f8743452f6e7e5c01e2352bc81f971d6 *DESCRIPTION
60da859463482a7ed89f264766728188 *LICENSE
e3c92641fe8ebd8d8340d7d2c8b3fdf5 *NAMESPACE
70ec9073dd5bbd3bf215c18256a233f9 *NEWS
0f038bb75b805b6d2309896d9c739eeb *R/AlphaSimR.R
2de82903acde5ca592d7e5b5e422a6c6 *R/Class-HybridPop.R
3a0eba4c7c69e89683a2fd386e39d9a2 *R/Class-LociMap.R
362a1d63ec27633fe09ecf8fd70a3f46 *R/Class-Pop.R
e25cede84cd87c826e3c49e95f963b0e *R/Class-RRsol.R
42228fede55e7b82f3ecd6089ecc9e50 *R/Class-SimParam.R
3219f9bd674d42a42d16d39399664982 *R/GS.R
044bb5293c58cd0c2ec05900e0452294 *R/OCS.R
ad0831a61e2dc834bea38113320ca0c4 *R/RcppExports.R
82f008b7766eb6ebe0ee76a0e439900f *R/crossing.R
ecd401d02fc9930ed1530d34b224ad40 *R/founderPop.R
7a698c9c674c3cd99df2db7e99de9196 *R/hybrids.R
a2308a83fb20c1a922c1a944ecd56346 *R/mergePops.R
95eda88b7320b45ae2247dd3cd1fe5ea *R/misc.R
1fb2901c6372a179fb3666b08d38998c *R/phenotypes.R
3349663a478aa21fbc68edc01ead38fe *R/polyploids.R
1d8d65da9f3fc433645a0adbcb071558 *R/popSummary.R
c0c27cc19e37f4f68aedf156581a351f *R/pullGeno.R
c2e9b28d3f48d0d56482de323feb45cb *R/selection.R
baf5f2caa8fdc9d81e75928298e3bac5 *R/writeRecords.R
da260f740e07c7455a614cbe01e26d7b *README.md
07260c6d31d701fa2d9a7cb90b7f3a2a *build/vignette.rds
c56d8dd12a1bd0477532f17dcfbff0c6 *cleanup
4fe28a8960b3f873d0b853c1127022d0 *configure
cbc30c3bdb80a0ba152033e4d689da20 *configure.ac
9be964c4daef73aa035a6aecc42a12b9 *inst/CITATION
a9eff901e41bcc9721efdd0b085ba0dd *inst/doc/intro.R
8890eebb84665107d7e684461741ec9a *inst/doc/intro.Rmd
0197b60ec82d42f47b972918b67834c5 *inst/doc/intro.html
41d9bac5bd56c1722ba82f7848b0d0d3 *inst/doc/traits.Rmd
6cee18b95f9b19d539444ebda64f80d0 *inst/doc/traits.pdf
7ba1882717551a79164414656b7bd69e *man/AlphaSimR-package.Rd
05adeab03e3e93b87c5ea41b250a1d1e *man/HybridPop-class.Rd
3c7a7578a962f050a42e8075761dc5ac *man/LociMap-class.Rd
167c91aaf1dc72aa04114726b157465e *man/MapPop-class.Rd
6b3250081169b2ea446cd84d110a2674 *man/MegaPop-class.Rd
334d3a1836465ca0fdff78df45381c51 *man/NamedMapPop-class.Rd
6c016366f90c926e6cca7a2a8f604b67 *man/Pop-class.Rd
3f63cd162601537411c4a9e0cc40d20b *man/RRBLUP.Rd
9de64196fd9f796d0c02c58e15397e57 *man/RRBLUP2.Rd
66e4f17eaa6a9edf00adc9294309cd78 *man/RRBLUPMemUse.Rd
67e2b13a75bac8ad28e63fc1d055af3f *man/RRBLUP_D.Rd
134b63d389c3f56cf807384835aa8752 *man/RRBLUP_D2.Rd
e62f1b6391460d70dd13b6090716b7bc *man/RRBLUP_GCA.Rd
ce140ec4be4a1e98b1cb3f74be854c1e *man/RRBLUP_GCA2.Rd
f4fe740e0e3e35e3d1f6633feb378fed *man/RRBLUP_SCA.Rd
550c7c1015f4c541e39c6cd77c4b1c6e *man/RRBLUP_SCA2.Rd
1d59a38a5a921455c14050a4afda5fcb *man/RRsol-class.Rd
e159add32388a82153c197e7fdb5c8b2 *man/RawPop-class.Rd
a9cd759b8e3c29568f5ec51b8d3fccb8 *man/SimParam.Rd
f5a23eb46fc22e13be18d74462f777c6 *man/TraitA-class.Rd
07344a77efe749c6a815f50d117f0ffb *man/TraitA2-class.Rd
7ca9144a1cfb396019445142d151dd2d *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
08fb2f155339df42abc4c9cefe665356 *man/attrition.Rd
0a25bf0f3803e38a6ef56d4deab315dd *man/bv.Rd
99df81be9209fb4be580017133045d0d *man/cChr.Rd
585623bda575ff90082bdcb49d1494b0 *man/calcGCA.Rd
d3554dccd76c3e5439962c6b89c65c1a *man/dd.Rd
fdad7c1aad6e3d4223256f1e0eabbf1c *man/doubleGenome.Rd
56f60780aaa59c624f082f6e8bf50f68 *man/ebv.Rd
3e0b539c9a9e15eafd15977e8bffcb51 *man/editGenome.Rd
5aba60f9e9c7039a708dcbea9d13af8e *man/editGenomeTopQtl.Rd
c31eb75c89319fed7384cdecc919aa60 *man/fastRRBLUP.Rd
f3acc20679df9f345b56e6e04c84c554 *man/genParam.Rd
cb153ab178b58bc71973787300de641f *man/genicVarA.Rd
b0d16ae1626b6bc2cf7c1dd6a520604b *man/genicVarAA.Rd
0a4a1baba2cd2393cf6ca9ba4b740260 *man/genicVarD.Rd
d6f93417f52db384611fe57ec70bd867 *man/genicVarG.Rd
730893ddac2fd0f72a9856afcedd75f9 *man/getNumThreads.Rd
1c3e2eea3dc913d79bc03ef9d7ace65c *man/getQtlMap.Rd
0f314150f47954e65de863a8b5b9d9bb *man/getSnpMap.Rd
9d67d3dea8a516cf3df611f463e38290 *man/gv.Rd
e8763f0dcc13e1ec535333f3709c1d23 *man/hybridCross.Rd
7e2f81064532350abaf6ff6eedd8959d *man/makeCross.Rd
9d886c8641b3b7d0cf1659f55e6486bd *man/makeCross2.Rd
5f50e7bc73fb5f4d69aeea1cb07d8fe3 *man/makeDH.Rd
1197d8790fe2c2ce80a2ba90b3f368c5 *man/meanG.Rd
6a7988b3d377a691fa42fb932056156d *man/meanP.Rd
d79da2db340f7d12e7212ebe9f0aa0b5 *man/mergeGenome.Rd
87c41767b308de52b67264a41f1f29b8 *man/mergePops.Rd
573df50ea78db6a234b19454d0d9cd1d *man/mutate.Rd
8748a0734fa05837da542f4068995721 *man/nInd.Rd
fdfc2bc75f5cedf3aaea1646558d34df *man/newMapPop.Rd
4ad14dc13dd2f5a5b6869235856f731c *man/newMegaPop.Rd
48e73b6a772ec93435bb3695ad2964c9 *man/newPop.Rd
992be14f2b4d8d15781af84fa7e2b6a8 *man/pedigreeCross.Rd
3a22bd04002fa459703faafc9e54c4c5 *man/pheno.Rd
456e31e7d92ef0cd2418028e322f301a *man/popVar.Rd
18d90ae1a75ff553a914fc930a65ec7c *man/pullIbdHaplo.Rd
1a7dc8cd658d8d44c9a463ff17e506b0 *man/pullQtlGeno.Rd
5fa604adc5f9a23334d1f1113f19464c *man/pullQtlHaplo.Rd
d1e6630072d66d4fcf0a4d3e738938b6 *man/pullSegSiteGeno.Rd
b056c0fa39fb37ab4d869ed453f1e292 *man/pullSegSiteHaplo.Rd
0810e8f7d4de9242cdba659fab92f9c5 *man/pullSnpGeno.Rd
edf5d38966bf97fe5d8c91217fdc9b75 *man/pullSnpHaplo.Rd
31837e5c385adc353a8cca839fa29829 *man/quickHaplo.Rd
124820e21796207bb8fd9134bb034b70 *man/randCross.Rd
50ff5cf7d3616ac73c31f3ba176569c9 *man/randCross2.Rd
982fd72e788eebcacca73b66699e8369 *man/reduceGenome.Rd
29bc964c0c1f0eae2c1cf875686606e7 *man/resetPop.Rd
a4d1b6522ffd618fbe955c8a19248ea4 *man/runMacs.Rd
27fa188c99fd675f32fea74392ccd8ba *man/runMacs2.Rd
4b7d578f9130bf4f833e2c0f4d4c2d7c *man/sampleHaplo.Rd
a8168ec598ebe589f34bb74758a1d60f *man/selIndex.Rd
1e6a20c079f6f3a69afaa25c7be3c49a *man/selInt.Rd
dfc2cd3df5b0bb73cee169f48bfd59dd *man/selectCross.Rd
74c6c93063f33c21eaeb8865809374e9 *man/selectFam.Rd
0e21a224666f4ebd44c492617fc80629 *man/selectInd.Rd
48b9edd6e3123b5514d9c86edffa56c7 *man/selectOP.Rd
f16ff52706e731774dd7eb82dd0f96ce *man/selectWithinFam.Rd
e1d8abe8e4f12fa506fe39eae1831ca4 *man/self.Rd
0217d67a246e43e6e37109a49269fcf2 *man/setEBV.Rd
fdda2406f25f279e2244187f168054f9 *man/setPheno.Rd
652d17881101563a2802358068e01525 *man/setPhenoGCA.Rd
4cafe268aa63f75ba2d7be217021db89 *man/setPhenoProgTest.Rd
8aa528591ee30195624b74ecd3544083 *man/smithHazel.Rd
b01abb6f7261f5be9d41346be5547c7e *man/solveMKM.Rd
82e9eac92b294c09c31d710ff995ba06 *man/solveMVM.Rd
dc2ed17feabd1249a26c4293e4e0d65d *man/solveRRBLUP.Rd
567cd1a161aa94379e58451bdfc3742c *man/solveRRBLUPMK.Rd
82883ade0d74aaa230f46e4f8423109e *man/solveRRBLUPMV.Rd
f1c35930220d32344074a0ce02a359cb *man/solveRRBLUP_EM.Rd
e024e77528bf1d6695eb3951140c6132 *man/solveRRBLUP_EM2.Rd
7d29c6e88a805266550743ae8c6f6949 *man/solveRRBLUP_EM3.Rd
bfb598d531d852c7221b3ab3c6ea8fca *man/solveUVM.Rd
8874c0f0560a1459e2d518c42b49faf4 *man/usefulness.Rd
3de2c81c763d94741a26c964abfb24bc *man/varA.Rd
4377c51a6900f41311c68f88c29592c5 *man/varAA.Rd
08d8292cc66f4f0ca147d31b9fdf074f *man/varD.Rd
1e15e29b4a0afb2bbb2b080f20cc34b2 *man/varG.Rd
ffa793a62b26b0b34f210bedd05d7f3c *man/varP.Rd
5c7c577dd6f563a84adc010b3d01110c *man/writePlink.Rd
57ff62a05b5a11a33018c5d16b51d00f *man/writeRecords.Rd
797c1ffa27e871218d033acd0c7a7c43 *src/MME.cpp
8538ea3f1a25c4ea2751911e6b2f15ac *src/Makevars.in
bee230df6ebea3196c0fe754585c486a *src/Makevars.win
cf3685ceaeedda7efae36aacf6a9578c *src/OCS.cpp
4d493197d09805b54ce09ed972785f53 *src/RcppExports.cpp
0df51bf31db1d146db87c2918b195cb6 *src/algorithm.cpp
7605ca8c267200bd65a36fd07f21c720 *src/alphaSuite.cpp
3ea5fa5fe51978446b386a3e43ad0dc4 *src/alphasimr.h
ac21ab2b6921b841c7aae524978da921 *src/calcGenParam.cpp
610876505ca439dd6ac7a6d714d79f8d *src/constants.h
19bec8e7a4529b63371f5a1bc4e14aed *src/datastructures.cpp
0542140f567dff5a603b4ae050ed007c *src/getGeno.cpp
67d6bf84c189d66c12b89f1e7ca2611e *src/getGeno.h
004ad186eb2b3e64807c952361c6579f *src/getGv.cpp
3bc1990c304c6ba088debe85f870d174 *src/getHybridGv.cpp
44f58b23fffa62127d1e2d8da262cf64 *src/ibd.cpp
01bc55b26cebde0586191c3758e05e9a *src/meiosis.cpp
4b1c5ce975bf5dd606d0dd4a0f25b40d *src/misc.cpp
8d66d82082726c3b41a4c63bbc35d462 *src/misc.h
e4a088c01ee18fdb6f60d0b5f3fcf624 *src/optimize.cpp
e6422fe7abd7b30c55ca07dbce1a574d *src/optimize.h
de99601cbd273c390472ba25b2415d20 *src/packHaplo.cpp
32495301a4daf3f2660a1f2ad93d1b4d *src/plink.cpp
6b7e6a65de4909fb16da0c5eab71f5ab *src/simulator.cpp
1c3c458c34552c84c3a70ac3323c3fe2 *src/simulator.h
4a3a208fecda1f56b904e4ca6e75e8b2 *tests/testthat.R
5fab3f8f009828821c9a862de52fe6ec *tests/testthat/test-addTrait.R
a7fb30cd87e01bc677d4dac1c22d2e30 *tests/testthat/test-crossing.R
7388e41ca9468b96d34719303acd35ac *tests/testthat/test-editGenome.R
5e83513609571979a72ad26a02112155 *tests/testthat/test-hybrids.R
5cb19d7769b660f96d79c3cd492ca391 *tests/testthat/test-statistics.R
18b101cdae30f7f6b9631913df0ff633 *vignettes/AlphaSimR.bib
8890eebb84665107d7e684461741ec9a *vignettes/intro.Rmd
41d9bac5bd56c1722ba82f7848b0d0d3 *vignettes/traits.Rmd
