d2ab8ed3f7f16da554265cc3b81bd420 *DESCRIPTION
60da859463482a7ed89f264766728188 *LICENSE
6e6364a851942cfdb7ed4e80442ce74d *NAMESPACE
2c6665ee46262f1646a01023ebe0ec52 *NEWS.md
e8a4e394c6f0bef82f353a76d5961e5f *R/AlphaSimR.R
6428607d5b4dd87f12f7118befa48b0e *R/Class-HybridPop.R
d62d99a444d7d6a2661140ce7346c509 *R/Class-LociMap.R
fda318783037988f41524063e876ccfd *R/Class-Pop.R
4daea4514899d855f937bf415361096a *R/Class-RRsol.R
39bb4c9d3f47ecbbc4f7f59e0907afc1 *R/Class-SimParam.R
87b83e9a252b00c161bb8c499078f4d0 *R/GS.R
07d4e431bcd5003562fd24ca38d632b1 *R/RcppExports.R
54f0ee8cebb6b5bad09235a376334261 *R/crossing.R
e201201b1adb84aca931f7507b666a37 *R/founderPop.R
83ad4ad3735c6cfaa1b7fed19b04dd1c *R/hybrids.R
ef2a45a9ea96e9beb2019905c2c7381c *R/importData.R
f1a158e7cbc594a1ee3be2fc55d007db *R/mergePops.R
3f9ea9290d951cdbee01faa5c4d8f70e *R/misc.R
bb5afff6be5e72bb8e91ee3d36fa5464 *R/phenotypes.R
e2e4d63bd37ee04022ea9acc46b187e5 *R/polyploids.R
9ee2c01ca623f7a4ef6fe88675ba190d *R/popSummary.R
b6e60d4fd37426c674e15e6e8aaed687 *R/pullGeno.R
9c8d7f1860ea8970d9a0c6cf3aa0fcb1 *R/selection.R
b0690de78dc6b600d37e76b81537122c *R/writePlink.R
3efdfc14d65482e05962b775d383b2d6 *R/writeRecords.R
71d7fb802a7ca15f94cb7aebf7d1892f *README.md
33ba034708f5758e137f9736a34b31e6 *build/partial.rdb
48f068af78ea6143b1c24e42dee6d367 *build/vignette.rds
df0862a37870968febcd53e6f989bfa7 *inst/CITATION
757f00f13de5ddf3a0e939019f588b5f *inst/REFERENCES.bib
8bbe9b83b5257d48939e8fc6c91ff99c *inst/doc/AlphaSimR.R
7e2c9d0f6e2f491ba92e1344a911567e *inst/doc/AlphaSimR.Rmd
3bc16aea8d13e6e7a919b648413ecea0 *inst/doc/AlphaSimR.html
41d9bac5bd56c1722ba82f7848b0d0d3 *inst/doc/traits.Rmd
e6014a03a2f9c85356869207e9a7d663 *inst/doc/traits.pdf
d25371b175fda87a284c66bc201d8fc2 *man/AlphaSimR-package.Rd
21124b1441bf63288a37b9c711e9c93d *man/HybridPop-class.Rd
7b2a9e11a704b1b19c3646ca06d2cfe4 *man/LociMap-class.Rd
1e4e9e828f4191762dd493292c3ec49d *man/MapPop-class.Rd
ec82db79c9e4984023d01542ff993264 *man/MultiPop-class.Rd
85ca7654382a579ab0aa466ae6578f1e *man/NamedMapPop-class.Rd
15ca1c3a1ca6270dd62207c3a2ff9f5d *man/Pop-class.Rd
add7c0202847c14455daa9f9ba08ae6c *man/RRBLUP.Rd
a374d7eb43bf5c45c754bab29d50c898 *man/RRBLUP2.Rd
3031cfff58695fa07a4cd0f4512ef479 *man/RRBLUPMemUse.Rd
f7af479aed1608aae9c0568eae8dcdaf *man/RRBLUP_D.Rd
34011b7216e253837ffb1e19824e3c69 *man/RRBLUP_D2.Rd
0a3fa0dc5fe19c97c35a88c4bedfb143 *man/RRBLUP_GCA.Rd
a6d33586e718bc8cd6d3b5c959dcb301 *man/RRBLUP_GCA2.Rd
d0fdd704685f70de8aacce04e5a07b83 *man/RRBLUP_SCA.Rd
336df501411dfe1a36f3e604ac1996c2 *man/RRBLUP_SCA2.Rd
8f06d16c1e0c2c6f9620fcbec169e636 *man/RRsol-class.Rd
328cb795c1c97ecbfc05f869fd898fb0 *man/RawPop-class.Rd
9bb517ad5120bbe28b2e98477fcab96e *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
91e578fb5addf0da670bebee29b2c127 *man/addError.Rd
9b62ea2224e075f9908eb27179aebb3e *man/addSegSite.Rd
29a3686f1de2d2ad695cbca22f5c484d *man/asCategorical.Rd
2eb31c509cad70c326992409492b734b *man/attrition.Rd
bc6177243845a1c8e3cda85a604ae0cb *man/bv.Rd
49d111cc2cd5fab6f8ef4a050034e5b5 *man/cChr.Rd
f99469b0b681b5bc0713f0e856a28c8a *man/calcGCA.Rd
01254697898088c78d473555f917a961 *man/calcPheno.Rd
08da8e25442e91194b73dfc351cff0d0 *man/checkSexes.Rd
f5f4253f3e76048aae84723ac229e5dc *man/convertTraitsToNames.Rd
f4c0c95de3d7e3d5bcbcaa69ffb84793 *man/dd.Rd
25a7ab4f31660e2cdac2f97d9a140caf *man/dot-newPop.Rd
81a203ba92eabe9ae6b521d372a12fff *man/doubleGenome.Rd
53a4d8651ea5875a3f99bc74887ccc53 *man/ebv.Rd
df1c12a1bcaf21bffe89f43da826da43 *man/editGenome.Rd
6b5ca5a8ff85a0e2ef9caab74c1df405 *man/editGenomeTopQtl.Rd
6127a72921a75c975f0ddee919a95ddc *man/fastRRBLUP.Rd
2db7bf891a8a926542a914eaee807d15 *man/findLociMapSuperset.Rd
b922d81c7aec6373645c8cbc47dc9250 *man/findQtlIndex.Rd
088d8c36452df8773e1e278d7e056153 *man/genParam.Rd
3a6bb3c4194e1dc261284ef8b3e1609a *man/genicVarA.Rd
504476a00ef620ded094f4913fa62159 *man/genicVarAA.Rd
043911f79b604c559a981f28002cef9d *man/genicVarD.Rd
fd2b207d32ad4afd8665393cc64c68aa *man/genicVarG.Rd
7e96b2d9393115180b1a31d7b45eb8e3 *man/getCandidates.Rd
279a0cc03c795ef34bedab068667e1ee *man/getFam.Rd
3fafa171caf57a4a593d348b06ad4696 *man/getGenMap.Rd
e480ec07eaa930ac04c8b69124ba8215 *man/getLociNames.Rd
d33aa1ee61d9bb98a08bae4ca283d6ec *man/getNumThreads.Rd
7246a534db8cb486e25bdeb004e77b80 *man/getPed.Rd
2aef70a7249098e05715ae51e2b43565 *man/getQtlMap.Rd
257bd10afa018dc06a5ad7e224c322f9 *man/getResponse.Rd
96f4c3de7a5d6b41c663a85040028a90 *man/getSnpMap.Rd
000cd8ba1859e9980d235f057962df24 *man/gv.Rd
ae9374dc8adbaf5973bc7cd53fc3f7cf *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
e9e9ee53d405b445dbe428f8b40c9f1d *man/mapLoci.Rd
17ffd2b485c095b2958da287c56e75ee *man/meanEBV.Rd
41ba0e75b6d017aa9cc9956fb4b675c5 *man/meanG.Rd
3deb646833c8bc5af52c34e97eb931b9 *man/meanP.Rd
86dc15d543e1f82c0257ae77574a3276 *man/mergeGenome.Rd
3837bcbd7b91f08b0eb3ff5f6fc3e975 *man/mergePops.Rd
ea3520a0ae442fb04c3d579860ceb8cb *man/mutate.Rd
24d3640b91f3827b57a7f694cd2d95ba *man/nInd.Rd
50c1328c8212aac3337875adf6eb176f *man/newEmptyPop.Rd
c75df87bca2f3a877b48aaf0beb716ad *man/newMapPop.Rd
9f4ed2dbfbadd1068ba8c0f58ab0b074 *man/newMultiPop.Rd
2abb11e38e54bc115ccde876e24ceb0b *man/newPop.Rd
4730e192735ad52aea040245fe0affb4 *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
192b99b1fb422bdb8f86d90057d01e9b *man/quickHaplo.Rd
c5eb8d0b6d57ef5bd6fcef48fcfc183e *man/randCross.Rd
efb37145e7c54daac12be59c4decca9e *man/randCross2.Rd
236e4d4294cbc07d5b60dbcad9412ddb *man/reduceGenome.Rd
9ff41591ce4b8ac1bb5e869d3601f929 *man/resetPop.Rd
c4222f759b068dba4ef1602f0ffb52d2 *man/rnormWithSeed.Rd
217d0fd28673ab1e6cf6102baf1f68cb *man/runMacs.Rd
68cbf69ae2e7f2ab30a1dafa95190644 *man/runMacs2.Rd
e824e552ea82bd3723f2b856e61425d3 *man/sampAddEff.Rd
6f031b28cfb00ec4fbe5b820582fd883 *man/sampDomEff.Rd
24a0931d44894d718e57d74ae6fe59db *man/sampEpiEff.Rd
5541a15fb63ed3081a41746da7c32d25 *man/sampleHaplo.Rd
0b64e285a188db25922f8cdb86565c0d *man/selIndex.Rd
61c034d133826de06fab410848787dd8 *man/selInt.Rd
d112563a318b792fecaf4dc13e94780a *man/selectCross.Rd
e8d2475cc1e9d8c2e08b75402796e5f2 *man/selectFam.Rd
36c02cf92c0fd8cad71e9650fe05aae8 *man/selectInd.Rd
ac79ac788cb7c98c207550772a42eb8f *man/selectLoci.Rd
673d12b3a6d8651fc9878a418094273a *man/selectOP.Rd
3d887c68515287af135561058a1f0184 *man/selectWithinFam.Rd
e81c0f73b56e18c9808ba55764eaa9df *man/self.Rd
8726b33275d1fd4b2fe1536ce7aa75b1 *man/setEBV.Rd
64dd5e30b978c7faad65ce85a67b240c *man/setMarkerHaplo.Rd
5becf8fee192f58816cb2cc57b511cd1 *man/setPheno.Rd
1ebb2323b1150aa0ef9564f4a4fb4a1a *man/setPhenoGCA.Rd
ea31c0e7fe65e1d5b0cb0a435c49a219 *man/setPhenoProgTest.Rd
8dc3559388f8141c0e6125a640af218f *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
e69ff860e97019c48e93e70c4734af2a *man/transMat.Rd
2afed976f1265a14ce725731c615c32b *man/usefulness.Rd
465b3f1bbc52457eb35e4c6beb25bbff *man/varA.Rd
14aec53e8f40875f4176418631af9529 *man/varAA.Rd
c70090bc47f0af6e7c7cbd7994c3bc00 *man/varD.Rd
243488592d24521ca176d02ee660d258 *man/varEBV.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
74cb2674972c8188b81b92c78bf9ce64 *src/RcppExports.cpp
822f71748798f68d98df82dd6b98bb9b *src/algorithm.cpp
244533d36f33bfa0686163d270f7e579 *src/alphaSuite.cpp
3ea5fa5fe51978446b386a3e43ad0dc4 *src/alphasimr.h
79f3c7660a58f60959c913d8ee320d35 *src/altAddTraitAD.cpp
689153b05dde5146d925fededd45528e *src/calcGenParam.cpp
610876505ca439dd6ac7a6d714d79f8d *src/constants.h
72e1755d9fa0b18527066cd5ee8701de *src/datastructures.cpp
6dc110010aa9a9edbce024d9cba98a48 *src/getGeno.cpp
67d6bf84c189d66c12b89f1e7ca2611e *src/getGeno.h
da41d6a4c209ba0977bb6dd4b54a925a *src/getGv.cpp
c91455fc8cc42234129fc0258c4849eb *src/getHybridGv.cpp
0510886067800e833b187a3e48c0bb67 *src/ibd.cpp
b1df05d1b9cd357be8f85af10125854a *src/meiosis.cpp
2e1c2afeb5030cc5b8d181aaea634120 *src/misc.cpp
8d66d82082726c3b41a4c63bbc35d462 *src/misc.h
e4a088c01ee18fdb6f60d0b5f3fcf624 *src/optimize.cpp
e6422fe7abd7b30c55ca07dbce1a574d *src/optimize.h
de99601cbd273c390472ba25b2415d20 *src/packHaplo.cpp
0c5ba054e3f0ffb4d68007f986a7f5f1 *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
5d674c8e09b802369c208ceb16097622 *tests/testthat/test-misc.R
1a31b4160bd42d96b2e0987c3a13e27d *tests/testthat/test-phenotypes.R
a8d62333ae8959adf3b6d8c33b9ee03b *tests/testthat/test-selection.R
5cb19d7769b660f96d79c3cd492ca391 *tests/testthat/test-statistics.R
7e2c9d0f6e2f491ba92e1344a911567e *vignettes/AlphaSimR.Rmd
3073638765feb6c928efcaeed5bfe1d0 *vignettes/AlphaSimR.bib
e150b43e239428514fe6ffbaac302585 *vignettes/articles/GeneticRecombination.Rmd
a7db9496bc03ebc70a02e42dac9f196d *vignettes/articles/Genome.Rmd
54a13c53b4fbbe5c71bec17b4e8420ed *vignettes/articles/ImportRealData.Rmd
1fb555f935ffbc2f5b4e58920f62f83c *vignettes/articles/SimulatePlantBreedingProgram.Rmd
fd0c94041b21b4a607f4faae416f219d *vignettes/articles/ToDo
41d9bac5bd56c1722ba82f7848b0d0d3 *vignettes/traits.Rmd
