4be95bfe5393b4ad0d988f9076587813 *DESCRIPTION
479cda305f23caf8bd3f42caa2013c3e *NAMESPACE
c3bdce8419097ef74d75dedfadbb2264 *NEWS.md
d778a01442f62a331f42f43636d35c9a *R/as.newick.R
791804c313fb1e1bc68e7c5b95ecc92d *R/calc_candidate_regions.R
f64accc80d3c07213985e6eebd0969a7 *R/calc_ehh.R
adf2e4d9478c23d89b6a1f64cbb8e645 *R/calc_ehhs.R
7fc6137f3a9052c916c600103630f747 *R/calc_furcation.R
8652c8e385335d536e351d10ccba7767 *R/calc_haplen.R
647a736449be2f7cb9ef08fc31691ad5 *R/calc_pairwise_haplen.R
c0a7134ed354a1cc6e2d92cff7cb528b *R/calc_region_stats.R
aebc3fea50b8605b1d1aa3aaf21776bd *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
6eebd3fac16bb154d1ea834dd0289c26 *R/ies2xpehh.R
0b91ea1dff6639b4c3b4f13dea539637 *R/ihh2ihs.R
1fc5288e0bd273f896e5daef79a8838e *R/ines2rsb.R
1ab4dd6448b5781c7abf510cd5be6750 *R/make.example.files.R
f1138821f4d4882da57c5499764342fd *R/manhattanplot.R
de8aebb14b907da33b6e6483acb05467 *R/plot.ehh.R
c461be69e8d0960110dbd2e2c214c809 *R/plot.ehhs.R
f8018a6adb6442dd197b00f6f50d62d4 *R/plot.furcation.R
562bf90c94616972a745c618e3002078 *R/plot.haplen.R
46f5794ea7ee74e36c779522aa2d6ab2 *R/plot.haplohh.R
d0c64f19c95d71847c72b56a14db8de9 *R/rehh.R
e232bea3e5d1d83fdf560f24d01deb18 *R/scan_hh.R
f31185006802c7467a9f6a8cc8c92fa8 *R/scan_hh_full.R
d857d3be60093cc3900f1d221fd867fc *R/subset.haplohh.R
9d53dfc94e3a08334b06091ab986217d *R/update_haplohh.R
8228a460ed62d771a05ec3e1e9a7cb59 *build/vignette.rds
bbd50c8eb813216188dce7896d1490d3 *data/datalist
91be48fb8754c805321891b9374459f3 *data/haplohh_cgu_bta12.RData
8439f1531106aeabce40b21067a1ac5e *inst/CITATION
ae04d6c09732f0e29be34d966896d3d4 *inst/doc/examples.R
347ed7fd5246ab0a51b07eb65c551f51 *inst/doc/examples.Rmd
a66b153a90d0c7ba1cfc0e6d7d993e13 *inst/doc/examples.html
0aca4270ed980c2b91db059f72ce8512 *inst/doc/rehh.R
0cb9f06cbea7141d8522641178da4b54 *inst/doc/rehh.Rmd
4c42ce24a6e5e3c0f331df7518413c4d *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
e444d999cd7277d08690d6031446baf1 *inst/extdata/ms.out
3f1bb468e3b3346d7925ed893f668d22 *man/allelefurcation-class.Rd
e43b5b616e972b190f596b0791aafdcb *man/as.newick.Rd
7d199b2def3e6d19e90ffa4128531956 *man/calc_candidate_regions.Rd
9a1d4d2573383b1af915cd9740433948 *man/calc_ehh.Rd
877765521fdd1bc21f0fad429f434980 *man/calc_ehhs.Rd
c933fc808090cbc1cade18247471df48 *man/calc_furcation.Rd
12a719a71c961a21e8de7f5146ac1dc2 *man/calc_haplen.Rd
36e5218744298abe44f67dbfb6d4c599 *man/calc_pairwise_haplen.Rd
2acaa7c3c89fcb46f3c7e4f370160986 *man/calc_region_stats.Rd
aae72c0cb9f1bffb913dd8b13d534125 *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
b240d6b987257834ba5e9815aadfc537 *man/haplohh_cgu_bta12.Rd
8f39cb0fa8ff33094b34f5cc094afa8d *man/ies2xpehh.Rd
53e588ceb4a78d806505251b4fb6f763 *man/ihh2ihs.Rd
5823cdec432bbd985be9063d46fc6af0 *man/ines2rsb.Rd
2449dbe55eb56665554d7fc8ee255766 *man/make.example.files.Rd
704045fb4408191c2962598b09080c7c *man/manhattanplot.Rd
96922dd9dbc33bcb024a69e3ec308be7 *man/plot.ehh.Rd
0091288c2de9b5c909c4f135dd87b1ad *man/plot.ehhs.Rd
c7933322276a4b8fa37433e050766c4d *man/plot.furcation.Rd
939fa1dcc75eacda1eef877ee99c9e7b *man/plot.haplen.Rd
cd8682e4686cbe6130490e25a8e79301 *man/plot.haplohh.Rd
9d5eba020ec22ee48ef012d9f1a54d70 *man/rehh-package.Rd
0b3af48394811f7b7e481ca6fd7c63fd *man/remove.example.files.Rd
a67e3e8c460d7f55dde5243edf351c6c *man/scan_hh.Rd
9894dd029348f74ae46e2fb658289e24 *man/scan_hh_full.Rd
ce6e4d831dabbd3ded45ea6a4cdbf433 *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
d5c7bc8c7d80203979aa6a9237e9346d *src/CALL_PAIRWISE_HAPLEN.c
997866feb635416dba2745e1275b33f0 *src/CALL_SCAN_HH.c
34549fcae56fa1cf4325ed1c9870b376 *src/CALL_SCAN_HH2.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
8ea79b7de0fcb35f571962e17f7567fb *src/calc_pairwise_haplen.c
00d18c8e73beb8a0c8351110060f1219 *src/calc_pairwise_haplen.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
b6ca1e604a504ee2fdb7aff7621ce855 *src/init.c
77f8dc940762ed75f438205732206fc7 *src/integrate.c
40f968c6eb88192b40c247c6b9cd6492 *src/integrate.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
b333feb96e38279b41a60f9fcb93dd65 *tests/testthat/test_data2haplohh.R
a57d331f176ddaa7e7a19fb056cd2626 *tests/testthat/test_error_messages.R
3c553b425c68132fe5a74a06fc85d3e4 *tests/testthat/test_examples.R
6adc3c44917659c38b0adddbbf254f18 *tests/testthat/test_furcation.R
83461c197932114fbb6185821cdae353 *tests/testthat/test_ihh2ihs.R
09bd1fc643230fc24c90aac2c2d2f035 *tests/testthat/test_scan_full.R
06e74a8f326b2099d3ef7b77c1664a89 *tests/testthat/test_scan_hh.R
347ed7fd5246ab0a51b07eb65c551f51 *vignettes/examples.Rmd
80ac2e78110aa3e54fb5ce824bd5574f *vignettes/genetics.csl
0cb9f06cbea7141d8522641178da4b54 *vignettes/rehh.Rmd
0ae5b0965175c9ae6cbc11dd9bf5adc5 *vignettes/vignette.bib
