bc810cac4bb9753eb50fe9ef698d63b1 *DESCRIPTION
60da859463482a7ed89f264766728188 *LICENSE
91a80586bde2d33c659cf33625c4cee8 *NAMESPACE
b4ba9b6e4e12c145452424468ecdeb3b *NEWS.md
e8a4e394c6f0bef82f353a76d5961e5f *R/AlphaSimR.R
6428607d5b4dd87f12f7118befa48b0e *R/Class-HybridPop.R
d62d99a444d7d6a2661140ce7346c509 *R/Class-LociMap.R
cfe8d5d03ed82cbf588234d4ca180927 *R/Class-Pop.R
4daea4514899d855f937bf415361096a *R/Class-RRsol.R
85cb6efa37042ce8fbad29b0e887044c *R/Class-SimParam.R
da841e792311dee0de8710b290fc485b *R/GS.R
bff257b488577c646ff6b985a0a10e30 *R/RcppExports.R
6bd88ebcf73fbff2a3626ef6d26694d7 *R/crossing.R
c1240a439a87c85ac54c8fb7cf544407 *R/founderPop.R
9716c541615dd38ef33c3159f57ccd7a *R/hybrids.R
6bf6aa9e0adb28eb3a2b62e483814e45 *R/importData.R
7242d2d8fe529229fa1744522a391c60 *R/mergePops.R
cafcf44e390f586e6d00b1cbb9d840dc *R/misc.R
9ad0102b079edd89770e2a5004b149d4 *R/phenotypes.R
67ab42450baffba75791eb1c7063145b *R/polyploids.R
040bc39e50526e7d95de4de48d07dce6 *R/popSummary.R
c4c5b9f98189f520da790d335a997c09 *R/pullGeno.R
c49d468a1f99ec90110f341b7e398f54 *R/selection.R
a613c961a548d4f37cc877b6e8e81b6e *R/writePlink.R
baf5f2caa8fdc9d81e75928298e3bac5 *R/writeRecords.R
290190d76e657dec65992da46616d745 *README.md
afc6c6784aedb0f13915179106609a66 *build/partial.rdb
d3d6cdd3ae9c17f3d704e0aeb040359e *build/vignette.rds
b1e9d1f2a12cf4ca3fced3bbc60a519c *inst/CITATION
462f5871a36e971b44d355f47f21b68d *inst/REFERENCES.bib
a9eff901e41bcc9721efdd0b085ba0dd *inst/doc/intro.R
8890eebb84665107d7e684461741ec9a *inst/doc/intro.Rmd
3db2dff3d8180c5d1cb7132010aeaa9e *inst/doc/intro.html
41d9bac5bd56c1722ba82f7848b0d0d3 *inst/doc/traits.Rmd
844e47b5fc613ed3bf4bf68ba267980b *inst/doc/traits.pdf
06486e81fc36371197d4d190b6069d5a *man/AlphaSimR-package.Rd
21124b1441bf63288a37b9c711e9c93d *man/HybridPop-class.Rd
7b2a9e11a704b1b19c3646ca06d2cfe4 *man/LociMap-class.Rd
1e4e9e828f4191762dd493292c3ec49d *man/MapPop-class.Rd
3c36fdfccb0a605b559a3cc4f52c3b59 *man/MegaPop-class.Rd
85ca7654382a579ab0aa466ae6578f1e *man/NamedMapPop-class.Rd
bb463d494d36d5f05afd3378cab398b5 *man/Pop-class.Rd
224e4b38a715379041e4969733b5eba6 *man/RRBLUP.Rd
0ee6e8cb48d131951fa9d6d2f0f1ff1f *man/RRBLUP2.Rd
f21ef20e9442a58540f898ee897f7188 *man/RRBLUPMemUse.Rd
e3cefd7b9d93b57482bf65b88f12d059 *man/RRBLUP_D.Rd
902dcc5c25ae3f1660ca2622daa4d9fe *man/RRBLUP_D2.Rd
857e1b120613f7f632ee4901df611295 *man/RRBLUP_GCA.Rd
330ca571bbd80487558590daa6d1d38c *man/RRBLUP_GCA2.Rd
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f00ab95d4a51220e21a18f6759bf20e3 *man/RRBLUP_SCA2.Rd
8f06d16c1e0c2c6f9620fcbec169e636 *man/RRsol-class.Rd
328cb795c1c97ecbfc05f869fd898fb0 *man/RawPop-class.Rd
3326b0fda2fb2f10805b89ab0ad42e7b *man/SimParam.Rd
54a729944d353cea045e029a66ca91a9 *man/TraitA-class.Rd
c810f2d604e261da077ff74ce4d6e3ab *man/TraitA2-class.Rd
7e836a223c1e5d6addcb016e8efda195 *man/TraitA2D-class.Rd
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6ad81040a08cbc8ff796caf1111c4d4a *man/TraitADE-class.Rd
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733c8567fa5933ff12bac22e5e072132 *man/TraitADG-class.Rd
7fefdbe540a760c9d7d93ec813664fcf *man/TraitAE-class.Rd
cfdc85c73ff965721b7a1cd66e7b6676 *man/TraitAEG-class.Rd
bb54b6af17e1cbebffbe194912fbf036 *man/TraitAG-class.Rd
153e31b6b786f6c7396047357c84b373 *man/aa.Rd
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f2aee1ebae8038ba7b77072ca6cfb8f6 *man/attrition.Rd
3c1d79628594abee5ba6bfe2820349a7 *man/bv.Rd
49d111cc2cd5fab6f8ef4a050034e5b5 *man/cChr.Rd
63f1eff276978fb7fc0822ff4ecfc29b *man/calcGCA.Rd
ab4366f48fef9c74e856956dc92be6c5 *man/dd.Rd
38605c10d38d1895edb357444d3ed6ea *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
3fafa171caf57a4a593d348b06ad4696 *man/getGenMap.Rd
254af751b19e143c78b6da3d51de5c7c *man/getMisc.Rd
d33aa1ee61d9bb98a08bae4ca283d6ec *man/getNumThreads.Rd
f573aa171b59ca107df88c39b7c7fef6 *man/getPed.Rd
031735c9192b032862a36ac923c10a6f *man/getQtlMap.Rd
46b116b185d6fb7c5d7b0ee31630b05e *man/getSnpMap.Rd
42f8ef7916942e71222ff543bb123639 *man/gv.Rd
9c274778fbf4c04b824d7e80b2ac9165 *man/hybridCross.Rd
d2a37c81eb8273d2667d619face41b55 *man/importGenMap.Rd
8b125d39347ffd8bf6bc96f1d5c6e4d0 *man/importHaplo.Rd
fc31f02e9060779bd566b5386b5f3b2b *man/importInbredGeno.Rd
f28184d816a76a41f86fb1e60c0dbb8f *man/isFemale.Rd
01d26fdf412da45dd68547234fbc3c0b *man/isPop.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
64da04cba7361e0fba3088a0fe202c3b *man/newEmptyPop.Rd
70b6db24f3f2f228f1d36203331ed0dd *man/newMapPop.Rd
ed510b0e5a9708bd3962605fd60ab160 *man/newMegaPop.Rd
0a0688ca8182b300486b38ca6bfcf0ee *man/newPop.Rd
1bca84bf6864945fd9cc0216105e40ad *man/pedigreeCross.Rd
a398bdcfc27f5959dc9d0b89b21db592 *man/pheno.Rd
c3e189b2e18f6672c4587987ee39f02e *man/popVar.Rd
58f85f272fea643a7de55cac1f7d2516 *man/pullIbdHaplo.Rd
219e7ede43e9508d2e2a8f15b82e663a *man/pullMarkerGeno.Rd
c3f9cf6daa977bdfa017cb6e0d07247b *man/pullMarkerHaplo.Rd
99cbe724406eef480d17b7fa09b81c3b *man/pullQtlGeno.Rd
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51973d60c8da78d795ffa80c19b14d39 *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
9ff41591ce4b8ac1bb5e869d3601f929 *man/resetPop.Rd
8d101281840e44de6ad9b275ca29381c *man/runMacs.Rd
009d0abf94217d06e39e52241bf08ec1 *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
64dd5e30b978c7faad65ce85a67b240c *man/setMarkerHaplo.Rd
e42c464b5b27dba29fdcf7f3d4a2be12 *man/setMisc.Rd
953ff6e499514ed1a90cddc545e4f4ab *man/setPheno.Rd
b57eb45aa87e20a8d96419d9fb2e3aaa *man/setPhenoGCA.Rd
bf7f88cd0a0044ba8197cef231526751 *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
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639acee156bbf96d21978f26892e967b *man/transMat.Rd
9b24faa550310e08703e894f355bd83d *man/usefulness.Rd
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3f6793dafc60d62f8210da381c189ab8 *man/varD.Rd
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39a629f2f28183231ea573e6fd6b0870 *man/writePlink.Rd
7267a12e18775a193159f89af98f72b2 *man/writeRecords.Rd
dbf50b2637b36da7127b67c94d6e6e48 *src/MME.cpp
efae3959806667aa05f2d1ec183b1270 *src/Makevars
efae3959806667aa05f2d1ec183b1270 *src/Makevars.win
65dafc3dc853fef69ccbdd53afa1db45 *src/RcppExports.cpp
e873dd0a2ae2f3a5c6b206cb980efb91 *src/algorithm.cpp
244533d36f33bfa0686163d270f7e579 *src/alphaSuite.cpp
3ea5fa5fe51978446b386a3e43ad0dc4 *src/alphasimr.h
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
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e6422fe7abd7b30c55ca07dbce1a574d *src/optimize.h
de99601cbd273c390472ba25b2415d20 *src/packHaplo.cpp
8c04cd5d91ae77f6305a1dfc6611bc20 *src/simulator.cpp
1c3c458c34552c84c3a70ac3323c3fe2 *src/simulator.h
4a3a208fecda1f56b904e4ca6e75e8b2 *tests/testthat.R
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2f5692b123f0ec3b3745471636a26094 *tests/testthat/test-crossing.R
7388e41ca9468b96d34719303acd35ac *tests/testthat/test-editGenome.R
5e83513609571979a72ad26a02112155 *tests/testthat/test-hybrids.R
5c4808e635c24e7b6f11e58940fc2cf5 *tests/testthat/test-importData.R
5cb19d7769b660f96d79c3cd492ca391 *tests/testthat/test-statistics.R
3073638765feb6c928efcaeed5bfe1d0 *vignettes/AlphaSimR.bib
8890eebb84665107d7e684461741ec9a *vignettes/intro.Rmd
41d9bac5bd56c1722ba82f7848b0d0d3 *vignettes/traits.Rmd
