36b32bb5087c96ea1ac0ff9f6da263ad *DESCRIPTION
60535cbfb654e4815b8af2877be13a28 *NAMESPACE
f00cbd8a8f7dd3d1cb5fc4f33278ddb0 *NEWS.md
49fb7dde709b7d56d950cfa481eee11e *R/as.newick.R
c489a95c70ee3f7a9b21c5e4e1701e00 *R/calc_candidate_regions.R
a5184787be940979ca4d87c32a69a6c5 *R/calc_ehh.R
d846b662a796c555a11a05a253237219 *R/calc_ehhs.R
7fc6137f3a9052c916c600103630f747 *R/calc_furcation.R
8652c8e385335d536e351d10ccba7767 *R/calc_haplen.R
1b9d3c5e76519a3101f08b58125167d3 *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
39ac154b20c0400cd5632b5268de2892 *R/make.example.files.R
14aae5afa388353eb0abee02d930773c *R/manhattanplot.R
de8aebb14b907da33b6e6483acb05467 *R/plot.ehh.R
c461be69e8d0960110dbd2e2c214c809 *R/plot.ehhs.R
f8018a6adb6442dd197b00f6f50d62d4 *R/plot.furcation.R
562bf90c94616972a745c618e3002078 *R/plot.haplen.R
f0e6d5dc46aa06ec2aa75a551187cee9 *R/plot.haplohh.R
b0695663334e80f7f38654bd355b7c32 *R/rehh.R
eb17387a546704c5510ba46856b6ca93 *R/scan_hh.R
50902c106c1f1a7e23f3534f6f639290 *R/scan_hh_full.R
c8aaf488db328f7ea21ecb7ea309e4ee *R/subset.haplohh.R
9d53dfc94e3a08334b06091ab986217d *R/update_haplohh.R
28612d69e6e3c076a5bac689ddabec2b *build/vignette.rds
bbd50c8eb813216188dce7896d1490d3 *data/datalist
91be48fb8754c805321891b9374459f3 *data/haplohh_cgu_bta12.RData
8439f1531106aeabce40b21067a1ac5e *inst/CITATION
ec7fb3bdabc787abe3be7512729a1e2f *inst/doc/examples.R
4d69844ff06315aff3356db7f85edd4c *inst/doc/examples.Rmd
f302ed194a63104b910a55c3fece8680 *inst/doc/examples.html
e4ac37fc09893fb1d5297d231923ba02 *inst/doc/rehh.R
602994925b401f0fe98262d30ff9d6e8 *inst/doc/rehh.Rmd
d993e482746096b0acbbba51cf4870d3 *inst/doc/rehh.html
529c33971c081bacc8d00072aac22b20 *inst/extdata/bta12_cgu.vcf.gz
1a13676197023c7796532d96aeff7f76 *inst/extdata/example1.hap
98aedc74c294ec4769b8e3272200fbbe *inst/extdata/example1.map
ef932b5c063861aae607ee0a93f33fb1 *inst/extdata/example1.vcf
259361a2879d15a50f494d8cb2322f95 *inst/extdata/example2.hap
05fcdbaf97aff8c6125dff9c40770538 *inst/extdata/example2.map
5e14d8117c9a49dac08ad3970a046373 *inst/extdata/example2.vcf
47a95eddad7ca90f68a4c35e671957b2 *inst/extdata/example_neutral.vcf
9adc5ae193051f554e00eda74567486e *inst/extdata/example_sweep.vcf
ab2d39dc100928b7c1e3a510287bb4c1 *inst/extdata/example_sweep_with_recombination.vcf
e444d999cd7277d08690d6031446baf1 *inst/extdata/ms.out
3f1bb468e3b3346d7925ed893f668d22 *man/allelefurcation-class.Rd
e43b5b616e972b190f596b0791aafdcb *man/as.newick.Rd
7d199b2def3e6d19e90ffa4128531956 *man/calc_candidate_regions.Rd
8ce616089d0acc6279c8acaaf2b30cb7 *man/calc_ehh.Rd
35d1ec2b344079cf92df525bf932c1d1 *man/calc_ehhs.Rd
c933fc808090cbc1cade18247471df48 *man/calc_furcation.Rd
12a719a71c961a21e8de7f5146ac1dc2 *man/calc_haplen.Rd
e6f80fc8df2c011ea38bd46d54b06a74 *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
9bf74e16a8816a0fd0f39fa67e879924 *man/make.example.files.Rd
af0baef3fee7a181c0b995d3bc65b5e0 *man/manhattanplot.Rd
96922dd9dbc33bcb024a69e3ec308be7 *man/plot.ehh.Rd
0091288c2de9b5c909c4f135dd87b1ad *man/plot.ehhs.Rd
c7933322276a4b8fa37433e050766c4d *man/plot.furcation.Rd
939fa1dcc75eacda1eef877ee99c9e7b *man/plot.haplen.Rd
090eca9f26b95024ee2aca3f483caf52 *man/plot.haplohh.Rd
07fab15f3017f348fcafac0dec82ac39 *man/rehh-package.Rd
0b3af48394811f7b7e481ca6fd7c63fd *man/remove.example.files.Rd
c7d8274a12c1b590ad9f210db5bfa52c *man/scan_hh.Rd
f0afc4cb433d9c6b7fddb600605d1ef7 *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
af8abfa9ecc355a7bd825358ef3afe5e *src/CALL_FURCATION.c
28bb39004e7d75cb01ff08c952148e6e *src/CALL_INTEGRAL.c
60d65393e0384e62cb72f308058ef007 *src/CALL_PAIRWISE_HAPLEN.c
997866feb635416dba2745e1275b33f0 *src/CALL_SCAN_HH.c
fe0c7dcc2bb11ae05b3ea7080d5aa7d7 *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
0f2d4d7ffafcef03cde572357aa3508e *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
c94ab72e812c9daf632b2acb919aa436 *tests/testthat/test_scan_full.R
06e74a8f326b2099d3ef7b77c1664a89 *tests/testthat/test_scan_hh.R
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test_scan_hh_full.log
2641e6bbf68bdd6c97280b3a86dfedcc *tests/testthat/test_sfs_tests.R
4d69844ff06315aff3356db7f85edd4c *vignettes/examples.Rmd
80ac2e78110aa3e54fb5ce824bd5574f *vignettes/genetics.csl
602994925b401f0fe98262d30ff9d6e8 *vignettes/rehh.Rmd
dc13674ff5df93035a03384f762a946f *vignettes/vignette.bib
