b4a13b46435ee6bf5d833f395b22475e *DESCRIPTION
bc6dc567e323431fe65668a75863c4e8 *LICENSE
4c75b7d6717101eac58f7cec341cf60b *NAMESPACE
0431903bc66cc8ca1d5a0f713394cf80 *NEWS
69dd3e9d5ed92830671c6d240664dbc0 *R/AlphaSimR.R
8659ce4816a3766a1b2cc51814efd74a *R/Class-HybridPop.R
69db222aa3443258b9d60c40dbfee5fc *R/Class-LociMap.R
d1a00951f0e751bdde686c6899483ad1 *R/Class-Pop.R
f125252ceffb869465421b27757769ed *R/Class-RRsol.R
fb9fa7f1257387eee652a95528b40847 *R/Class-SimParam.R
abe8569d58020da53c0fb4caf33425e4 *R/GS.R
77e3da04fc89d28cb95625cda784c676 *R/RcppExports.R
7bdbb93cdbee4f83e7496dab55760f3f *R/crossing.R
02a5267e9dd76ded32f005b0cd9e873e *R/founderPop.R
e0c27f934d5e35ea033b6224635da75a *R/hybrids.R
f19b7025666e4cfa6761b2cbde5d6f40 *R/mergePops.R
ff440a259ae072cf7b5f8e3909680e46 *R/misc.R
a73765ded8f0866b90195b19e1b3dfd5 *R/phenotypes.R
0fdf867e11677b7de60ba9a4ab04f85f *R/popSummary.R
460d0c8ba7afa3e24de69bd8daa780f1 *R/pullGeno.R
d8a4bda57967757b97ed38bf75a580d3 *R/selection.R
6867b1a85517896e1c8169138c3d8919 *R/writeRecords.R
4a519ea5a539fdd8b6701d57bc4e40f5 *README.md
12a0b2317453e9d6f1b02284e7e72126 *build/vignette.rds
c56d8dd12a1bd0477532f17dcfbff0c6 *cleanup
4fe28a8960b3f873d0b853c1127022d0 *configure
cbc30c3bdb80a0ba152033e4d689da20 *configure.ac
bfe828238328d45f2cfd1dd79000e0f3 *inst/doc/intro.R
0466ecf912e093e4d09125728eae378c *inst/doc/intro.Rmd
15f8bb81f5177b3245e66f503fd8b9f9 *inst/doc/intro.html
b9f4e4b10b0e5801e4426ce83ec3893e *inst/doc/traits.Rmd
65dbf9ca0136e969971061ab52a9ebe5 *inst/doc/traits.pdf
594ebf59d58c52509b571ba71683e043 *man/AlphaSimR.Rd
e1d4cd37aa0cfcac23003b1a43e89a7b *man/HybridPop-class.Rd
3c7a7578a962f050a42e8075761dc5ac *man/LociMap-class.Rd
4c6c112dcef4b66c9c1958612a704370 *man/MapPop-class.Rd
16247ac8d94614b9113c5cb1bd277312 *man/Pop-class.Rd
c29cdffe8448af3139e7b8853a4d5c4d *man/RRBLUP.Rd
90639d2f526f6c45c2e905709eeeacfd *man/RRBLUP2.Rd
66e4f17eaa6a9edf00adc9294309cd78 *man/RRBLUPMemUse.Rd
b626a3e3e6531c17e2cadb90c31716d4 *man/RRBLUP_D.Rd
6ef9b7022d5888c6728f33dd3c0630cb *man/RRBLUP_D2.Rd
e1ce07926ca47ca4a6b161c4018636a5 *man/RRBLUP_GCA.Rd
73260a7af926c6368f33dcf04ab53dd4 *man/RRBLUP_GCA2.Rd
424cb9e50ba0e6e6942ae178f363a624 *man/RRBLUP_SCA.Rd
4cc9cb2f588af3b3dc80c6200b011a98 *man/RRBLUP_SCA2.Rd
1d59a38a5a921455c14050a4afda5fcb *man/RRsol-class.Rd
858e6b2c964b99ec43c20c483db0ad00 *man/RawPop-class.Rd
b848082aa0ae94891d135395509588b3 *man/SimParam.Rd
b5967e097338a8f3f40ef2df81da6aa2 *man/SimParam_addSnpChip.Rd
f242d6425de21dda369b948c226eb3ff *man/SimParam_addStructuredSnpChips.Rd
38b9ca6176e9c1e860085b093b556156 *man/SimParam_addTraitA.Rd
14573ef804b36be8c676a0d5abf3748f *man/SimParam_addTraitAD.Rd
110a6335764362aec521d2340dc999d0 *man/SimParam_addTraitADE.Rd
7d2e6a8404d9776345c190a820a9936b *man/SimParam_addTraitADEG.Rd
dd5eb0d4e692710a3cee2a01c9b61cc2 *man/SimParam_addTraitADG.Rd
b061e9a4021ee9efa16bac5033e56edf *man/SimParam_addTraitAE.Rd
c74127fdbf344c91ea913f042e76f11e *man/SimParam_addTraitAEG.Rd
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
e737131452a18c91db57c0256e7caf05 *man/SimParam_restrSegSites.Rd
1c0d7703c5f5977272bb900f29987472 *man/SimParam_setCorE.Rd
95347352443f738b4bc47a284afe4cfc *man/SimParam_setGender.Rd
ad6a543831a049dab3383ad60a0fbf46 *man/SimParam_setMeiosis.Rd
406b1249c05afb2e4a69a5c6b4804dea *man/SimParam_setTrackPed.Rd
b5924e214146f939a200db54a78f4a9d *man/SimParam_setTrackRec.Rd
b1630e4d5973349763257c948e59da85 *man/SimParam_setVarE.Rd
0f9ff6a4a9171042ac61a44fa571f3a0 *man/SimParam_switchFemaleMap.Rd
35ee86d17c2aafa3552984cec1ad0411 *man/SimParam_switchFounderPop.Rd
c68802f8388675dfc58b3f05ad53fcfb *man/SimParam_switchGenMap.Rd
f7cc13579a28e3e597fe411ee44640d5 *man/SimParam_switchMaleMap.Rd
24e28a8e60a86ee20f4feae20b268b66 *man/SimParam_switchSnpChip.Rd
d86d276aed7e9bc2f08e9bbb0a6a141e *man/SimParam_switchTrait.Rd
f5a23eb46fc22e13be18d74462f777c6 *man/TraitA-class.Rd
ddbd0d5b74d693198c82df8ed24e189b *man/TraitA2-class.Rd
79e31eaa82c485d477f8a788a3fcdff5 *man/TraitA2D-class.Rd
08eb03b1e8c3e69e9669bb77b4576117 *man/TraitAD-class.Rd
8eba42ed44ba1dd50404c1a881d218ce *man/TraitADE-class.Rd
8f822f81643e617ca3bcd8223a2884ae *man/TraitADEG-class.Rd
edf038fef2b0612c1cd9c80ccbc09c32 *man/TraitADG-class.Rd
91a6cb995d3b5846e2eea484c3c6f2f8 *man/TraitAE-class.Rd
bf61bed0891bd74e7eda5b39e3e369f1 *man/TraitAEG-class.Rd
e8a83a532a55fbf7d45de9afbe2ad31f *man/TraitAG-class.Rd
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
7a63cf38a359d04b184694a970599a9c *man/genParam.Rd
cb153ab178b58bc71973787300de641f *man/genicVarA.Rd
b0d16ae1626b6bc2cf7c1dd6a520604b *man/genicVarAA.Rd
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
171946cc0158346c68921ee8a6325a5b *man/makeDH.Rd
1197d8790fe2c2ce80a2ba90b3f368c5 *man/meanG.Rd
6a7988b3d377a691fa42fb932056156d *man/meanP.Rd
81ec60a40e10c6b6b4d2e5efc8587d6f *man/mergePops.Rd
573df50ea78db6a234b19454d0d9cd1d *man/mutate.Rd
8748a0734fa05837da542f4068995721 *man/nInd.Rd
7bbbe95866e6c4a96f433ce97b9fe266 *man/newMapPop.Rd
9a3954e7784adfd4c539f5bfbf5c1660 *man/newPop.Rd
7c7c0536156c8e55ebd9ab5a111a2137 *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
acac3589a886ab0ecd4743d7b2fcdcf1 *man/self.Rd
3c63c1f5fafd6e4f2e801d3f0fd8dab3 *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
672b5743ae7945dfaca51c6f728df034 *src/MME.cpp
8538ea3f1a25c4ea2751911e6b2f15ac *src/Makevars.in
bee230df6ebea3196c0fe754585c486a *src/Makevars.win
4efb0afa4eaaa1475a229f5bd562de10 *src/RcppExports.cpp
b61f0f447c96bb61936383f891a43799 *src/algorithm.cpp
54edda62673404d4e1619c64bf1984b9 *src/alphaSuite.cpp
3ea5fa5fe51978446b386a3e43ad0dc4 *src/alphasimr.h
1008b9bf72d00ec2accf940838502464 *src/calcGenParam.cpp
610876505ca439dd6ac7a6d714d79f8d *src/constants.h
abf8ee1ff272e3d1724c15ef80dd552b *src/datastructures.cpp
b9d8e9083cd8173c1f0cecf67b6d74ef *src/getGeno.cpp
67d6bf84c189d66c12b89f1e7ca2611e *src/getGeno.h
7e6914a52186c4665c7797e6d4936a74 *src/getGv.cpp
ff92baca0004548d3b27d6bb38db81e4 *src/getHybridGv.cpp
5d4ec0019ce6007762d16be272e554f4 *src/init.c
3aefbf28f3b5ea357a4780716ebc69be *src/meiosis.cpp
ba24b533871432b8621ec2ed7e17861c *src/misc.cpp
bc0c25734b5a070b832badb4367459c2 *src/misc.h
e4a088c01ee18fdb6f60d0b5f3fcf624 *src/optimize.cpp
e6422fe7abd7b30c55ca07dbce1a574d *src/optimize.h
d3f61e7d24bafbb9c0801e745856af9e *src/packHaplo.cpp
85c5466d7e98701f4a2b98762fefeb3b *src/plink.cpp
0a1c479fa66a26fa3440b32b0432f85f *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
a83fc05efb785e2b6864c79f67a2ffe7 *vignettes/AlphaSimR.bib
0466ecf912e093e4d09125728eae378c *vignettes/intro.Rmd
b9f4e4b10b0e5801e4426ce83ec3893e *vignettes/traits.Rmd
