951ae8249e740b637ec1a6efa23ac693 *DESCRIPTION
60da859463482a7ed89f264766728188 *LICENSE
3aad54c680a72aaa9b38b57d047ec7df *NAMESPACE
ca78c11c09e433e0a058bea36b4f4e97 *NEWS
2b931c35068df81230045290f3dabcac *R/AlphaSimR.R
2af4e3bf8235212fd56619007e1594b8 *R/Class-HybridPop.R
baee606336f6beb1e67ec0b960049f39 *R/Class-LociMap.R
6fa3c3532152a7df64600b0137ad0ddb *R/Class-Pop.R
4daea4514899d855f937bf415361096a *R/Class-RRsol.R
fc516735d8160a59e8f4affbdf853ab3 *R/Class-SimParam.R
b28465d9213c1b660c26ddf931c6e332 *R/GS.R
ad0831a61e2dc834bea38113320ca0c4 *R/RcppExports.R
6bd88ebcf73fbff2a3626ef6d26694d7 *R/crossing.R
a7ded543b9d77046c484ab3411fca869 *R/founderPop.R
be2ecefe7284d4027cc5fa3fbca47eb2 *R/hybrids.R
b94b4d8be013a35606c3d16871a13a5a *R/importData.R
47f805eb690582b60f299ee9fe80ec3f *R/mergePops.R
e6342ce62431f0724f4b9ccfdec6a7c9 *R/misc.R
dd3aefc2846630ca127d96f9b5ffd5f6 *R/phenotypes.R
67ab42450baffba75791eb1c7063145b *R/polyploids.R
040bc39e50526e7d95de4de48d07dce6 *R/popSummary.R
0fe74f84a1f82c669f0075a8431a1fb1 *R/pullGeno.R
c49d468a1f99ec90110f341b7e398f54 *R/selection.R
baf5f2caa8fdc9d81e75928298e3bac5 *R/writeRecords.R
da260f740e07c7455a614cbe01e26d7b *README.md
5a3dc0234a88f74f692067da4f19f766 *build/vignette.rds
9be964c4daef73aa035a6aecc42a12b9 *inst/CITATION
a9eff901e41bcc9721efdd0b085ba0dd *inst/doc/intro.R
8890eebb84665107d7e684461741ec9a *inst/doc/intro.Rmd
87c903cbd8beba4f898e0fe9cbef4cc2 *inst/doc/intro.html
41d9bac5bd56c1722ba82f7848b0d0d3 *inst/doc/traits.Rmd
0199a90311d36327e9634b8b7a30bc05 *inst/doc/traits.pdf
fee089b9cafb164eee51ac0393c989e6 *man/AlphaSimR-package.Rd
d8b97c4d5a683e658669ad8ac7a3b4f6 *man/HybridPop-class.Rd
7b2a9e11a704b1b19c3646ca06d2cfe4 *man/LociMap-class.Rd
4dd3371830b52716c15b37421b7f4edf *man/MapPop-class.Rd
19c8795e3147eb6717a70e1a338c2452 *man/MegaPop-class.Rd
d6e4903c3edde5fe0ac517fd9535c9c5 *man/NamedMapPop-class.Rd
29a426d9ac55612b537501b4add75fc9 *man/Pop-class.Rd
094b0650cf9ed11e55f70438d9130bf8 *man/RRBLUP.Rd
cdbe8de4b216d15e0b57c73721bdc3bf *man/RRBLUP2.Rd
f21ef20e9442a58540f898ee897f7188 *man/RRBLUPMemUse.Rd
db9ebac04b6e25e872f3040f490b98b4 *man/RRBLUP_D.Rd
ee6e3dbf198657888d3df80f04c7c08f *man/RRBLUP_D2.Rd
f9de029254499ccef22db61ca3345d3b *man/RRBLUP_GCA.Rd
722f143217a0e4fd1fd76062f761a071 *man/RRBLUP_GCA2.Rd
d85c534767a2cd7098dccf67dc121a32 *man/RRBLUP_SCA.Rd
f939f4b8bd8c2076dc2fc65639b69a52 *man/RRBLUP_SCA2.Rd
8f06d16c1e0c2c6f9620fcbec169e636 *man/RRsol-class.Rd
8ed75d4b0b8af7058cc5abfd30f3de58 *man/RawPop-class.Rd
24d925ff09e387d4bdae0896fe91c701 *man/SimParam.Rd
57614a59940cb71bbb378707076f77b5 *man/TraitA-class.Rd
af7e93d9660f6dc5c6a27be509726891 *man/TraitA2-class.Rd
60c08840559549fd59adf7b5fc643d16 *man/TraitA2D-class.Rd
797fd4c0b41399cbc85b251e4a48511a *man/TraitAD-class.Rd
b511269a570f3a7a58c7699d1ed7f731 *man/TraitADE-class.Rd
334780eec7d4fefa5d5e728c4a7bfa7c *man/TraitADEG-class.Rd
ee6c6debfdd36bcaec4951a3c5375f4f *man/TraitADG-class.Rd
752424c80e9cead070a5c96db7155dc7 *man/TraitAE-class.Rd
a282c81977ca7eef43b1ba655f7e2e61 *man/TraitAEG-class.Rd
97f64df0061093ea150818c61fc2a3f0 *man/TraitAG-class.Rd
153e31b6b786f6c7396047357c84b373 *man/aa.Rd
f2aee1ebae8038ba7b77072ca6cfb8f6 *man/attrition.Rd
3c1d79628594abee5ba6bfe2820349a7 *man/bv.Rd
a51fef468cd2daed15e434ee35a0106f *man/cChr.Rd
63f1eff276978fb7fc0822ff4ecfc29b *man/calcGCA.Rd
ab4366f48fef9c74e856956dc92be6c5 *man/dd.Rd
88d1b0fd63b525590767c577ec3db499 *man/dot-newPop.Rd
3fb0939dc02fae27c90687f653e24482 *man/doubleGenome.Rd
4a8716c5137ef826edc670bd4c1b6419 *man/ebv.Rd
0354ca6782f4640ce62168bb4c5fa654 *man/editGenome.Rd
f1a197c4f8cc8e9a44c482932432396d *man/editGenomeTopQtl.Rd
8e3f9c34b7b8fce757e2ec16c4fe4c25 *man/fastRRBLUP.Rd
6cb1e69132ea7c784cca20baccf76e5f *man/genParam.Rd
185ccf2b86824f6f9dde454d50dd98cd *man/genicVarA.Rd
a7f069fde33e1a9f8abcf0b996758e36 *man/genicVarAA.Rd
8eef48851ed58e6064ffc7d1e7043b69 *man/genicVarD.Rd
59dd7bc0a8dda00adb1643580832b215 *man/genicVarG.Rd
254af751b19e143c78b6da3d51de5c7c *man/getMisc.Rd
d33aa1ee61d9bb98a08bae4ca283d6ec *man/getNumThreads.Rd
031735c9192b032862a36ac923c10a6f *man/getQtlMap.Rd
46b116b185d6fb7c5d7b0ee31630b05e *man/getSnpMap.Rd
42f8ef7916942e71222ff543bb123639 *man/gv.Rd
9c274778fbf4c04b824d7e80b2ac9165 *man/hybridCross.Rd
5eba4ba604a6a2116929fb7351ed4c53 *man/importGenMap.Rd
514a4fef647eabe3019abbe97472c7f5 *man/importHaplo.Rd
0815157e0b2eacd320c94532e362f22a *man/importInbredGeno.Rd
959dd78900475758d267ec8545658bd6 *man/isFemale.Rd
a0bf94f71531e081d04443a3e3097c8b *man/makeCross.Rd
0640d92a77bf9458967611c048ec00b9 *man/makeCross2.Rd
1e9f601984ae471094d49fe0551914c4 *man/makeDH.Rd
1122a4b4672ea876c25fe791aeb30c4b *man/meanG.Rd
d65462143caf3e96a8b684712bbbb0c4 *man/meanP.Rd
33a99d00127721843b5e4a2c60fb5a89 *man/mergeGenome.Rd
4ae04a1166deede602c6fb55d6688b36 *man/mergePops.Rd
c4860dce5f2d31f5618bd9ef675f48d4 *man/mutate.Rd
ae4f3b5a5e61042360f26ffcc5d6588a *man/nInd.Rd
70b6db24f3f2f228f1d36203331ed0dd *man/newMapPop.Rd
8f48b92a8bc98a6b8960e6439f0ec5ff *man/newMegaPop.Rd
f5cd8d11c228f3cd2baf16035aacbc46 *man/newPop.Rd
1bca84bf6864945fd9cc0216105e40ad *man/pedigreeCross.Rd
a398bdcfc27f5959dc9d0b89b21db592 *man/pheno.Rd
c3e189b2e18f6672c4587987ee39f02e *man/popVar.Rd
58f85f272fea643a7de55cac1f7d2516 *man/pullIbdHaplo.Rd
f43b3bbb52f219076eede8267d54bfa6 *man/pullMarkerGeno.Rd
f3c9fa9f5aa4a1aa6ed529d54b56b192 *man/pullMarkerHaplo.Rd
99cbe724406eef480d17b7fa09b81c3b *man/pullQtlGeno.Rd
d32416e9c638be38be0936065d7b3394 *man/pullQtlHaplo.Rd
b590236d710a22180c0ad2cc4540ae01 *man/pullSegSiteGeno.Rd
2ab0dbbc281ae1c000c76dc0c7c88bd1 *man/pullSegSiteHaplo.Rd
4fa74e00099ed21d96fd319bdfb56034 *man/pullSnpGeno.Rd
c8ed379407d2e21d735c16f7120b8f71 *man/pullSnpHaplo.Rd
c7bc3efdf89354b72d2dedf83924bcdc *man/quickHaplo.Rd
252f5d5d6e2822a461bc70acf38829ac *man/randCross.Rd
3428dee487fed14b6b0ae1e456b48553 *man/randCross2.Rd
b22fd3fd8886af511da7a2135f401f3a *man/reduceGenome.Rd
398ed604c18aa6cf5838ffac45e31759 *man/resetPop.Rd
63ca174dbfc5b302a0f5a16e8d03fa13 *man/runMacs.Rd
d17ecb32febe2b058a8ea12ed691ad8d *man/runMacs2.Rd
9f7ee8cb642c7fce7d83da192172040e *man/sampleHaplo.Rd
c01680dc8f4bf7918ba7a5836044f37e *man/selIndex.Rd
61c034d133826de06fab410848787dd8 *man/selInt.Rd
e4fed9ff9855dbc5ea656206e63da73a *man/selectCross.Rd
d512c431c88df07a73c45ffdbe180bbc *man/selectFam.Rd
ba30feaa217448783066c35d50629379 *man/selectInd.Rd
fa4985291a8ee3f075dec8ea437a92a7 *man/selectOP.Rd
25fc5a792de02b8baedee221ea315aaf *man/selectWithinFam.Rd
0540230a6bfb1a0cd850367ab5b66e1f *man/self.Rd
7fad3e112b88da09e5aa5cf169808731 *man/setEBV.Rd
e42c464b5b27dba29fdcf7f3d4a2be12 *man/setMisc.Rd
8887ede61fc5fc5a357d025769648c16 *man/setPheno.Rd
d57f1e986f68bfc655457329d8a58e86 *man/setPhenoGCA.Rd
f09e4a3514128f029d117685ed719572 *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
2d6016974fa7090c581563e803e12ef0 *man/transMat.Rd
9b24faa550310e08703e894f355bd83d *man/usefulness.Rd
0937145ba1e35fee49a3ec930544321d *man/varA.Rd
7b3f76288208510586e2ed3881d50e90 *man/varAA.Rd
3f6793dafc60d62f8210da381c189ab8 *man/varD.Rd
b1b31f14fa2bfc588e862abc0a67fdcb *man/varG.Rd
c219ffdc3c777f7c6c5b9b58481bbefb *man/varP.Rd
14ee73305bf4b0834fbf00303cd35717 *man/writePlink.Rd
7267a12e18775a193159f89af98f72b2 *man/writeRecords.Rd
797c1ffa27e871218d033acd0c7a7c43 *src/MME.cpp
efae3959806667aa05f2d1ec183b1270 *src/Makevars
efae3959806667aa05f2d1ec183b1270 *src/Makevars.win
4d493197d09805b54ce09ed972785f53 *src/RcppExports.cpp
e873dd0a2ae2f3a5c6b206cb980efb91 *src/algorithm.cpp
7605ca8c267200bd65a36fd07f21c720 *src/alphaSuite.cpp
3ea5fa5fe51978446b386a3e43ad0dc4 *src/alphasimr.h
ac21ab2b6921b841c7aae524978da921 *src/calcGenParam.cpp
610876505ca439dd6ac7a6d714d79f8d *src/constants.h
1bf302f7b64658b19e300c8579a81731 *src/datastructures.cpp
76ab822cac025cf60b3cc263ac7287f8 *src/getGeno.cpp
67d6bf84c189d66c12b89f1e7ca2611e *src/getGeno.h
004ad186eb2b3e64807c952361c6579f *src/getGv.cpp
c91455fc8cc42234129fc0258c4849eb *src/getHybridGv.cpp
8450ae3689f6212bf3c549db50714848 *src/ibd.cpp
86eb4cadc0bf257aa3eeb85d01bc8cdf *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
e56892d7f4cad6dfc993b42b1b404e77 *tests/testthat/test-addTrait.R
2f5692b123f0ec3b3745471636a26094 *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
