26015c771fd5525798c03f1cd54ca8f2 *DESCRIPTION
60da859463482a7ed89f264766728188 *LICENSE
0f15967c56db577a1bfb4c2dbce07ecf *NAMESPACE
ae94237c82eaf7b7194779a4ece606cf *NEWS.md
e8a4e394c6f0bef82f353a76d5961e5f *R/AlphaSimR.R
6428607d5b4dd87f12f7118befa48b0e *R/Class-HybridPop.R
d62d99a444d7d6a2661140ce7346c509 *R/Class-LociMap.R
65ba4c8b13c52e1bb247a89f51b8507e *R/Class-Pop.R
4daea4514899d855f937bf415361096a *R/Class-RRsol.R
495678f637f8dc018c6272013047d9bd *R/Class-SimParam.R
307d52b96218e04ca732691ca7e745cd *R/GS.R
4dc8eb931188f3ae697408b589008aab *R/RcppExports.R
8fb3f25ebd00c23ab6227393be06a918 *R/crossing.R
6d63b9ec6a022803cbba574b1c01670c *R/founderPop.R
bd264d97c0fa7e3bdc5d6b7da67127db *R/hybrids.R
02ce84f37243b846fe26b9fc6e4de0b0 *R/importData.R
f81c1240b9e23d3c56f00ab3cac57483 *R/mergePops.R
717797b958a97d672dfdd055d312efe0 *R/misc.R
88fe24188c336dd790714fd01c30543f *R/phenotypes.R
89e3728e2332b236378cd791d5d0141f *R/polyploids.R
90f5541db0e712616c67e3456bb519a9 *R/popSummary.R
ac495a0c33eba34e9b65e273b6d4df53 *R/pullGeno.R
634ef0de9cab7cf2aec914f8d929cc3d *R/selection.R
b0690de78dc6b600d37e76b81537122c *R/writePlink.R
3efdfc14d65482e05962b775d383b2d6 *R/writeRecords.R
71d7fb802a7ca15f94cb7aebf7d1892f *README.md
5e451144636e65f018fd7465f0675b6f *build/partial.rdb
81288097aaed39a4070215b4db8e1a59 *build/vignette.rds
b1e9d1f2a12cf4ca3fced3bbc60a519c *inst/CITATION
462f5871a36e971b44d355f47f21b68d *inst/REFERENCES.bib
27dabe3ee39e9e538504b1c66808454a *inst/doc/intro.R
7e2c9d0f6e2f491ba92e1344a911567e *inst/doc/intro.Rmd
4a3c2fd6496187756effac63e4edf839 *inst/doc/intro.html
41d9bac5bd56c1722ba82f7848b0d0d3 *inst/doc/traits.Rmd
3dac9664c818196f64d7b4165552f3c7 *inst/doc/traits.pdf
4c0ffe276edfc27a50ed5c517c0027b1 *man/AlphaSimR-package.Rd
21124b1441bf63288a37b9c711e9c93d *man/HybridPop-class.Rd
7b2a9e11a704b1b19c3646ca06d2cfe4 *man/LociMap-class.Rd
1e4e9e828f4191762dd493292c3ec49d *man/MapPop-class.Rd
bca342988da7ba4bfe37520b9ca5bad5 *man/MultiPop-class.Rd
85ca7654382a579ab0aa466ae6578f1e *man/NamedMapPop-class.Rd
059719a71cb7fdda06994b3e131f454a *man/Pop-class.Rd
026b00dd1983a8a17488e853f5e5e806 *man/RRBLUP.Rd
e6a50aef385554f9b135e34c8f818a74 *man/RRBLUP2.Rd
f21ef20e9442a58540f898ee897f7188 *man/RRBLUPMemUse.Rd
74d83c271698e1e33e70f4cd01c8cbce *man/RRBLUP_D.Rd
a95c1f1a0d3399de9a8e4ad0984dd33d *man/RRBLUP_D2.Rd
662e83cf387f4b1be9f3e44acc5561cd *man/RRBLUP_GCA.Rd
f8d7a3f2e8fab8304e22c9423ff909de *man/RRBLUP_GCA2.Rd
fee3e2c440a26666962492b2d37a3b62 *man/RRBLUP_SCA.Rd
2e21a60609949816b48394d14889fe66 *man/RRBLUP_SCA2.Rd
8f06d16c1e0c2c6f9620fcbec169e636 *man/RRsol-class.Rd
328cb795c1c97ecbfc05f869fd898fb0 *man/RawPop-class.Rd
59e77448220041d5f2974305d3722466 *man/SimParam.Rd
54a729944d353cea045e029a66ca91a9 *man/TraitA-class.Rd
c810f2d604e261da077ff74ce4d6e3ab *man/TraitA2-class.Rd
7e836a223c1e5d6addcb016e8efda195 *man/TraitA2D-class.Rd
a5fb48edfeb3774bafebf6be3d88ccad *man/TraitAD-class.Rd
6ad81040a08cbc8ff796caf1111c4d4a *man/TraitADE-class.Rd
f631b47cc20247be023e4835f3a1a1d3 *man/TraitADEG-class.Rd
733c8567fa5933ff12bac22e5e072132 *man/TraitADG-class.Rd
7fefdbe540a760c9d7d93ec813664fcf *man/TraitAE-class.Rd
cfdc85c73ff965721b7a1cd66e7b6676 *man/TraitAEG-class.Rd
bb54b6af17e1cbebffbe194912fbf036 *man/TraitAG-class.Rd
557367f5d69d956901aa67b47e2bf36d *man/aa.Rd
e83d92c2ab7d6f251d3883e6ebb7e146 *man/addSegSite.Rd
8d6448d067414e0f374df31dacdb1554 *man/attrition.Rd
bc6177243845a1c8e3cda85a604ae0cb *man/bv.Rd
49d111cc2cd5fab6f8ef4a050034e5b5 *man/cChr.Rd
f99469b0b681b5bc0713f0e856a28c8a *man/calcGCA.Rd
f4c0c95de3d7e3d5bcbcaa69ffb84793 *man/dd.Rd
38605c10d38d1895edb357444d3ed6ea *man/dot-newPop.Rd
81a203ba92eabe9ae6b521d372a12fff *man/doubleGenome.Rd
53a4d8651ea5875a3f99bc74887ccc53 *man/ebv.Rd
ae3eee3d2cdb3c17be0e3966abd3eabc *man/editGenome.Rd
5e71cf2a654f5dd28ee008ee02aa7351 *man/editGenomeTopQtl.Rd
e0c0cbd1fb3ad1a21805ab903f34fb9c *man/fastRRBLUP.Rd
02d0ac09b9a920f6c2390f78b8f36e6f *man/genParam.Rd
3a6bb3c4194e1dc261284ef8b3e1609a *man/genicVarA.Rd
504476a00ef620ded094f4913fa62159 *man/genicVarAA.Rd
043911f79b604c559a981f28002cef9d *man/genicVarD.Rd
fd2b207d32ad4afd8665393cc64c68aa *man/genicVarG.Rd
3fafa171caf57a4a593d348b06ad4696 *man/getGenMap.Rd
e596a0ecc94456f6cdee7cf77468df0b *man/getMisc.Rd
d33aa1ee61d9bb98a08bae4ca283d6ec *man/getNumThreads.Rd
f573aa171b59ca107df88c39b7c7fef6 *man/getPed.Rd
2aef70a7249098e05715ae51e2b43565 *man/getQtlMap.Rd
96f4c3de7a5d6b41c663a85040028a90 *man/getSnpMap.Rd
000cd8ba1859e9980d235f057962df24 *man/gv.Rd
60b06075be6580d49be9218cbab2f81a *man/hybridCross.Rd
d2a37c81eb8273d2667d619face41b55 *man/importGenMap.Rd
8b125d39347ffd8bf6bc96f1d5c6e4d0 *man/importHaplo.Rd
fc31f02e9060779bd566b5386b5f3b2b *man/importInbredGeno.Rd
f28184d816a76a41f86fb1e60c0dbb8f *man/isFemale.Rd
01d26fdf412da45dd68547234fbc3c0b *man/isPop.Rd
0fa687239d14587b3a68d41142a7a441 *man/makeCross.Rd
059634cca577a0c9e4250e71e3aef24e *man/makeCross2.Rd
58e58de64365c78c21b4564941750153 *man/makeDH.Rd
41ba0e75b6d017aa9cc9956fb4b675c5 *man/meanG.Rd
3deb646833c8bc5af52c34e97eb931b9 *man/meanP.Rd
86dc15d543e1f82c0257ae77574a3276 *man/mergeGenome.Rd
b1973674c28f51762ec0cba28af5c699 *man/mergePops.Rd
f114a49c4554774870057a4b8cdf1819 *man/mutate.Rd
24d3640b91f3827b57a7f694cd2d95ba *man/nInd.Rd
50c1328c8212aac3337875adf6eb176f *man/newEmptyPop.Rd
70b6db24f3f2f228f1d36203331ed0dd *man/newMapPop.Rd
9f4ed2dbfbadd1068ba8c0f58ab0b074 *man/newMultiPop.Rd
0a0688ca8182b300486b38ca6bfcf0ee *man/newPop.Rd
db62a16b03f969a947a5fc3b606cf4aa *man/pedigreeCross.Rd
5ba9a4e2aed9e3902f90e46faa19e75a *man/pheno.Rd
c3e189b2e18f6672c4587987ee39f02e *man/popVar.Rd
60260d5c07a945434574e73b06df27f1 *man/pullIbdHaplo.Rd
8f3c4a3c2fca0fdfb98069018657e126 *man/pullMarkerGeno.Rd
6d9c4652f799295cfa82341a2fe800f3 *man/pullMarkerHaplo.Rd
546fb983146d25ec0e4c423625c668d6 *man/pullQtlGeno.Rd
5a6983f42dc39c2792a4a45ec9952e82 *man/pullQtlHaplo.Rd
f78ab5c392233d2cbf61096981d89d25 *man/pullSegSiteGeno.Rd
a579b218f97c525403c39527a8a554a4 *man/pullSegSiteHaplo.Rd
e8d11694947a0ac32282e67a5568b2d3 *man/pullSnpGeno.Rd
2d4334ef4286573f31fe74ac82a393ac *man/pullSnpHaplo.Rd
c7bc3efdf89354b72d2dedf83924bcdc *man/quickHaplo.Rd
c5eb8d0b6d57ef5bd6fcef48fcfc183e *man/randCross.Rd
efb37145e7c54daac12be59c4decca9e *man/randCross2.Rd
236e4d4294cbc07d5b60dbcad9412ddb *man/reduceGenome.Rd
9ff41591ce4b8ac1bb5e869d3601f929 *man/resetPop.Rd
ae96ba90f5bbf90ac60a78084e78bf36 *man/runMacs.Rd
77de232102fc49035d0b0996783c6d60 *man/runMacs2.Rd
fcc70adb1e6fb7528210802a5ffebfb7 *man/sampleHaplo.Rd
d519a1f0ed0caa1aba9170b40cf580ef *man/selIndex.Rd
61c034d133826de06fab410848787dd8 *man/selInt.Rd
d112563a318b792fecaf4dc13e94780a *man/selectCross.Rd
d44abaad2a3c4ce33cf7c9f41cd85e70 *man/selectFam.Rd
17d7a4d5118a0ead42f071d8a39f0d76 *man/selectInd.Rd
f2711e9c34e9d772e3aaae4bdd07dac7 *man/selectOP.Rd
ce5994f996e518da222b2b12fa9f2711 *man/selectWithinFam.Rd
e81c0f73b56e18c9808ba55764eaa9df *man/self.Rd
f3a67b9278765c320ab615590f7acc27 *man/setEBV.Rd
64dd5e30b978c7faad65ce85a67b240c *man/setMarkerHaplo.Rd
4f8cac84822b00b1da84902f4b320ef2 *man/setMisc.Rd
5becf8fee192f58816cb2cc57b511cd1 *man/setPheno.Rd
1ebb2323b1150aa0ef9564f4a4fb4a1a *man/setPhenoGCA.Rd
ea31c0e7fe65e1d5b0cb0a435c49a219 *man/setPhenoProgTest.Rd
ff3cc00610ce0a9250e96766e3567885 *man/smithHazel.Rd
ba190c1d8d5ed2d3ee0d462196fef4e1 *man/solveMKM.Rd
564008025f09d68b0f16e74a1b7d0b50 *man/solveMVM.Rd
e0a3b7882b22977b8b8f2c73ed127b71 *man/solveRRBLUP.Rd
57a76761cde382f792e6396aabebbd61 *man/solveRRBLUPMK.Rd
c7c853e43d26d0cf2cced60e8a25847f *man/solveRRBLUPMV.Rd
659b0e636e4b5f4794748f4ef8db52d6 *man/solveRRBLUP_EM.Rd
97cd79c7fd5c9f8dc06224463e0ef59a *man/solveRRBLUP_EM2.Rd
efed6f4b229973533abbac5c3b3cb8b5 *man/solveRRBLUP_EM3.Rd
abffef8e7a09150d3832a8492a7a63fd *man/solveUVM.Rd
639acee156bbf96d21978f26892e967b *man/transMat.Rd
a1f58fb28fb5a4fad0cc100c7e8069aa *man/usefulness.Rd
465b3f1bbc52457eb35e4c6beb25bbff *man/varA.Rd
14aec53e8f40875f4176418631af9529 *man/varAA.Rd
c70090bc47f0af6e7c7cbd7994c3bc00 *man/varD.Rd
329368575776709ef37ed7b68b5aef02 *man/varG.Rd
3339e8716cd54c0f5aefb1b2b0a6dbe8 *man/varP.Rd
e88ea7a690aa85b8061975995faaceef *man/writePlink.Rd
7267a12e18775a193159f89af98f72b2 *man/writeRecords.Rd
dbf50b2637b36da7127b67c94d6e6e48 *src/MME.cpp
efae3959806667aa05f2d1ec183b1270 *src/Makevars
efae3959806667aa05f2d1ec183b1270 *src/Makevars.win
1a346af3ccf680b99b5ca6fbc30f6a60 *src/RcppExports.cpp
e873dd0a2ae2f3a5c6b206cb980efb91 *src/algorithm.cpp
244533d36f33bfa0686163d270f7e579 *src/alphaSuite.cpp
3ea5fa5fe51978446b386a3e43ad0dc4 *src/alphasimr.h
79f3c7660a58f60959c913d8ee320d35 *src/altAddTraitAD.cpp
2cc0edef6a2b9afdfef04b3c32da5ac2 *src/calcGenParam.cpp
610876505ca439dd6ac7a6d714d79f8d *src/constants.h
72e1755d9fa0b18527066cd5ee8701de *src/datastructures.cpp
6dc110010aa9a9edbce024d9cba98a48 *src/getGeno.cpp
67d6bf84c189d66c12b89f1e7ca2611e *src/getGeno.h
004ad186eb2b3e64807c952361c6579f *src/getGv.cpp
c91455fc8cc42234129fc0258c4849eb *src/getHybridGv.cpp
0510886067800e833b187a3e48c0bb67 *src/ibd.cpp
2bfd6bbbb58ea9d4d4330a40be480bf6 *src/meiosis.cpp
2e1c2afeb5030cc5b8d181aaea634120 *src/misc.cpp
8d66d82082726c3b41a4c63bbc35d462 *src/misc.h
e4a088c01ee18fdb6f60d0b5f3fcf624 *src/optimize.cpp
e6422fe7abd7b30c55ca07dbce1a574d *src/optimize.h
de99601cbd273c390472ba25b2415d20 *src/packHaplo.cpp
8c04cd5d91ae77f6305a1dfc6611bc20 *src/simulator.cpp
1c3c458c34552c84c3a70ac3323c3fe2 *src/simulator.h
4a3a208fecda1f56b904e4ca6e75e8b2 *tests/testthat.R
e79d818fc206eae256d8ab81d1050524 *tests/testthat/test-addTrait.R
ad78e420165ae3c767cc3b4ea9eea2a5 *tests/testthat/test-crossing.R
3cf3dd4910f344a29f7dbbed56e009e6 *tests/testthat/test-editGenome.R
8b6ba6fdcad9d802b789b5ab76cf19bb *tests/testthat/test-hybrids.R
8063566e5fbdb35ca33fb6908fc1fc36 *tests/testthat/test-importData.R
5cb19d7769b660f96d79c3cd492ca391 *tests/testthat/test-statistics.R
3073638765feb6c928efcaeed5bfe1d0 *vignettes/AlphaSimR.bib
7e2c9d0f6e2f491ba92e1344a911567e *vignettes/intro.Rmd
41d9bac5bd56c1722ba82f7848b0d0d3 *vignettes/traits.Rmd
