 56 84 102 92 120 -9 88 100 4
80 102 54 82 102 92 116 -9 86 104 4
88 104 56 84 102 92 120 -9 88 100 4
86 102 56 80 102 90 116 90 86 100 5
88 104 54 80 102 90 116 92 86 100 5
86 102 56 80 104 90 116 90 86 100 5
88 102 54 80 102 90 116 92 86 100 5
88 102 56 80 100 90 118 90 88 104 1
80 102 54 82 102 92 116 90 86 104 1
88 102 56 80 100 90 118 90 88 104 1
80 102 54 82 102 92 116 90 86 104 1
88 -9 56 84 102 92 120 90 88 100 2
86 -9 56 80 102 90 116 90 86 102 2
88 -9 56 84 102 92 120 90 88 100 2
86 -9 56 80 102 90 116 90 86 100 2
88 102 54 82 102 90 116 92 86 102 3
88 102 56 80 100 90 118 90 88 104 3
88 102 54 80 102 90 116 92 86 102 3
88 102 56 80 100 90 118 90 88 104 3
80 102 54 82 102 92 116 -9 86 104 4
88 104 56 84 102 92 120 -9 88 100 4
80 102 54 82 102 92 116 -9 86 104 4
88 104 56 84 102 92 120 -9 88 100 4
86 102 56 80 102 90 116 90 86 100 5
88 104 54 80 102 90 116 92 86 100 5
86 102 56 80 104 90 116 90 86 100 5
88 102 54 80 102 90 116 92 86 100 5

20
inst/ext/ExamplesDataFormatting/Example data in BAPS format for group-wise clustering of diploid individuals.txt → inst/testdata/ExamplesDataFormatting/Example data in BAPS format for group-wise clustering of diploid individuals.txt vendored
View file

@ -1,10 +1,10 @@
-9 102 56 80 100 90 118 90 88 104 1
-9 102 54 82 102 92 116 90 86 104 1
88 104 56 84 102 -9 120 90 88 100 1
86 102 56 80 102 -9 116 90 86 100 1
88 102 54 80 102 90 116 92 -9 100 2
88 102 56 80 100 90 118 90 -9 104 2
80 102 54 82 102 92 116 90 86 104 2
88 104 56 84 102 92 120 90 88 100 2
86 102 56 80 -9 90 116 90 86 100 3
88 102 54 80 -9 90 116 92 86 100 3
-9 102 56 80 100 90 118 90 88 104 1
-9 102 54 82 102 92 116 90 86 104 1
88 104 56 84 102 -9 120 90 88 100 1
86 102 56 80 102 -9 116 90 86 100 1
88 102 54 80 102 90 116 92 -9 100 2
88 102 56 80 100 90 118 90 -9 104 2
80 102 54 82 102 92 116 90 86 104 2
88 104 56 84 102 92 120 90 88 100 2
86 102 56 80 -9 90 116 90 86 100 3
88 102 54 80 -9 90 116 92 86 100 3

10
inst/ext/ExamplesDataFormatting/Example data in BAPS format for group-wise clustering of haploid individuals.txt → inst/testdata/ExamplesDataFormatting/Example data in BAPS format for group-wise clustering of haploid individuals.txt vendored
View file

@ -1,5 +1,5 @@
88 102 56 80 100 90 118 -9 88 104 1
80 102 54 82 102 92 116 90 86 104 1
88 104 56 84 102 -9 120 90 88 100 2
86 102 56 80 102 90 116 90 86 100 2
88 102 -9 80 102 90 116 92 86 100 3
88 102 56 80 100 90 118 -9 88 104 1
80 102 54 82 102 92 116 90 86 104 1
88 104 56 84 102 -9 120 90 88 100 2
86 102 56 80 102 90 116 90 86 100 2
88 102 -9 80 102 90 116 92 86 100 3

40
inst/ext/ExamplesDataFormatting/Example data in BAPS format for group-wise clustering of tetraploid individuals.txt → inst/testdata/ExamplesDataFormatting/Example data in BAPS format for group-wise clustering of tetraploid individuals.txt vendored
View file

@ -1,20 +1,20 @@
88 102 56 80 100 90 118 90 88 104 1
80 102 54 82 102 92 116 90 86 104 1
88 102 56 80 100 90 118 90 88 104 1
80 102 54 82 102 92 116 90 86 104 1
88 -9 56 84 102 92 120 90 88 100 1
86 -9 56 80 102 90 116 90 86 102 1
88 -9 56 84 102 92 120 90 88 100 1
86 -9 56 80 102 90 116 90 86 100 1
88 102 54 82 102 90 116 92 86 102 2
88 102 56 80 100 90 118 90 88 104 2
88 102 54 80 102 90 116 92 86 102 2
88 102 56 80 100 90 118 90 88 104 2
80 102 54 82 102 92 116 -9 86 104 2
88 104 56 84 102 92 120 -9 88 100 2
80 102 54 82 102 92 116 -9 86 104 2
88 104 56 84 102 92 120 -9 88 100 2
86 102 56 80 102 90 116 90 86 100 3
88 104 54 80 102 90 116 92 86 100 3
86 102 56 80 104 90 116 90 86 100 3
88 102 54 80 102 90 116 92 86 100 3
88 102 56 80 100 90 118 90 88 104 1
80 102 54 82 102 92 116 90 86 104 1
88 102 56 80 100 90 118 90 88 104 1
80 102 54 82 102 92 116 90 86 104 1
88 -9 56 84 102 92 120 90 88 100 1
86 -9 56 80 102 90 116 90 86 102 1
88 -9 56 84 102 92 120 90 88 100 1
86 -9 56 80 102 90 116 90 86 100 1
88 102 54 82 102 90 116 92 86 102 2
88 102 56 80 100 90 118 90 88 104 2
88 102 54 80 102 90 116 92 86 102 2
88 102 56 80 100 90 118 90 88 104 2
80 102 54 82 102 92 116 -9 86 104 2
88 104 56 84 102 92 120 -9 88 100 2
80 102 54 82 102 92 116 -9 86 104 2
88 104 56 84 102 92 120 -9 88 100 2
86 102 56 80 102 90 116 90 86 100 3
88 104 54 80 102 90 116 92 86 100 3
86 102 56 80 104 90 116 90 86 100 3
88 102 54 80 102 90 116 92 86 100 3

40
inst/ext/ExamplesDataFormatting/Example data in FASTA format for clustering of haploid individuals.fasta → inst/testdata/ExamplesDataFormatting/Example data in FASTA format for clustering of haploid individuals.fasta vendored
View file

@ -1,20 +1,20 @@
>1
AACGAAACGATCGCGTCACCGGAACGTTGTCCGTCTCGAATAGCACTGTGGGAACGTGTTTTACATTCGT
TAGTAACATGGTCAGCTGCTCATCCGTATT
>2
ATCAGCAAACGAGAAGTTGCAGAGGTCTTTGGTTTGAGCATTGCCCCCATACAATCGACTTCTGGCCTGG
AATGCACCACAAACATACCCCACAGGCTCG
>3
GCTTTTACTAAGGCCTATCGGATTCAACGTCACTAAGACTCGGCACTAACAGGCCGTTGTAAGCCGCTCT
GTCTGAGTATGGATGGTGGAGGCGGAGCCG
>4
ACCTGGACCTCTGTATTAACGGCTGTGATTCTGAGGGGGGTATCGCAGCGCACTTTCTAGCTATATCACG
CAAGGATAAAGTTCACCCATCACGTTGACC
>5
ACAATACGTCATCCACACCGCGCCTATGGAAGAATTTGCCCTTTCGGCGACAGCCCATGCTGTCAAGGAG
GTAACATAGCTACCAGGTCCCATTCCAGGA
>1
AACGAAACGATCGCGTCACCGGAACGTTGTCCGTCTCGAATAGCACTGTGGGAACGTGTTTTACATTCGT
TAGTAACATGGTCAGCTGCTCATCCGTATT
>2
ATCAGCAAACGAGAAGTTGCAGAGGTCTTTGGTTTGAGCATTGCCCCCATACAATCGACTTCTGGCCTGG
AATGCACCACAAACATACCCCACAGGCTCG
>3
GCTTTTACTAAGGCCTATCGGATTCAACGTCACTAAGACTCGGCACTAACAGGCCGTTGTAAGCCGCTCT
GTCTGAGTATGGATGGTGGAGGCGGAGCCG
>4
ACCTGGACCTCTGTATTAACGGCTGTGATTCTGAGGGGGGTATCGCAGCGCACTTTCTAGCTATATCACG
CAAGGATAAAGTTCACCCATCACGTTGACC
>5
ACAATACGTCATCCACACCGCGCCTATGGAAGAATTTGCCCTTTCGGCGACAGCCCATGCTGTCAAGGAG
GTAACATAGCTACCAGGTCCCATTCCAGGA

16
inst/ext/ExamplesDataFormatting/Example of a BAPS formatted diploid sequence file for clustering with linked loci.txt → inst/testdata/ExamplesDataFormatting/Example of a BAPS formatted diploid sequence file for clustering with linked loci.txt vendored
View file

@ -1,8 +1,8 @@
CTAACGCTTGAGCTTATTGCTGCAGCGCAGAAAGTAGGTAAAACGTGTGCATTCGTTGATGCGGAA 1
GCACTTGACCCTATCTACGCTCAAAAGCTTGGTGTTGATATTGACGCTTTGCTTGTATCTCAACCT 1
GATACGGGTGAACAAGCTCTAGAAATTTGTGATGCACTGGCTCGTTCAGGTGCTATCGATGTTCTT 2
GTTATCTAC--GGTTGCTGCACTAACACCT-AGCTGAGATCGA-GGCGAAATGGGCGATAGCCACA 2
CTAACGCTTGAGCTTATTGCTGCAGCGCAGAAAGTAGGTAAAACGTGTGCATTCGTTGATGCGGAA 3
GCACTTGACCCTATCTACGCTCAAAAGCTTGGTGTTGATATTGACGCTTTGCTTGTATCTCAACCT 3
GATACGGGTGAACAAGCTCTAGAAATTTGTGATGCACTGGCTCGTTCAGGTGCTATCGATGTTCTT 4
GTTATCTAC--GGTTGCTGCACTAACACCT-AGCTGAGATCGA-GGCGAAATGGGCGATAGCCACA 4
CTAACGCTTGAGCTTATTGCTGCAGCGCAGAAAGTAGGTAAAACGTGTGCATTCGTTGATGCGGAA 1
GCACTTGACCCTATCTACGCTCAAAAGCTTGGTGTTGATATTGACGCTTTGCTTGTATCTCAACCT 1
GATACGGGTGAACAAGCTCTAGAAATTTGTGATGCACTGGCTCGTTCAGGTGCTATCGATGTTCTT 2
GTTATCTAC--GGTTGCTGCACTAACACCT-AGCTGAGATCGA-GGCGAAATGGGCGATAGCCACA 2
CTAACGCTTGAGCTTATTGCTGCAGCGCAGAAAGTAGGTAAAACGTGTGCATTCGTTGATGCGGAA 3
GCACTTGACCCTATCTACGCTCAAAAGCTTGGTGTTGATATTGACGCTTTGCTTGTATCTCAACCT 3
GATACGGGTGAACAAGCTCTAGAAATTTGTGATGCACTGGCTCGTTCAGGTGCTATCGATGTTCTT 4
GTTATCTAC--GGTTGCTGCACTAACACCT-AGCTGAGATCGA-GGCGAAATGGGCGATAGCCACA 4

8
inst/ext/ExamplesDataFormatting/Example of a BAPS formatted haploid sequence file for clustering with linked loci.txt → inst/testdata/ExamplesDataFormatting/Example of a BAPS formatted haploid sequence file for clustering with linked loci.txt vendored
View file

@ -1,4 +1,4 @@
CTAACGCTTGAGCTTATTGCTGCAGCGCAGAAAGTAGGTAAAACGTGTGCATTCGTTGATGCGGAA 1
GATACGGGTGAACAAGCTCTAGAAATTTGTGATGCACTGGCTCGTTCAGGTGCTATCGATGTTCTT 2
CTAACGCTTGAGCTTATTGCTGCAGCGCAGAAAGTAGGTAAAACGTGTGCATTCGTTGATGCGGAA 3
GTTATCTAC--GGTTGCTGCACTAACACCT-AGCTGAGATCGA-GGCGAAATGGGCGATAGCCACA 4
CTAACGCTTGAGCTTATTGCTGCAGCGCAGAAAGTAGGTAAAACGTGTGCATTCGTTGATGCGGAA 1
GATACGGGTGAACAAGCTCTAGAAATTTGTGATGCACTGGCTCGTTCAGGTGCTATCGATGTTCTT 2
CTAACGCTTGAGCTTATTGCTGCAGCGCAGAAAGTAGGTAAAACGTGTGCATTCGTTGATGCGGAA 3
GTTATCTAC--GGTTGCTGCACTAACACCT-AGCTGAGATCGA-GGCGAAATGGGCGATAGCCACA 4

32
inst/ext/ExamplesDataFormatting/Example of a BAPS formatted tetraploid sequence file for clustering with linked loci.txt → inst/testdata/ExamplesDataFormatting/Example of a BAPS formatted tetraploid sequence file for clustering with linked loci.txt vendored
View file

@ -1,16 +1,16 @@
CTAACGCTTGAGCTTATTGCTGCAGCGCAGAAAGTAGGTAAAACGTGTGCATTCGTTGATGCGGAA 1
GCACTTGACCCTATCTACGCTCAAAAGCTTGGTGTTGATATTGACGCTTTGCTTGTATCTCAACCT 1
GATACGGGTGAACAAGCTCTAGAAATTTGTGATGCACTGGCTCGTTCAGGTGCTATCGATGTTCTT 1
GTTATTGACTCGGTTGCTGCACTAACACCT-AGCTGAGATCGA-GGCGAAATGGGCGATAGCCACA 1
TATCTAC--GAGCTTATTGCTGCAGCGCAGAAAGTAGGTAAAACGTGTGCATTCGTTGATGCGGAA 2
GCACTTGACCCTATCTACGCTCAAAAGCTTGGTGTTGATATTGACGCTTTGCTTGTATCTCAACCT 2
GATACGGGTGAACAAGCTCTAGAAATTTGTGATGCACTGGCTCGTTCAGGTGCTATCGATGTTCTT 2
GTTATCTAC--GGTTGCTGCACTAACACCT-AGCTGAGATCGA-GGCGAAATGGGCGATAGCCACA 2
CTAACGCTTGAGCTTATTGCTGCAGCGCAGAAAGTAGGTAAAACGTGTGCATTCGTTGATGCGGAA 3
GCACTTGACCCTATCTACGCTCAAAAGCTTGGTGTTGATATTGACGCTTTGCTTGTATCTCAACCT 3
GATACGGGTGAACAAGCTCTAGAAATTTGTGATGCACTGGCTCGTTCAGGTGCTATCGATGTTCTT 3
GTTATTGACTCGGTTGCTGCACTAACACCT-AGCTGAGATCGA-GGCGAAATGGGCGATAGCCACA 3
TATCTAC--GAGCTTATTGCTGCAGCGCAGAAAGTAGGTAAAACGTGTGCATTCGTTGATGCGGAA 4
GCACTTGACCCTATCTACGCTCAAAAGCTTGGTGTTGATATTGACGCTTTGCTTGTATCTCAACCT 4
GATACGGGTGAACAAGCTCTAGAAATTTGTGATGCACTGGCTCGTTCAGGTGCTATCGATGTTCTT 4
GTTATCTAC--GGTTGCTGCACTAACACCT-AGCTGAGATCGA-GGCGAAATGGGCGATAGCCACA 4
CTAACGCTTGAGCTTATTGCTGCAGCGCAGAAAGTAGGTAAAACGTGTGCATTCGTTGATGCGGAA 1
GCACTTGACCCTATCTACGCTCAAAAGCTTGGTGTTGATATTGACGCTTTGCTTGTATCTCAACCT 1
GATACGGGTGAACAAGCTCTAGAAATTTGTGATGCACTGGCTCGTTCAGGTGCTATCGATGTTCTT 1
GTTATTGACTCGGTTGCTGCACTAACACCT-AGCTGAGATCGA-GGCGAAATGGGCGATAGCCACA 1
TATCTAC--GAGCTTATTGCTGCAGCGCAGAAAGTAGGTAAAACGTGTGCATTCGTTGATGCGGAA 2
GCACTTGACCCTATCTACGCTCAAAAGCTTGGTGTTGATATTGACGCTTTGCTTGTATCTCAACCT 2
GATACGGGTGAACAAGCTCTAGAAATTTGTGATGCACTGGCTCGTTCAGGTGCTATCGATGTTCTT 2
GTTATCTAC--GGTTGCTGCACTAACACCT-AGCTGAGATCGA-GGCGAAATGGGCGATAGCCACA 2
CTAACGCTTGAGCTTATTGCTGCAGCGCAGAAAGTAGGTAAAACGTGTGCATTCGTTGATGCGGAA 3
GCACTTGACCCTATCTACGCTCAAAAGCTTGGTGTTGATATTGACGCTTTGCTTGTATCTCAACCT 3
GATACGGGTGAACAAGCTCTAGAAATTTGTGATGCACTGGCTCGTTCAGGTGCTATCGATGTTCTT 3
GTTATTGACTCGGTTGCTGCACTAACACCT-AGCTGAGATCGA-GGCGAAATGGGCGATAGCCACA 3
TATCTAC--GAGCTTATTGCTGCAGCGCAGAAAGTAGGTAAAACGTGTGCATTCGTTGATGCGGAA 4
GCACTTGACCCTATCTACGCTCAAAAGCTTGGTGTTGATATTGACGCTTTGCTTGTATCTCAACCT 4
GATACGGGTGAACAAGCTCTAGAAATTTGTGATGCACTGGCTCGTTCAGGTGCTATCGATGTTCTT 4
GTTATCTAC--GGTTGCTGCACTAACACCT-AGCTGAGATCGA-GGCGAAATGGGCGATAGCCACA 4

16
inst/ext/ExamplesDataFormatting/Example of a fasta formatted sequence file for gene recA.txt → inst/testdata/ExamplesDataFormatting/Example of a fasta formatted sequence file for gene recA.txt vendored
View file

@ -1,8 +1,8 @@
>RecA-1
CTAACGCTTGAGCTTATT-CTGCAGCCAAATTCGTATGAAAATTGGTGTAATGTTCGGTAACCTAACGCTTGAGCTTATT-CTGCAGCCAAATTCGTATGAAAATTGGTGTAATGTTCGGTAAC
>RecA-2
CTAACGCTTGAGCTTATTGCTGCAGCACAGA-AGTGGGCAAAACGTGTGCATTCGTCGATGCCTAACGCTTGAGCTTATT-CTGCAGCCAAATTCGTATGAAAATTGGTGTAATGTTCGGTAAC
>RecA-3
CTAACGC--GAGCTTATT-CTGCAGCCAAATTCGTATGAAAATTGGTGTAATGTTCGGTAACCTAACGCTTGAGCTTATT-CTGCAGCCAAATTCGTATGAAAATTGGTGTAATGTTCGGTAAC
>RecA-4
CTAACGCTTGAGCTTATTGCTGCAGCACAGA-AGTGGGCAAAACGTGTGCATTCGTCGATGCCTAACGCTTGAGCTTATT-CTGCAGCCAAATTCGTATGAAAATTGGTGTAATGTTCGGTAAC
>RecA-1
CTAACGCTTGAGCTTATT-CTGCAGCCAAATTCGTATGAAAATTGGTGTAATGTTCGGTAACCTAACGCTTGAGCTTATT-CTGCAGCCAAATTCGTATGAAAATTGGTGTAATGTTCGGTAAC
>RecA-2
CTAACGCTTGAGCTTATTGCTGCAGCACAGA-AGTGGGCAAAACGTGTGCATTCGTCGATGCCTAACGCTTGAGCTTATT-CTGCAGCCAAATTCGTATGAAAATTGGTGTAATGTTCGGTAAC
>RecA-3
CTAACGC--GAGCTTATT-CTGCAGCCAAATTCGTATGAAAATTGGTGTAATGTTCGGTAACCTAACGCTTGAGCTTATT-CTGCAGCCAAATTCGTATGAAAATTGGTGTAATGTTCGGTAAC
>RecA-4
CTAACGCTTGAGCTTATTGCTGCAGCACAGA-AGTGGGCAAAACGTGTGCATTCGTCGATGCCTAACGCTTGAGCTTATT-CTGCAGCCAAATTCGTATGAAAATTGGTGTAATGTTCGGTAAC

0
inst/ext/ExamplesDataFormatting/Example of a file specifying gene boundaries for a concatenated sequence in BAPS format.txt → inst/testdata/ExamplesDataFormatting/Example of a file specifying gene boundaries for a concatenated sequence in BAPS format.txt vendored
View file

20
inst/ext/ExamplesDataFormatting/Example of a partition file for admixture analysis based on user-specified populations.txt → inst/testdata/ExamplesDataFormatting/Example of a partition file for admixture analysis based on user-specified populations.txt vendored
View file

@ -1,10 +1,10 @@
1
1
2
2
2
2
2
3
3
3
1
1
2
2
2
2
2
3
3
3

10
inst/ext/ExamplesDataFormatting/Example of an MLST profile file for 6 genes.txt → inst/testdata/ExamplesDataFormatting/Example of an MLST profile file for 6 genes.txt vendored
View file

@ -1,5 +1,5 @@
ST Isolate Species Adk GyrB Hsp60 Mdh Pgi RecA
1 1A1 My. splendidone 1 1 1 1 1 1
2 1B1 A. dent 2 2 2 2 2 2
3 1B2 A. dent 3 3 3 3 3 3
4 1A5 D. gently 4 4 4 4 4 4
ST Isolate Species Adk GyrB Hsp60 Mdh Pgi RecA
1 1A1 My. splendidone 1 1 1 1 1 1
2 1B1 A. dent 2 2 2 2 2 2
3 1B2 A. dent 3 3 3 3 3 3
4 1A5 D. gently 4 4 4 4 4 4

44290
inst/ext/ExamplesDataFormatting/Example of hierBAPS input in FASTA format.fa → inst/testdata/ExamplesDataFormatting/Example of hierBAPS input in FASTA format.fa vendored
View file

File diff suppressed because it is too large Load diff

0
inst/ext/ExamplesDataFormatting/Example of hierBAPS input in XLS format.xls → inst/testdata/ExamplesDataFormatting/Example of hierBAPS input in XLS format.xls vendored
View file

6
inst/ext/ExamplesDataFormatting/Example of sample population index file to be used with BAPS formatted data.txt → inst/testdata/ExamplesDataFormatting/Example of sample population index file to be used with BAPS formatted data.txt vendored
View file

@ -1,3 +1,3 @@
1
3
5
1
3
5

4
inst/ext/ExamplesDataFormatting/Example of sample population names file to be used with BAPS formatted data.txt → inst/testdata/ExamplesDataFormatting/Example of sample population names file to be used with BAPS formatted data.txt vendored
View file

@ -1,3 +1,3 @@
Example population 1
Example population 2
Example population 1
Example population 2
Example population 3

50
inst/ext/ExamplesDataFormatting/Example pre-grouped sample data in GENEPOP format for Trained clustering.txt → inst/testdata/ExamplesDataFormatting/Example pre-grouped sample data in GENEPOP format for Trained clustering.txt vendored
View file

@ -1,25 +1,25 @@
Sample data for trained clustering
1
2
3
4
5
6
7
8
9
10
POP
AreaUnknown_11, 1717 1010 1717 0404 0505 0606 0808 1010 0707 1212
AreaUnknown_12, 1515 1212 1414 0404 0505 0606 1919 1010 0707 1414
AreaUnknown_13, 1717 0303 1515 0404 0505 0606 1414 1010 0707 1212
POP
AreaUnknown_24, 1311 1205 1212 0302 0505 0606 1313 1005 0707 1107
AreaUnknown_25, 1306 0707 1212 0505 0603 0808 1109 1003 0000 0806
POP
AreaUnknown_36, 0909 0606 1212 0404 0606 0808 1717 1001 0909 1308
POP
AreaUnknown_47, 1507 1208 1212 0404 0202 0101 1915 1510 0202 0705
AreaUnknown_48, 1507 1313 1212 0202 0202 0101 1414 1510 0202 0704
AreaUnknown_49, 0907 0907 1212 0404 0202 0101 1908 0000 0202 1507
AreaUnknown_410, 1109 1918 1512 0505 0505 0000 1605 0706 0707 0505
Sample data for trained clustering
1
2
3
4
5
6
7
8
9
10
POP
AreaUnknown_11, 1717 1010 1717 0404 0505 0606 0808 1010 0707 1212
AreaUnknown_12, 1515 1212 1414 0404 0505 0606 1919 1010 0707 1414
AreaUnknown_13, 1717 0303 1515 0404 0505 0606 1414 1010 0707 1212
POP
AreaUnknown_24, 1311 1205 1212 0302 0505 0606 1313 1005 0707 1107
AreaUnknown_25, 1306 0707 1212 0505 0603 0808 1109 1003 0000 0806
POP
AreaUnknown_36, 0909 0606 1212 0404 0606 0808 1717 1001 0909 1308
POP
AreaUnknown_47, 1507 1208 1212 0404 0202 0101 1915 1510 0202 0705
AreaUnknown_48, 1507 1313 1212 0202 0202 0101 1414 1510 0202 0704
AreaUnknown_49, 0907 0907 1212 0404 0202 0101 1908 0000 0202 1507
AreaUnknown_410, 1109 1918 1512 0505 0505 0000 1605 0706 0707 0505

62
inst/ext/ExamplesDataFormatting/Example sample data in GENEPOP format for Trained clustering.txt → inst/testdata/ExamplesDataFormatting/Example sample data in GENEPOP format for Trained clustering.txt vendored
View file

@ -1,31 +1,31 @@
Sample data for trained clustering
1
2
3
4
5
6
7
8
9
10
POP
AreaUnknown1, 1717 1010 1717 0404 0505 0606 0808 1010 0707 1212
POP
AreaUnknown2, 1515 1212 1414 0404 0505 0606 1919 1010 0707 1414
POP
AreaUnknown3, 1717 0303 1515 0404 0505 0606 1414 1010 0707 1212
POP
AreaUnknown4, 1311 1205 1212 0302 0505 0606 1313 1005 0707 1107
POP
AreaUnknown5, 1306 0707 1212 0505 0603 0808 1109 1003 0000 0806
POP
AreaUnknown6, 0909 0606 1212 0404 0606 0808 1717 1001 0909 1308
POP
AreaUnknown7, 1507 1208 1212 0404 0202 0101 1915 1510 0202 0705
POP
AreaUnknown8, 1507 1313 1212 0202 0202 0101 1414 1510 0202 0704
POP
AreaUnknown9, 0907 0907 1212 0404 0202 0101 1908 0000 0202 1507
POP
AreaUnknown10, 1109 1918 1512 0505 0505 0000 1605 0706 0707 0505
Sample data for trained clustering
1
2
3
4
5
6
7
8
9
10
POP
AreaUnknown1, 1717 1010 1717 0404 0505 0606 0808 1010 0707 1212
POP
AreaUnknown2, 1515 1212 1414 0404 0505 0606 1919 1010 0707 1414
POP
AreaUnknown3, 1717 0303 1515 0404 0505 0606 1414 1010 0707 1212
POP
AreaUnknown4, 1311 1205 1212 0302 0505 0606 1313 1005 0707 1107
POP
AreaUnknown5, 1306 0707 1212 0505 0603 0808 1109 1003 0000 0806
POP
AreaUnknown6, 0909 0606 1212 0404 0606 0808 1717 1001 0909 1308
POP
AreaUnknown7, 1507 1208 1212 0404 0202 0101 1915 1510 0202 0705
POP
AreaUnknown8, 1507 1313 1212 0202 0202 0101 1414 1510 0202 0704
POP
AreaUnknown9, 0907 0907 1212 0404 0202 0101 1908 0000 0202 1507
POP
AreaUnknown10, 1109 1918 1512 0505 0505 0000 1605 0706 0707 0505

0
inst/ext/ExamplesDataFormatting/Example test data in XLS format for Trained clustering.xls → inst/testdata/ExamplesDataFormatting/Example test data in XLS format for Trained clustering.xls vendored
View file

0
inst/ext/ExamplesDataFormatting/Example training data in XLS format for Trained clustering.xls → inst/testdata/ExamplesDataFormatting/Example training data in XLS format for Trained clustering.xls vendored
View file

0
inst/ext/ExamplesDataFormatting/Notes.md → inst/testdata/ExamplesDataFormatting/Notes.md vendored
View file

216
inst/ext/GENEPOP_format_trained_clustering.gen → inst/testdata/datasets-for-future-releases/GENEPOP_format_trained_clustering.gen vendored
View file

@ -1,108 +1,108 @@
Baseline data for trained clustering
1
2
3
4
5
6
7
8
9
10
POP
Area1_1, 1717 1111 0000 0404 0505 0606 0707 1212 0707 1212
Area1_2, 0909 1010 0505 0404 0505 1010 0707 1111 0707 1212
Area1_3, 0000 1010 1414 0404 0505 0606 1111 1212 0707 1212
Area1_4, 1111 1010 1515 0404 0101 0606 1313 1111 0707 0808
Area1_5, 0101 1010 1212 0404 0505 0606 0909 1212 0707 1212
Area1_6, 1111 1010 1414 0404 0505 0606 1111 1212 0707 1010
Area1_7, 1515 1010 0707 0404 0505 0606 0707 1212 0707 1212
Area1_8, 1515 1212 0606 0404 0505 0606 1616 1212 0707 1010
Area1_9, 0909 1010 1010 0404 0505 0606 1919 1212 0707 1010
Area1_10, 0000 0000 0000 0404 0505 0606 1111 1010 0707 0000
Area1_11, 0000 0000 0000 0404 0505 0505 1919 1212 0404 1111
Area1_12, 1515 1010 0606 0404 0505 0606 1616 1212 0202 1212
Area1_13, 1515 1010 1515 0404 0505 0606 0707 0606 0707 1212
Area1_14, 0505 1010 1919 0404 0202 0606 1111 1010 0202 1212
Area1_15, 1111 1010 1414 0404 0505 0606 1616 0606 0707 1212
Area1_16, 1515 1212 0000 0404 0505 0606 1919 1212 0707 1212
Area1_17, 1515 1010 1515 0404 0505 0606 1919 1212 0707 1212
Area1_18, 1515 1010 1212 0404 0505 0606 0909 1212 0707 1010
Area1_19, 1515 1212 0606 0404 0505 0606 1515 1212 0707 1212
Area1_20, 1717 1414 1717 0404 0505 0606 0808 1212 0707 0808
Area1_21, 1515 1212 1212 0404 0505 0606 0808 1818 0707 1212
Area1_22, 1313 1111 1212 0404 0505 0606 1313 1212 0707 1212
Area1_23, 1515 1212 1212 0404 0505 0606 1313 1010 0707 1212
Area1_24, 0000 0000 0000 0404 0505 0606 1919 1212 0404 0000
Area1_25, 0000 0000 0000 0404 0202 0101 1919 1919 0707 1212
Area1_26, 1313 1010 0202 0404 0505 0606 1717 1212 0707 1212
POP
Area2_1, 1706 0505 1212 0404 0606 0808 1309 1111 0909 1413
Area2_2, 1511 0707 1209 0404 0602 0808 1111 1004 0902 1310
Area2_3, 1711 0000 1412 0402 0000 0000 1913 1002 0000 1313
Area2_4, 1715 1515 1412 0404 0505 0604 1313 1010 1007 1309
Area2_5, 1515 1515 1412 0404 0505 0606 1515 1111 0707 0908
Area2_6, 1309 0000 1212 0404 0603 0802 1311 1204 0903 1309
Area2_7, 1313 0505 1212 0404 0606 0808 1616 1414 0909 1206
Area2_8, 1307 0707 1212 0404 0606 0808 1313 1004 0909 1313
Area2_9, 0000 1212 1209 0404 0505 0606 0000 1106 0707 1208
Area2_10, 1307 0000 1212 0404 0606 0806 1313 1005 0909 1111
Area2_11, 0000 0707 1409 0505 0606 0808 1616 1110 0909 1309
Area2_12, 1807 0000 1212 0505 0606 0000 0909 0401 0909 1309
Area2_13, 1511 1212 1212 0404 0505 0604 1313 1110 0707 1210
Area2_14, 1111 1515 1412 0505 0606 0808 1414 1004 0909 1313
Area2_15, 1817 0707 1212 0505 0707 0909 1111 1004 0909 1313
Area2_16, 1913 1511 1212 0404 0606 0000 0909 1212 0909 1313
Area2_17, 1515 0000 0000 0000 0505 1006 1313 1005 0707 1212
Area2_18, 0707 0606 1408 0404 0202 0101 1313 1615 0202 1307
Area2_19, 0707 1309 0909 0502 0202 0101 2009 1510 0202 0704
POP
Area3_1, 1507 0706 1212 0202 0202 0000 0905 1409 0202 0707
Area3_2, 1507 1313 1212 0202 0202 0101 1613 1510 0202 0807
Area3_3, 1313 1414 1212 0404 0202 0101 1909 1510 0202 0704
Area3_4, 1515 0909 1212 0502 0202 0101 1409 1210 0202 0807
Area3_5, 1515 0808 1212 0502 0202 0101 1111 1510 0202 1007
Area3_6, 1306 0909 1212 0202 0202 0101 0807 1512 0202 0707
Area3_7, 0000 1009 1212 0404 0202 0101 1109 0702 0202 0808
Area3_8, 1507 0606 1212 0404 0202 0101 1908 1409 0202 0707
Area3_9, 1515 0606 1212 0202 0202 0101 0909 1510 0202 1207
Area3_10, 1307 1010 1412 0202 0202 0101 1709 1615 0202 1207
Area3_11, 1307 1005 1212 0404 0202 0101 1709 1510 0202 0703
Area3_12, 1109 0902 1212 0404 0202 0101 0909 1002 0202 1207
Area3_13, 1307 0606 1412 0404 0202 0101 0807 1515 0202 1207
Area3_14, 1717 1407 1212 0404 0202 0101 1107 1409 0202 0805
Area3_15, 1307 1007 1412 0404 0505 0101 0909 0000 0202 0807
Area3_16, 1811 0000 1212 0404 0505 0000 1515 0707 0000 1212
Area3_17, 1907 1414 1512 0402 0705 0000 0000 0000 0909 1212
POP
Area4_1, 1311 2019 1212 0404 0505 0000 1919 0707 0707 1109
Area4_2, 1309 2018 1512 0404 0505 0000 1919 0808 0707 1111
Area4_3, 1509 2118 1212 0404 0505 0000 1515 0707 0707 1107
Area4_4, 1715 2221 1512 0404 0505 0000 1919 0707 0707 1111
Area4_5, 1515 2121 1512 0404 0505 0000 1515 0707 0606 0707
Area4_6, 1717 2222 1512 0404 0505 0000 1913 0707 0707 0907
Area4_7, 1715 2221 1512 0404 0505 0000 1313 0707 0606 1111
Area4_8, 1813 2320 1512 0404 0505 0000 1515 0707 0707 1107
Area4_9, 1311 2019 1512 0404 0505 0000 1515 0707 0707 1111
Area4_10, 1311 2019 1512 0000 0505 0000 1313 0707 0707 0909
Area4_11, 1111 2625 0000 0000 0505 0606 0707 0903 0505 0505
Area4_12, 0907 2724 0000 0404 0505 0605 1914 1105 0505 0707
Area4_13, 1511 1610 1212 0404 0505 0605 1513 1105 1107 0704
Area4_14, 1513 0404 1111 0404 0505 0606 1515 1111 1207 1107
Area4_15, 1311 1616 1212 0404 0505 0606 1313 1111 0707 1107
Area4_16, 1109 0606 1212 0404 0000 0000 1515 0902 0807 0505
Area4_17, 1107 1004 1506 0404 0505 0606 1515 1212 0707 1108
Area4_18, 1107 0904 1512 0404 0505 0606 1913 1105 1107 1107
Area4_19, 1109 1313 1212 0404 0505 0606 1915 1111 1007 1107
Area4_20, 1711 1604 1212 0404 0505 0606 1915 1212 1107 1007
Area4_21, 1111 0606 1515 0404 0505 0606 1707 1009 0807 0502
Area4_22, 1311 0603 1512 0404 0505 0606 1714 0707 0807 0501
POP
Area5_1, 0711 1212 1513 0202 0707 0808 1408 0000 0909 1210
Area5_2, 1118 0101 1212 0202 0803 0901 0808 0000 1101 1211
Area5_3, 1518 0000 1512 0404 0707 0806 0909 0000 0909 1212
Area5_4, 1309 0000 1512 0202 0606 0707 1508 0000 0808 1204
Area5_5, 0718 0000 1512 0402 0707 0806 0707 0000 0909 1208
Area5_6, 1818 1414 1212 0404 0707 0000 1916 0000 0909 1208
Area5_7, 1318 1313 1212 0404 0606 0000 1908 0000 0808 1008
Area5_8, 1818 0000 1212 0404 0000 0806 1616 0000 0808 1212
Baseline data for trained clustering
1
2
3
4
5
6
7
8
9
10
POP
Area1_1, 1717 1111 0000 0404 0505 0606 0707 1212 0707 1212
Area1_2, 0909 1010 0505 0404 0505 1010 0707 1111 0707 1212
Area1_3, 0000 1010 1414 0404 0505 0606 1111 1212 0707 1212
Area1_4, 1111 1010 1515 0404 0101 0606 1313 1111 0707 0808
Area1_5, 0101 1010 1212 0404 0505 0606 0909 1212 0707 1212
Area1_6, 1111 1010 1414 0404 0505 0606 1111 1212 0707 1010
Area1_7, 1515 1010 0707 0404 0505 0606 0707 1212 0707 1212
Area1_8, 1515 1212 0606 0404 0505 0606 1616 1212 0707 1010
Area1_9, 0909 1010 1010 0404 0505 0606 1919 1212 0707 1010
Area1_10, 0000 0000 0000 0404 0505 0606 1111 1010 0707 0000
Area1_11, 0000 0000 0000 0404 0505 0505 1919 1212 0404 1111
Area1_12, 1515 1010 0606 0404 0505 0606 1616 1212 0202 1212
Area1_13, 1515 1010 1515 0404 0505 0606 0707 0606 0707 1212
Area1_14, 0505 1010 1919 0404 0202 0606 1111 1010 0202 1212
Area1_15, 1111 1010 1414 0404 0505 0606 1616 0606 0707 1212
Area1_16, 1515 1212 0000 0404 0505 0606 1919 1212 0707 1212
Area1_17, 1515 1010 1515 0404 0505 0606 1919 1212 0707 1212
Area1_18, 1515 1010 1212 0404 0505 0606 0909 1212 0707 1010
Area1_19, 1515 1212 0606 0404 0505 0606 1515 1212 0707 1212
Area1_20, 1717 1414 1717 0404 0505 0606 0808 1212 0707 0808
Area1_21, 1515 1212 1212 0404 0505 0606 0808 1818 0707 1212
Area1_22, 1313 1111 1212 0404 0505 0606 1313 1212 0707 1212
Area1_23, 1515 1212 1212 0404 0505 0606 1313 1010 0707 1212
Area1_24, 0000 0000 0000 0404 0505 0606 1919 1212 0404 0000
Area1_25, 0000 0000 0000 0404 0202 0101 1919 1919 0707 1212
Area1_26, 1313 1010 0202 0404 0505 0606 1717 1212 0707 1212
POP
Area2_1, 1706 0505 1212 0404 0606 0808 1309 1111 0909 1413
Area2_2, 1511 0707 1209 0404 0602 0808 1111 1004 0902 1310
Area2_3, 1711 0000 1412 0402 0000 0000 1913 1002 0000 1313
Area2_4, 1715 1515 1412 0404 0505 0604 1313 1010 1007 1309
Area2_5, 1515 1515 1412 0404 0505 0606 1515 1111 0707 0908
Area2_6, 1309 0000 1212 0404 0603 0802 1311 1204 0903 1309
Area2_7, 1313 0505 1212 0404 0606 0808 1616 1414 0909 1206
Area2_8, 1307 0707 1212 0404 0606 0808 1313 1004 0909 1313
Area2_9, 0000 1212 1209 0404 0505 0606 0000 1106 0707 1208
Area2_10, 1307 0000 1212 0404 0606 0806 1313 1005 0909 1111
Area2_11, 0000 0707 1409 0505 0606 0808 1616 1110 0909 1309
Area2_12, 1807 0000 1212 0505 0606 0000 0909 0401 0909 1309
Area2_13, 1511 1212 1212 0404 0505 0604 1313 1110 0707 1210
Area2_14, 1111 1515 1412 0505 0606 0808 1414 1004 0909 1313
Area2_15, 1817 0707 1212 0505 0707 0909 1111 1004 0909 1313
Area2_16, 1913 1511 1212 0404 0606 0000 0909 1212 0909 1313
Area2_17, 1515 0000 0000 0000 0505 1006 1313 1005 0707 1212
Area2_18, 0707 0606 1408 0404 0202 0101 1313 1615 0202 1307
Area2_19, 0707 1309 0909 0502 0202 0101 2009 1510 0202 0704
POP
Area3_1, 1507 0706 1212 0202 0202 0000 0905 1409 0202 0707
Area3_2, 1507 1313 1212 0202 0202 0101 1613 1510 0202 0807
Area3_3, 1313 1414 1212 0404 0202 0101 1909 1510 0202 0704
Area3_4, 1515 0909 1212 0502 0202 0101 1409 1210 0202 0807
Area3_5, 1515 0808 1212 0502 0202 0101 1111 1510 0202 1007
Area3_6, 1306 0909 1212 0202 0202 0101 0807 1512 0202 0707
Area3_7, 0000 1009 1212 0404 0202 0101 1109 0702 0202 0808
Area3_8, 1507 0606 1212 0404 0202 0101 1908 1409 0202 0707
Area3_9, 1515 0606 1212 0202 0202 0101 0909 1510 0202 1207
Area3_10, 1307 1010 1412 0202 0202 0101 1709 1615 0202 1207
Area3_11, 1307 1005 1212 0404 0202 0101 1709 1510 0202 0703
Area3_12, 1109 0902 1212 0404 0202 0101 0909 1002 0202 1207
Area3_13, 1307 0606 1412 0404 0202 0101 0807 1515 0202 1207
Area3_14, 1717 1407 1212 0404 0202 0101 1107 1409 0202 0805
Area3_15, 1307 1007 1412 0404 0505 0101 0909 0000 0202 0807
Area3_16, 1811 0000 1212 0404 0505 0000 1515 0707 0000 1212
Area3_17, 1907 1414 1512 0402 0705 0000 0000 0000 0909 1212
POP
Area4_1, 1311 2019 1212 0404 0505 0000 1919 0707 0707 1109
Area4_2, 1309 2018 1512 0404 0505 0000 1919 0808 0707 1111
Area4_3, 1509 2118 1212 0404 0505 0000 1515 0707 0707 1107
Area4_4, 1715 2221 1512 0404 0505 0000 1919 0707 0707 1111
Area4_5, 1515 2121 1512 0404 0505 0000 1515 0707 0606 0707
Area4_6, 1717 2222 1512 0404 0505 0000 1913 0707 0707 0907
Area4_7, 1715 2221 1512 0404 0505 0000 1313 0707 0606 1111
Area4_8, 1813 2320 1512 0404 0505 0000 1515 0707 0707 1107
Area4_9, 1311 2019 1512 0404 0505 0000 1515 0707 0707 1111
Area4_10, 1311 2019 1512 0000 0505 0000 1313 0707 0707 0909
Area4_11, 1111 2625 0000 0000 0505 0606 0707 0903 0505 0505
Area4_12, 0907 2724 0000 0404 0505 0605 1914 1105 0505 0707
Area4_13, 1511 1610 1212 0404 0505 0605 1513 1105 1107 0704
Area4_14, 1513 0404 1111 0404 0505 0606 1515 1111 1207 1107
Area4_15, 1311 1616 1212 0404 0505 0606 1313 1111 0707 1107
Area4_16, 1109 0606 1212 0404 0000 0000 1515 0902 0807 0505
Area4_17, 1107 1004 1506 0404 0505 0606 1515 1212 0707 1108
Area4_18, 1107 0904 1512 0404 0505 0606 1913 1105 1107 1107
Area4_19, 1109 1313 1212 0404 0505 0606 1915 1111 1007 1107
Area4_20, 1711 1604 1212 0404 0505 0606 1915 1212 1107 1007
Area4_21, 1111 0606 1515 0404 0505 0606 1707 1009 0807 0502
Area4_22, 1311 0603 1512 0404 0505 0606 1714 0707 0807 0501
POP
Area5_1, 0711 1212 1513 0202 0707 0808 1408 0000 0909 1210
Area5_2, 1118 0101 1212 0202 0803 0901 0808 0000 1101 1211
Area5_3, 1518 0000 1512 0404 0707 0806 0909 0000 0909 1212
Area5_4, 1309 0000 1512 0202 0606 0707 1508 0000 0808 1204
Area5_5, 0718 0000 1512 0402 0707 0806 0707 0000 0909 1208
Area5_6, 1818 1414 1212 0404 0707 0000 1916 0000 0909 1208
Area5_7, 1318 1313 1212 0404 0606 0000 1908 0000 0808 1008
Area5_8, 1818 0000 1212 0404 0000 0806 1616 0000 0808 1212

0
inst/ext/example_drosophila.Aligned.out.sam → inst/testdata/datasets-for-future-releases/example_drosophila.Aligned.out.sam vendored
View file

4
man/greedyMix.Rd
View file

@ -16,6 +16,10 @@ greedyMix(data, format, verbose = TRUE)
\description{
Clustering of individuals
}
\examples{
data <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS")
greedyMix(data)
}
\references{
Samtools: a suite of programs for interacting
with high-throughput sequencing data. <http://www.htslib.org/>

2
man/load_fasta.Rd
View file

@ -19,7 +19,7 @@ Loads a fasta file into matrix format ready for
running the hierBAPS algorithm.
}
\examples{
msa <- system.file("ext", "seqs.fa", package = "rBAPS")
msa <- system.file("extdata", "seqs.fa", package = "rBAPS")
snp.matrix <- load_fasta(msa)
}
\seealso{

4
tests/testthat/test-greedyMix.R
View file

@ -1,11 +1,11 @@
context("Auxiliary functions to greedyMix")
# Defining the relative path to current inst -----------------------------------
path_inst <- system.file("ext", "", package = "rBAPS")
path_inst <- system.file("extdata", "", package = "rBAPS")
# Reading datasets -------------------------------------------------------------
baps_diploid <- read.delim(
file = paste(path_inst, "BAPS_format_clustering_diploid.txt", sep = "/"),
file = file.path(path_inst, "BAPS_format_clustering_diploid.txt"),
sep = " ",
header = FALSE
)

2
tests/testthat/test-spatialMixture.R
View file

@ -79,7 +79,7 @@ test_that("lakseKlitik() and subfunctions produce expected output", {
})
test_that("testFastaData() produces same output as on MATLAB", {
msa <- system.file("ext", "seqs.fa", package = "rBAPS")
msa <- system.file("extdata", "seqs.fa", package = "rBAPS")
test_msa <- testFastaData(msa)
expect_equal(test_msa$ninds, 515)
expect_equal(dim(test_msa$data), c(515, 745))