926e50105f74aa7b29a1100d2e1d0757 *DESCRIPTION
bc6dc567e323431fe65668a75863c4e8 *LICENSE
a17559649973f98a4436914b05071069 *NAMESPACE
9db8035e10c4c62e33d95e92e6a9e921 *NEWS
350e7cc6c77dae52aed76a7797bf7df4 *R/AlphaSimR.R
8659ce4816a3766a1b2cc51814efd74a *R/Class-HybridPop.R
567bfaeb25af5104ce16849f1b3a6797 *R/Class-LociMap.R
3acd8bde857520044df183653d86991a *R/Class-Pop.R
236effa754e819397b9a520761b2e6d9 *R/Class-SimParam.R
2262e1e5d5c9414813179396c10cd8d3 *R/GS.R
03b99f8eeee075f3ee0baa99cdaf7853 *R/RcppExports.R
14a8cfc7fff5d5f3734b144dbebd60dd *R/crossing.R
0df6ba4e2c1096289523baa34989fc76 *R/founderPop.R
e0c27f934d5e35ea033b6224635da75a *R/hybrids.R
d4ab076ff911c9cb3524ff80533d9fc8 *R/mergePops.R
ac4c8a069aa5ba9b3ecb1066cf7a1a40 *R/misc.R
e0aa697944c313b4e00f3623e5b21c7d *R/phenotypes.R
3c0db9406fd82fd2f4def9b825698817 *R/popSummary.R
17e49e38b31e8dab60f0fa6157f8a9f9 *R/pullGeno.R
1fddd69b6469e5540959425a7eaab270 *R/selection.R
6867b1a85517896e1c8169138c3d8919 *R/writeRecords.R
4a519ea5a539fdd8b6701d57bc4e40f5 *README.md
684beb74fd8a66a90c4a7daf725361f8 *build/vignette.rds
c56d8dd12a1bd0477532f17dcfbff0c6 *cleanup
4fe28a8960b3f873d0b853c1127022d0 *configure
cbc30c3bdb80a0ba152033e4d689da20 *configure.ac
40474467915e180d4e4ad3b29de68343 *inst/doc/intro.R
0beb56c97558e40ddbd6de468e9e153d *inst/doc/intro.Rmd
7459d852a685cd1b994f5a5934ffd9ba *inst/doc/intro.html
594ebf59d58c52509b571ba71683e043 *man/AlphaSimR.Rd
c199152c28126477003c9336a0ab0bf2 *man/GCAsol-class.Rd
e1d4cd37aa0cfcac23003b1a43e89a7b *man/HybridPop-class.Rd
3c7a7578a962f050a42e8075761dc5ac *man/LociMap-class.Rd
6b2cb18244de4644a95aed067caed7c4 *man/MapPop-class.Rd
b865eb550e96836146728468221be855 *man/Pop-class.Rd
96e08e0c2ebdc32d4e01f25d193140f9 *man/RRBLUP.Rd
62ed5ca2ebce5bcefef8083b6168b9d4 *man/RRBLUP2.Rd
e6d28645c0c860d61ed27f714b4dce17 *man/RRBLUPMemUse.Rd
b50caa6200a75025767b2f5929385e10 *man/RRBLUP_D.Rd
acc01c8f1047261ebed778c30dec2f84 *man/RRBLUP_D2.Rd
caa4e0dcb9d23928b532d53f5afd88e7 *man/RRBLUP_GCA.Rd
f4494566d3c02c3e69702e10b7a14006 *man/RRBLUP_GCA2.Rd
99d56dba1ac9167ad4fb802bb734d54c *man/RRBLUP_SCA.Rd
e4e883653f9deae7994f8fd5b59e26e6 *man/RRDsol-class.Rd
a2f1480651949a8da409180ef36ae0d1 *man/RRsol-class.Rd
0fcd2315fcba1aa125de24c1ca1ca8eb *man/RawPop-class.Rd
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1bad73ae72e27dd30f8d52be04bce0fb *man/SimParam.Rd
b5967e097338a8f3f40ef2df81da6aa2 *man/SimParam_addSnpChip.Rd
f242d6425de21dda369b948c226eb3ff *man/SimParam_addStructuredSnpChips.Rd
38b9ca6176e9c1e860085b093b556156 *man/SimParam_addTraitA.Rd
14573ef804b36be8c676a0d5abf3748f *man/SimParam_addTraitAD.Rd
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3a471543fada48b9dd8493cd6de52c42 *man/SimParam_addTraitADEG.Rd
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9199dead7b506c99f93e90f1e6464ff9 *man/SimParam_addTraitAE.Rd
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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
64997b2fb8cc6ff746f1e46a7f80d31e *man/SimParam_setRecRatio.Rd
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b5924e214146f939a200db54a78f4a9d *man/SimParam_setTrackRec.Rd
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0f9ff6a4a9171042ac61a44fa571f3a0 *man/SimParam_switchFemaleMap.Rd
35ee86d17c2aafa3552984cec1ad0411 *man/SimParam_switchFounderPop.Rd
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f7cc13579a28e3e597fe411ee44640d5 *man/SimParam_switchMaleMap.Rd
24e28a8e60a86ee20f4feae20b268b66 *man/SimParam_switchSnpChip.Rd
d86d276aed7e9bc2f08e9bbb0a6a141e *man/SimParam_switchTrait.Rd
1ec419ca101a12084b88c67e862abf27 *man/TraitA-class.Rd
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8f822f81643e617ca3bcd8223a2884ae *man/TraitADEG-class.Rd
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c62494f3c98c186e43813afdda614a1c *man/aa.Rd
0a25bf0f3803e38a6ef56d4deab315dd *man/bv.Rd
585623bda575ff90082bdcb49d1494b0 *man/calcGCA.Rd
d3554dccd76c3e5439962c6b89c65c1a *man/dd.Rd
56f60780aaa59c624f082f6e8bf50f68 *man/ebv.Rd
e0544c5da87c09f533caa17bd5b2fff0 *man/editGenome.Rd
72e910b28b75fb4d3dd93d6cd8d6edc8 *man/editGenomeTopQtl.Rd
6ccd58a6aba6eb5be20b0dd9812e29af *man/fastRRBLUP.Rd
3d8e60c20d398fdbbfc408a9a88b079b *man/genParam.Rd
cb153ab178b58bc71973787300de641f *man/genicVarA.Rd
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0a4a1baba2cd2393cf6ca9ba4b740260 *man/genicVarD.Rd
d6f93417f52db384611fe57ec70bd867 *man/genicVarG.Rd
08d1eef5f8c45d3ad4067f03c21dca26 *man/getQtlMap.Rd
6f48d5a55f4cab6a65e346cd94033657 *man/getSnpMap.Rd
9d67d3dea8a516cf3df611f463e38290 *man/gv.Rd
6aa036b8b996b2452ac3d8aa40e76484 *man/hybridCross.Rd
93b33ad601e6c78eb4af800722a8a4f2 *man/makeCross.Rd
f14d882c6f95ae196f818a895510a933 *man/makeCross2.Rd
620348188de1f23eb7fe0837c1072590 *man/makeDH.Rd
1197d8790fe2c2ce80a2ba90b3f368c5 *man/meanG.Rd
6a7988b3d377a691fa42fb932056156d *man/meanP.Rd
81ec60a40e10c6b6b4d2e5efc8587d6f *man/mergePops.Rd
8748a0734fa05837da542f4068995721 *man/nInd.Rd
7bbbe95866e6c4a96f433ce97b9fe266 *man/newMapPop.Rd
9a3954e7784adfd4c539f5bfbf5c1660 *man/newPop.Rd
3ac7726e85db9634e347ca70f1a9e026 *man/pedigreeCross.Rd
3a22bd04002fa459703faafc9e54c4c5 *man/pheno.Rd
456e31e7d92ef0cd2418028e322f301a *man/popVar.Rd
88db8df349c5ec071a04dfca4f2236ac *man/pullIbdHaplo.Rd
1272ce29f3c6f38190f92283d052ed00 *man/pullMultipleSnpGeno.Rd
ec75361d9ab55aefc41572d327e93d87 *man/pullMultipleSnpHaplo.Rd
ec08e6fd2e3740f59a4ce9316df0c0e2 *man/pullQtlGeno.Rd
9203be661fff36baaba8d29b4dd1d0b5 *man/pullQtlHaplo.Rd
1672dfe9879119f77557a15ecd917f8b *man/pullSegSiteGeno.Rd
1a24b4f17353ef2d9c46fb6590849f4d *man/pullSegSiteHaplo.Rd
bcd2a477be31a5e8e3489d5d6f77f883 *man/pullSnpGeno.Rd
601cb055d67cf8e8609ed4d190731b75 *man/pullSnpHaplo.Rd
96e627ee9e8322e72072aee771c8f32a *man/quickHaplo.Rd
a30a05f1a3dad33f5f726a163cb7040e *man/randCross.Rd
6ed3d3ac43b0a1bbec525b4b706ec69d *man/randCross2.Rd
29bc964c0c1f0eae2c1cf875686606e7 *man/resetPop.Rd
c46e5e6ce3e9753c175b6ddd9e9b0e72 *man/runMacs.Rd
d2306ba933debe2758f66c3d0685e880 *man/runMacs2.Rd
b2a1c56ff99b09ed04cf344cd0cb2529 *man/sampleHaplo.Rd
a8168ec598ebe589f34bb74758a1d60f *man/selIndex.Rd
1e6a20c079f6f3a69afaa25c7be3c49a *man/selInt.Rd
7a4d4b98d9012b77bb4e44d2055b3b1d *man/selectCross.Rd
730854e1c1a3aa553d24f0a7e7dfc294 *man/selectFam.Rd
006c279d813d4476053f7fd7cb338391 *man/selectInd.Rd
aed09992838aa92cf84e542e157db49a *man/selectOP.Rd
829cfcddaafb9d06eae8ba3ad9402177 *man/selectWithinFam.Rd
d05b538da32f480398333a852abf5288 *man/self.Rd
2328596b69ca89a3b532733ca5e95016 *man/setEBV.Rd
3ced0e8684550b59bd5263140abef7e5 *man/setPheno.Rd
3e96631f09cbe96f34f62d8cab001e1e *man/setPhenoGCA.Rd
8aa528591ee30195624b74ecd3544083 *man/smithHazel.Rd
b73359161d900fba45407f0ca08f3d68 *man/usefulness.Rd
3de2c81c763d94741a26c964abfb24bc *man/varA.Rd
4377c51a6900f41311c68f88c29592c5 *man/varAA.Rd
08d8292cc66f4f0ca147d31b9fdf074f *man/varD.Rd
1e15e29b4a0afb2bbb2b080f20cc34b2 *man/varG.Rd
ffa793a62b26b0b34f210bedd05d7f3c *man/varP.Rd
10196e444497f3876711b0862d14226b *man/writePlink.Rd
1974a164c4d9477a89b8eb40d1d9d24a *man/writeRecords.Rd
4462a0d63dfbf701fb12923bfab05e62 *src/GEBV.cpp
62267ac88468235ab56d8f3e9887fb6e *src/MME.cpp
8538ea3f1a25c4ea2751911e6b2f15ac *src/Makevars.in
bee230df6ebea3196c0fe754585c486a *src/Makevars.win
7e5aa243052899b4befceb0fb106a137 *src/RcppExports.cpp
b61f0f447c96bb61936383f891a43799 *src/algorithm.cpp
54edda62673404d4e1619c64bf1984b9 *src/alphaSuite.cpp
b6bc5bd8eb92f89b559107dd876d8b72 *src/alphasimr.h
203b20d021a8c79a84fcf0be6f353863 *src/calcGenParam.cpp
610876505ca439dd6ac7a6d714d79f8d *src/constants.h
abf8ee1ff272e3d1724c15ef80dd552b *src/datastructures.cpp
00147893071ebe8d2b13a813649e72da *src/getGeno.cpp
8a55c25bcfb4e51b7845f31f16916c54 *src/getGeno.h
e6de871ca93ebecff5f2252693ee6b91 *src/getGv.cpp
ecf61e7e9523ec31e5402fc12686cc37 *src/getHybridGv.cpp
ccec50db757fcc492c863f7bb7cf4ced *src/init.c
8e822b196a96185d24215c2f31eab481 *src/meiosis.cpp
4171708418bd0fe7e0775ed9b485cb59 *src/misc.cpp
d7518d33d022918927c7193df327a457 *src/misc.h
e4a088c01ee18fdb6f60d0b5f3fcf624 *src/optimize.cpp
e6422fe7abd7b30c55ca07dbce1a574d *src/optimize.h
1562ad080a8cd6661a28bebfc2329648 *src/packHaplo.cpp
85c5466d7e98701f4a2b98762fefeb3b *src/plink.cpp
1ac2ade8317a6480ef58cc4322f0c7ce *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
99c25951014e3aaa5b43f90d15273327 *vignettes/bibliography.bib
0beb56c97558e40ddbd6de468e9e153d *vignettes/intro.Rmd
