11e4efc33ed9c4aaf1e7ac3fc0ff3179 *DESCRIPTION
bc6dc567e323431fe65668a75863c4e8 *LICENSE
9fdf9dbb97cb185bd7c8fdaaa747df69 *NAMESPACE
35e8446b27fbbc88b88d8e7b2f1bd06d *NEWS
69dd3e9d5ed92830671c6d240664dbc0 *R/AlphaSimR.R
8659ce4816a3766a1b2cc51814efd74a *R/Class-HybridPop.R
69db222aa3443258b9d60c40dbfee5fc *R/Class-LociMap.R
999772bc1950fff0def48314f56c631e *R/Class-Pop.R
f125252ceffb869465421b27757769ed *R/Class-RRsol.R
7168c330e17a12dc7f33e54faf85a47e *R/Class-SimParam.R
abe8569d58020da53c0fb4caf33425e4 *R/GS.R
55d95f0ebbc96cf5a84aa7622be2c9ff *R/RcppExports.R
cf59766d3689bd36b4e9a784fb60d480 *R/crossing.R
68c8d87e3fc47f53e269a4c0d6a6bd0d *R/founderPop.R
e0c27f934d5e35ea033b6224635da75a *R/hybrids.R
76fc4beda465f95f54b0defdb34af209 *R/mergePops.R
6b9f10ef567acff4b8c8a29c5c4e1b5e *R/misc.R
a73765ded8f0866b90195b19e1b3dfd5 *R/phenotypes.R
a1f21ca476b08b7f41bf992aadd7f56a *R/polyploids.R
0fdf867e11677b7de60ba9a4ab04f85f *R/popSummary.R
f9c99a0a0bcdf30e6dc492ac6b91e16c *R/pullGeno.R
d8a4bda57967757b97ed38bf75a580d3 *R/selection.R
6867b1a85517896e1c8169138c3d8919 *R/writeRecords.R
4a519ea5a539fdd8b6701d57bc4e40f5 *README.md
a8a8bfdb6c723e271ce7bfaa59afc0d2 *build/vignette.rds
c56d8dd12a1bd0477532f17dcfbff0c6 *cleanup
4fe28a8960b3f873d0b853c1127022d0 *configure
cbc30c3bdb80a0ba152033e4d689da20 *configure.ac
0b311a2b7099b549ded3000d603b540a *inst/doc/intro.R
0466ecf912e093e4d09125728eae378c *inst/doc/intro.Rmd
b9f181633e723ca60dc65aa8af712c3f *inst/doc/intro.html
b9f4e4b10b0e5801e4426ce83ec3893e *inst/doc/traits.Rmd
53ba74246e3e254ea088652924d4e916 *inst/doc/traits.pdf
8d42f75bc72876c4b27a909cfb11cb64 *man/AlphaSimR.Rd
e1d4cd37aa0cfcac23003b1a43e89a7b *man/HybridPop-class.Rd
3c7a7578a962f050a42e8075761dc5ac *man/LociMap-class.Rd
00aa7353e04e9cf92cdeb5aa181cce8f *man/MapPop-class.Rd
16247ac8d94614b9113c5cb1bd277312 *man/Pop-class.Rd
6bf8ebdf5de1a777cedbc07a253b0464 *man/RRBLUP.Rd
c8ebce085426a892dd8a48df9e97a640 *man/RRBLUP2.Rd
66e4f17eaa6a9edf00adc9294309cd78 *man/RRBLUPMemUse.Rd
91536887d72122a50879d0fcf2cc9e13 *man/RRBLUP_D.Rd
867b0b3b0162e37c5e6431024f70752f *man/RRBLUP_D2.Rd
fdc9ce455f9e1edaf729d2f999c6bb90 *man/RRBLUP_GCA.Rd
f9cb1a4a373a51ec227bb50288cafa00 *man/RRBLUP_GCA2.Rd
d632b7871436d2b07d89775a439bfa50 *man/RRBLUP_SCA.Rd
a37ab9842db7ee68e80753fe9d312879 *man/RRBLUP_SCA2.Rd
1d59a38a5a921455c14050a4afda5fcb *man/RRsol-class.Rd
858e6b2c964b99ec43c20c483db0ad00 *man/RawPop-class.Rd
13b0f398682c797616899618b74b73a0 *man/SimParam.Rd
2a2c1e692c0cd91edf3a9d5dff22ccce *man/SimParam_addSnpChip.Rd
f242d6425de21dda369b948c226eb3ff *man/SimParam_addStructuredSnpChips.Rd
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14573ef804b36be8c676a0d5abf3748f *man/SimParam_addTraitAD.Rd
110a6335764362aec521d2340dc999d0 *man/SimParam_addTraitADE.Rd
7d2e6a8404d9776345c190a820a9936b *man/SimParam_addTraitADEG.Rd
dd5eb0d4e692710a3cee2a01c9b61cc2 *man/SimParam_addTraitADG.Rd
b061e9a4021ee9efa16bac5033e56edf *man/SimParam_addTraitAE.Rd
c74127fdbf344c91ea913f042e76f11e *man/SimParam_addTraitAEG.Rd
25e02bdb8284265f63898fe341dd9e21 *man/SimParam_addTraitAG.Rd
bb7ae84b7ac1c6adef0af5e752d3aebb *man/SimParam_manAddSnpChip.Rd
40ad15741ad44b05c852c92b9adba467 *man/SimParam_manAddTrait.Rd
0f7064a244a21bbe4c3fac85a625673a *man/SimParam_new.Rd
a73e01d402dad73b6c60cc26d8bb41a6 *man/SimParam_removeFounderPop.Rd
996d8649e1db3ee852688b41aabd0e5d *man/SimParam_removeSnpChip.Rd
ee602aefb077514cdb186d17054377a0 *man/SimParam_removeTrait.Rd
092adc231d52b280625af67a6e84e059 *man/SimParam_rescaleTraits.Rd
1dfed52d928988656e65c3e58c7b8e42 *man/SimParam_resetPed.Rd
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1c0d7703c5f5977272bb900f29987472 *man/SimParam_setCorE.Rd
95347352443f738b4bc47a284afe4cfc *man/SimParam_setGender.Rd
ad6a543831a049dab3383ad60a0fbf46 *man/SimParam_setMeiosis.Rd
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b5924e214146f939a200db54a78f4a9d *man/SimParam_setTrackRec.Rd
b1630e4d5973349763257c948e59da85 *man/SimParam_setVarE.Rd
0f9ff6a4a9171042ac61a44fa571f3a0 *man/SimParam_switchFemaleMap.Rd
35ee86d17c2aafa3552984cec1ad0411 *man/SimParam_switchFounderPop.Rd
c68802f8388675dfc58b3f05ad53fcfb *man/SimParam_switchGenMap.Rd
f7cc13579a28e3e597fe411ee44640d5 *man/SimParam_switchMaleMap.Rd
24e28a8e60a86ee20f4feae20b268b66 *man/SimParam_switchSnpChip.Rd
d86d276aed7e9bc2f08e9bbb0a6a141e *man/SimParam_switchTrait.Rd
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ddbd0d5b74d693198c82df8ed24e189b *man/TraitA2-class.Rd
79e31eaa82c485d477f8a788a3fcdff5 *man/TraitA2D-class.Rd
08eb03b1e8c3e69e9669bb77b4576117 *man/TraitAD-class.Rd
8eba42ed44ba1dd50404c1a881d218ce *man/TraitADE-class.Rd
8f822f81643e617ca3bcd8223a2884ae *man/TraitADEG-class.Rd
edf038fef2b0612c1cd9c80ccbc09c32 *man/TraitADG-class.Rd
91a6cb995d3b5846e2eea484c3c6f2f8 *man/TraitAE-class.Rd
bf61bed0891bd74e7eda5b39e3e369f1 *man/TraitAEG-class.Rd
e8a83a532a55fbf7d45de9afbe2ad31f *man/TraitAG-class.Rd
c62494f3c98c186e43813afdda614a1c *man/aa.Rd
0a25bf0f3803e38a6ef56d4deab315dd *man/bv.Rd
3f07ca9e5e2d834949a9fc33ae91e59b *man/cChr.Rd
585623bda575ff90082bdcb49d1494b0 *man/calcGCA.Rd
d3554dccd76c3e5439962c6b89c65c1a *man/dd.Rd
fdad7c1aad6e3d4223256f1e0eabbf1c *man/doubleGenome.Rd
56f60780aaa59c624f082f6e8bf50f68 *man/ebv.Rd
e0544c5da87c09f533caa17bd5b2fff0 *man/editGenome.Rd
5aba60f9e9c7039a708dcbea9d13af8e *man/editGenomeTopQtl.Rd
0ac2f4fb82f6aa824a333e3ebabb7ea8 *man/fastRRBLUP.Rd
7a63cf38a359d04b184694a970599a9c *man/genParam.Rd
cb153ab178b58bc71973787300de641f *man/genicVarA.Rd
b0d16ae1626b6bc2cf7c1dd6a520604b *man/genicVarAA.Rd
0a4a1baba2cd2393cf6ca9ba4b740260 *man/genicVarD.Rd
d6f93417f52db384611fe57ec70bd867 *man/genicVarG.Rd
08d1eef5f8c45d3ad4067f03c21dca26 *man/getQtlMap.Rd
6f48d5a55f4cab6a65e346cd94033657 *man/getSnpMap.Rd
9d67d3dea8a516cf3df611f463e38290 *man/gv.Rd
e8763f0dcc13e1ec535333f3709c1d23 *man/hybridCross.Rd
93b33ad601e6c78eb4af800722a8a4f2 *man/makeCross.Rd
f14d882c6f95ae196f818a895510a933 *man/makeCross2.Rd
5f50e7bc73fb5f4d69aeea1cb07d8fe3 *man/makeDH.Rd
1197d8790fe2c2ce80a2ba90b3f368c5 *man/meanG.Rd
6a7988b3d377a691fa42fb932056156d *man/meanP.Rd
81ec60a40e10c6b6b4d2e5efc8587d6f *man/mergePops.Rd
573df50ea78db6a234b19454d0d9cd1d *man/mutate.Rd
8748a0734fa05837da542f4068995721 *man/nInd.Rd
7bbbe95866e6c4a96f433ce97b9fe266 *man/newMapPop.Rd
b07c4db91b8c250abd255251d8bf78ad *man/newPop.Rd
547df820ed7a668a3dc3cf48135cf296 *man/pedigreeCross.Rd
3a22bd04002fa459703faafc9e54c4c5 *man/pheno.Rd
456e31e7d92ef0cd2418028e322f301a *man/popVar.Rd
034d13ae6c84f2b4c8ce1564e7f24a96 *man/pullIbdHaplo.Rd
33fe8f6c0c8f5be2c0ea9387946f3062 *man/pullQtlGeno.Rd
dc0049de72df2ff400d9830339410d0e *man/pullQtlHaplo.Rd
1672dfe9879119f77557a15ecd917f8b *man/pullSegSiteGeno.Rd
1a24b4f17353ef2d9c46fb6590849f4d *man/pullSegSiteHaplo.Rd
bcd2a477be31a5e8e3489d5d6f77f883 *man/pullSnpGeno.Rd
663091837d50ecaa5750d4db7005a038 *man/pullSnpHaplo.Rd
31837e5c385adc353a8cca839fa29829 *man/quickHaplo.Rd
5a7c64962f182299eb46b3170d04f564 *man/randCross.Rd
56bb5d06085896f79178e9ce2efb1a84 *man/randCross2.Rd
ee53629c991daf0b9207c67fe871359f *man/reduceGenome.Rd
29bc964c0c1f0eae2c1cf875686606e7 *man/resetPop.Rd
a4d1b6522ffd618fbe955c8a19248ea4 *man/runMacs.Rd
27fa188c99fd675f32fea74392ccd8ba *man/runMacs2.Rd
a0b7854879b46cd6fd717b21a3763b94 *man/sampleHaplo.Rd
a8168ec598ebe589f34bb74758a1d60f *man/selIndex.Rd
1e6a20c079f6f3a69afaa25c7be3c49a *man/selInt.Rd
ec2ac42cc252e628e2bff6c44edc9c9a *man/selectCross.Rd
a7fb1a8c1564b36756f50137fbda5f53 *man/selectFam.Rd
83e13db983ade6c87bff8cd615e0f44c *man/selectInd.Rd
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7e17e12bf13f17eac3a753d407615bbd *man/selectWithinFam.Rd
719646dbd6619e3bcf398c024803a38c *man/self.Rd
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661a66128dd3be7d67d75476d9989caa *man/setPheno.Rd
392981c07bbacaced0045a27aaba27d0 *man/setPhenoGCA.Rd
8aa528591ee30195624b74ecd3544083 *man/smithHazel.Rd
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3de2c81c763d94741a26c964abfb24bc *man/varA.Rd
4377c51a6900f41311c68f88c29592c5 *man/varAA.Rd
08d8292cc66f4f0ca147d31b9fdf074f *man/varD.Rd
1e15e29b4a0afb2bbb2b080f20cc34b2 *man/varG.Rd
ffa793a62b26b0b34f210bedd05d7f3c *man/varP.Rd
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e5b0b2f51e4aa3395d131fdf60e66bd8 *man/writeRecords.Rd
672b5743ae7945dfaca51c6f728df034 *src/MME.cpp
8538ea3f1a25c4ea2751911e6b2f15ac *src/Makevars.in
bee230df6ebea3196c0fe754585c486a *src/Makevars.win
4cc194800fc8d0a444542e8b0741c292 *src/RcppExports.cpp
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54edda62673404d4e1619c64bf1984b9 *src/alphaSuite.cpp
3ea5fa5fe51978446b386a3e43ad0dc4 *src/alphasimr.h
1008b9bf72d00ec2accf940838502464 *src/calcGenParam.cpp
610876505ca439dd6ac7a6d714d79f8d *src/constants.h
abf8ee1ff272e3d1724c15ef80dd552b *src/datastructures.cpp
b9d8e9083cd8173c1f0cecf67b6d74ef *src/getGeno.cpp
67d6bf84c189d66c12b89f1e7ca2611e *src/getGeno.h
7e6914a52186c4665c7797e6d4936a74 *src/getGv.cpp
ff92baca0004548d3b27d6bb38db81e4 *src/getHybridGv.cpp
8be664bdd1cc88a47e3b3d229ead8ed0 *src/init.c
3a8ead4d1c23e0b7f755060cb159b3bd *src/meiosis.cpp
ba24b533871432b8621ec2ed7e17861c *src/misc.cpp
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e6422fe7abd7b30c55ca07dbce1a574d *src/optimize.h
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7339b189dd61b91ce697a86def4c7c84 *src/plink.cpp
0a1c479fa66a26fa3440b32b0432f85f *src/simulator.cpp
ab2471403bb60203f733aab07cda83ef *src/simulator.h
4f73537cef0969345caec0e220f40246 *tests/testthat.R
406f261d0ccaa6ebb600ad3a5a18b7eb *tests/testthat/test-addTrait.R
1d2b2a259611ce4a2cb23f4b4836e152 *tests/testthat/test-crossing.R
52dd0a931fa780e88030e065781d212f *tests/testthat/test-editGenome.R
8eb3290e50d471da265080b662b0dbee *tests/testthat/test-hybrids.R
00b8896df01ad62151adf7ccb8ddfc7e *tests/testthat/test-ibdRecHaplo.R
5012f419d470d6b08ebedda893cf41f4 *tests/testthat/test-statistics.R
a83fc05efb785e2b6864c79f67a2ffe7 *vignettes/AlphaSimR.bib
0466ecf912e093e4d09125728eae378c *vignettes/intro.Rmd
b9f4e4b10b0e5801e4426ce83ec3893e *vignettes/traits.Rmd
