b18ee41254334985b84872d14d1e4104 *DESCRIPTION
d0adce3125ea8bcd95e03f8db6ee4dcc *NAMESPACE
75926d2336fd08546adb50a6f52d7a30 *NEWS.md
49fb7dde709b7d56d950cfa481eee11e *R/as.newick.R
c83b36569ef092969fb85be359966389 *R/calc_candidate_regions.R
9c0b577529d2d26ab099268e4c111ef5 *R/calc_ehh.R
40408ee15f42b7870f0d9024c7bf83c9 *R/calc_ehhs.R
50ce4fa9eb3b1a07e202d4affb77cd5d *R/calc_furcation.R
8652c8e385335d536e351d10ccba7767 *R/calc_haplen.R
247396f8bc253bf053862e637dea9455 *R/calc_pairwise_haplen.R
c0a7134ed354a1cc6e2d92cff7cb528b *R/calc_region_stats.R
dc4dfe02470f10724b4702d7bad63153 *R/calc_sfs_tests.R
db41e0abae0d42d719592911a8db10d7 *R/data2haplohh.R
3caea4a19997c6f248290697f797b4a1 *R/distribplot.R
ef5e101f1c8c4891d5991bf2fd0257b4 *R/extract_regions.R
e5d4611c5eeb4e3f839683a3f665e214 *R/freqbinplot.R
810c2aca58d223d852d957d0fe236b0a *R/furcation-class.R
b9dd5b7b760f2fdb3441fcf332fd8f9a *R/haplohh-class.R
10eddc406dc337e263f6e745a1c8d002 *R/haplohh2sweepfinder.R
6eebd3fac16bb154d1ea834dd0289c26 *R/ies2xpehh.R
0b91ea1dff6639b4c3b4f13dea539637 *R/ihh2ihs.R
1fc5288e0bd273f896e5daef79a8838e *R/ines2rsb.R
66d755943656fb5f8fb45b373cd953a7 *R/make.example.files.R
14aae5afa388353eb0abee02d930773c *R/manhattanplot.R
9339d68928fd766fee69fd149f723d7a *R/plot.ehh.R
32c5f455b02f5e2b73e00ed6f0ad33d8 *R/plot.ehhs.R
f8018a6adb6442dd197b00f6f50d62d4 *R/plot.furcation.R
562bf90c94616972a745c618e3002078 *R/plot.haplen.R
f0e6d5dc46aa06ec2aa75a551187cee9 *R/plot.haplohh.R
e92f7f893d3c2ccc2376da60febaaf22 *R/rehh.R
553167f3f944f6b20c9e001831aeafe4 *R/scan_hh.R
0a334afc13bddfb3a4bbafd97c689800 *R/scan_hh_full.R
c8aaf488db328f7ea21ecb7ea309e4ee *R/subset.haplohh.R
9d53dfc94e3a08334b06091ab986217d *R/update_haplohh.R
76e123f5dcc8dee07678412adc0a2a84 *build/partial.rdb
5616aad233ef62b880626da9fe8951a4 *build/vignette.rds
bbd50c8eb813216188dce7896d1490d3 *data/datalist
91be48fb8754c805321891b9374459f3 *data/haplohh_cgu_bta12.RData
f8aaac10da55162c39eed71b63b48b27 *inst/CITATION
6485521fad51165614b58ca68de67935 *inst/doc/examples.R
b45e3b5e9ad67daaf4b9e747d5b79847 *inst/doc/examples.Rmd
468cf5ee4ded989b59dc75a2276c5f5d *inst/doc/examples.html
7cd4a3ca08da6c479abcef2edefbbca6 *inst/doc/rehh.R
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529c33971c081bacc8d00072aac22b20 *inst/extdata/bta12_cgu.vcf.gz
1a13676197023c7796532d96aeff7f76 *inst/extdata/example1.hap
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ef932b5c063861aae607ee0a93f33fb1 *inst/extdata/example1.vcf
259361a2879d15a50f494d8cb2322f95 *inst/extdata/example2.hap
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5e14d8117c9a49dac08ad3970a046373 *inst/extdata/example2.vcf
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ab2d39dc100928b7c1e3a510287bb4c1 *inst/extdata/example_sweep_with_recombination.vcf
e444d999cd7277d08690d6031446baf1 *inst/extdata/ms.out
3f1bb468e3b3346d7925ed893f668d22 *man/allelefurcation-class.Rd
e43b5b616e972b190f596b0791aafdcb *man/as.newick.Rd
a9492bcf882cc0ae0410a4320513336c *man/calc_candidate_regions.Rd
c66f09d880e374d123f74bd75af2ca12 *man/calc_ehh.Rd
ae5f180eb1f6e59a36cf3d6acfe3f5e3 *man/calc_ehhs.Rd
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12a719a71c961a21e8de7f5146ac1dc2 *man/calc_haplen.Rd
9811f91205297677d07a4cc4ae4fa838 *man/calc_pairwise_haplen.Rd
2acaa7c3c89fcb46f3c7e4f370160986 *man/calc_region_stats.Rd
d2af8949d1a198ab26bfe45434be5924 *man/calc_sfs_tests.Rd
827eda0a35e51d45916607f10511a564 *man/data2haplohh.Rd
de43ae62050ec49c91c44138fe93b67c *man/distribplot.Rd
d557df62cd52e701005da0a5f0d8ec7c *man/extract_regions.Rd
17a00bb024774a6d4ef9491306f79872 *man/freqbinplot.Rd
21f93e394201b1b91a9de96890fa918a *man/ftree-class.Rd
33ddd89f9f2b47889d3be980b70747a0 *man/furcation-class.Rd
128fede3b0de4f84512e35c295433af2 *man/haplen-class.Rd
9917b0686748d15925dc890f045a076d *man/haplohh-class.Rd
c4211206daf63a9bfea41eb968dc3fc6 *man/haplohh2sweepfinder.Rd
b240d6b987257834ba5e9815aadfc537 *man/haplohh_cgu_bta12.Rd
8f39cb0fa8ff33094b34f5cc094afa8d *man/ies2xpehh.Rd
53e588ceb4a78d806505251b4fb6f763 *man/ihh2ihs.Rd
5823cdec432bbd985be9063d46fc6af0 *man/ines2rsb.Rd
2db5c3f65561479d9fa83976bf560cfb *man/make.example.files.Rd
af0baef3fee7a181c0b995d3bc65b5e0 *man/manhattanplot.Rd
128187e64050278de6776963f877f7b7 *man/plot.ehh.Rd
a552752fd894e2f6679c0ea145db8eed *man/plot.ehhs.Rd
c7933322276a4b8fa37433e050766c4d *man/plot.furcation.Rd
939fa1dcc75eacda1eef877ee99c9e7b *man/plot.haplen.Rd
090eca9f26b95024ee2aca3f483caf52 *man/plot.haplohh.Rd
fd8d8a1994fb6b66bd49967188d12643 *man/rehh-package.Rd
0b3af48394811f7b7e481ca6fd7c63fd *man/remove.example.files.Rd
14cb4bb029c45bacf50242aea195a7cd *man/scan_hh.Rd
7fa05a9c88401629f0ef7c639662afc2 *man/scan_hh_full.Rd
3940df1de7b4ad97554a1d03ce8c64e1 *man/subset.haplohh.Rd
35d96dc7734635751107a32802c872c7 *man/update_haplohh.Rd
ea195efe5e62727303defe92c7dfd337 *src/CALL_ASNEWICK.c
3bbb1385892442008a3efa83ed14f25a *src/CALL_EHH.c
733a9d7f96da43cdd8127c4323bca3dc *src/CALL_EHHS.c
3519903a3d7178f8103833acded6863d *src/CALL_FURCATION.c
28bb39004e7d75cb01ff08c952148e6e *src/CALL_INTEGRAL.c
60d65393e0384e62cb72f308058ef007 *src/CALL_PAIRWISE_HAPLEN.c
1206ac4084e2a683023e476771881615 *src/CALL_SCAN_HH.c
307f8f701e59a3a2675f04b258c389e9 *src/CALL_SCAN_HH_FULL.c
63feb5cece836f3ef515492d15a166af *src/CALL_SFS_TESTS.c
95e3011e37d9dde0d75f3a3819b2acd3 *src/Makevars
fba8f42eba26752e28b32338665d7348 *src/asnewick.c
c091d180d8864d7f3eea26b915784877 *src/asnewick.h
4dc69d4f01f541f4c853e3b203dd1b6b *src/calc_ehh.c
531486c77dbdf0de5e131d173b0bb623 *src/calc_ehh.h
488527d4efa9758e655b44e672d47842 *src/calc_ehhs.c
27c58a2a27960458af14d7c61f0d155e *src/calc_ehhs.h
08642573b73421d2a0a401769bf8248b *src/calc_furcation.c
965b71b2edfd728a6a32472cda3e7713 *src/calc_furcation.h
a05f2b0184ce0b035a956723f6d92eda *src/calc_pairwise_haplen.c
3839049affccee8d202be5eb505d366d *src/calc_pairwise_haplen.h
e8a5d23d30265ed943365b58fc28f422 *src/calc_sfs_tests.c
b779fcb22524d83657d325d4245cbc99 *src/calc_sfs_tests.h
4c1d8febd6cd04df5b4d22a3e2bd2c09 *src/definitions.h
d42625e6350dcad51095cf22bf571db8 *src/haplotypes.c
976fa1c7e90f686dd57ee6229b12c43a *src/haplotypes.h
3b2551c14b264fae6d2301e2bf453699 *src/haplotypes_with_lengths.c
7e3b917788ab2161b5c399475c3c388a *src/haplotypes_with_lengths.h
d515074159b54f4e8fa71d847f0cc4e3 *src/haplotypes_with_nodes.c
b8718089aed1c9aadf83d877f9762a5c *src/haplotypes_with_nodes.h
29441637b9f2e8c074323b102c802683 *src/homozygosity.c
8a0372f7038e294975eba1db483598ca *src/homozygosity.h
625ba8904f1e83f49b398277e7a524d3 *src/init.c
77f8dc940762ed75f438205732206fc7 *src/integrate.c
40f968c6eb88192b40c247c6b9cd6492 *src/integrate.h
72a80b3450d690a6ac58609f94dd7fcb *src/sfs_moments.c
a3b3aeea2920660c6e293769c631b068 *src/sfs_moments.h
7d20b8af53a3a33835b45ed2dde1f2ff *tests/testthat.R
d10abdbe610dee90be8e7c6a1baf28da *tests/testthat/furcation_F1205400.newick
26f4662e29cc03d705c9c9e5d81046d6 *tests/testthat/serialized_furcation_F1205400.txt
49083b987e561c6043f9fd6937ad0fb6 *tests/testthat/serialized_furcation_example2_rs6_phased.txt
2bb21fd95588fe2c01e56123b749a71f *tests/testthat/serialized_furcation_example2_rs6_unphased.txt
7f87b223f6153b8926956609ba293241 *tests/testthat/setup.R
a177583dabfe62a659b2d0ff4e5829d8 *tests/testthat/teardown.R
28480da7351e2890c4f216147423154f *tests/testthat/test_calc_candidate_regions.R
f8a26c6ede3ff1c7bf965b3d3c9797ea *tests/testthat/test_data2haplohh.R
a57d331f176ddaa7e7a19fb056cd2626 *tests/testthat/test_error_messages.R
3c553b425c68132fe5a74a06fc85d3e4 *tests/testthat/test_examples.R
c5d51b0340ebb2dc628e911bcc259f82 *tests/testthat/test_furcation.R
83461c197932114fbb6185821cdae353 *tests/testthat/test_ihh2ihs.R
7aced03b8c5cc701485546241128fa10 *tests/testthat/test_scan_full.R
06e74a8f326b2099d3ef7b77c1664a89 *tests/testthat/test_scan_hh.R
2641e6bbf68bdd6c97280b3a86dfedcc *tests/testthat/test_sfs_tests.R
b45e3b5e9ad67daaf4b9e747d5b79847 *vignettes/examples.Rmd
80ac2e78110aa3e54fb5ce824bd5574f *vignettes/genetics.csl
2dc7b8118bbc3c1af4b2363b4573cc34 *vignettes/rehh.Rmd
bc1c9018757e8e4ec9605e787657c463 *vignettes/vignette.bib
