91a5cd149554ff2f5801d9f44aac90db *DESCRIPTION
ae857376acb740151284d7bb923255b6 *NAMESPACE
fbe3530a0a3391f1fe91a22084e9e345 *R/RcppExports.R
47948ddac862a20c296d07092d52fa73 *R/completeness.R
0e823e5814ff033fb8b5844f3b4cbdbb *R/conttac.R
e936a3e1a826d53f0ce468635b0e3736 *R/freqlist.R
c22fbb0ed9c06273f103e3d974e4590e *R/genecont.R
5ee7f764084356953b5fc3c577f42ab2 *R/genecontALT.R
e9d7b063526281d182dbdba9e139091c *R/getNe.R
3a44a59f6c311f6297ff0ebb2fcd702e *R/getcskip.R
606a863f464bb3129ec39b7c95518f97 *R/getskip.R
a2f24122671496d9b7f4dcc9eddc397f *R/haplofreq.R
adcf6116f1b140c7f7b840ea5fee2df1 *R/help.opticont.R
5b0dda3f315a0f920930dd32f6caef0d *R/help.opticont4mb.R
e48c7582d741eec28047ecc90b0db906 *R/kinlist.R
6010e8140b5f975a6ab75f086a149348 *R/kinwac.R
337833fa16126bd9cc4a121a14d8a009 *R/makeA.R
4fdc24f730479a9210f23b0d31cbfb17 *R/matings.R
09f0684aef18d837d139e06079efba08 *R/noffspring.R
fa5e5c6a4edf95ace6ea3e021329217d *R/onAttach.R
d2c8bc8838a98a99210658c34ac358c3 *R/opticomp.R
73562171813d78fe4bc81cd7fa079321 *R/opticont.R
b6f589dc94902d9a919faec241bf9d0d *R/opticont4mb.R
9cbd07a914c9319d1c9f5208a68775cb *R/opticontx.R
072330784c15c1b4253350bb63ff9176 *R/pedBreedComp.R
e2276c02fb255f3d6b74351cc97fc07a *R/pedIBD.R
a76ec9091980a38b8a83ca50ad63efc7 *R/pedIBDatN.R
0acf0fecf7ad185a667a609a2805eb92 *R/pedIBDorM.R
9abe4b78368eca0dcca449896e69f4df *R/pedInbreeding.R
fa7a566f1bc97e2034d9b4b212f0f357 *R/pedplot.R
cef03d204b37cf438af624baa276d10b *R/plot.HaploFreq.R
71417c69e544c080dece6e350780833c *R/prePed.R
b0215d6cf961d8cab45e42f758c91e1b *R/read.indiv.R
d2a2d744a81640025a4b7d337eb041de *R/sampleIndiv.R
343fc1d7aae54f2031c097752fc98723 *R/segBreedComp.R
3ce7853ccc3f5e019bf56611f5ce49fd *R/segIBD.R
55d740609aa394e05d211735d2384f96 *R/segIBDandN.R
623ffe1029272174733646c4e1f00900 *R/segIBDatN.R
a52ab93b131a51117301d0e2a8b25d94 *R/segInbreeding.R
7cccbc923868b536209f389b6244904d *R/segN.R
c4a2a1d4f14ac74d774411bb6062cb69 *R/sim2dis.R
0ff7879d5b347cadf44e7358f3d6b630 *R/subPed.R
5ae28ef66444a069538076b31c31250c *R/summary.Pedig.R
1aa3cab22335a5b40ab37394a1cd9ed2 *R/summary.kinMatrices.R
03ebd88bc156f4636984b3c27434c871 *R/summary.opticont.R
86a0c50e6fb34c433c71fa139ce17618 *build/partial.rdb
a3ba110dc36b076adbcebb476393f299 *build/vignette.rds
a4d5a3f8eac0ad0b060bb83b5580415e *data/Cattle.rda
9ab775a1bfeddd429ce93e1ddb56ee0f *data/ExamplePed.rda
5fe9bd369c0bf382f62da1ebaa98d098 *data/Kin.rda
d2d70fbcbc358eaa62851134e907285f *data/PedigWithErrors.rda
41526e48e9e4c960d4c0f94e4a89c698 *data/Phen.rda
f77b43248a0cc36ac93bf5332baaad49 *data/map.rda
1d6d7e8544c4a7ff0cc1a8b84f4f5e79 *inst/doc/ocs-vignette.R
eae142b3e83fd8acc9860c551beecf1d *inst/doc/ocs-vignette.Rmd
1d2c7edd4e7a3c105a327abe5ecf67bd *inst/doc/ocs-vignette.html
237629b2d93ac6cc9a860b73b8923e70 *inst/doc/ped-vignette.R
a61ab0de1ccb4a5c8f5333c27b246a16 *inst/doc/ped-vignette.Rmd
bd9498a54c12fe120c9266148a75757f *inst/doc/ped-vignette.html
2fabb16514abdce4fb349d60a160294a *inst/doc/ped-vignette_files/figure-html/unnamed-chunk-4-1.png
2aa549bc3253666fffbbd2e168c47619 *inst/doc/ped-vignette_files/figure-html/unnamed-chunk-7-1.png
609b6cb6a3216733a31972ef59f9103f *inst/doc/seg-vignette.R
4e7b390aa7157ac941a6114bcd03dec2 *inst/doc/seg-vignette.Rmd
18d319b9fbb15b1a9ba3ce99deac515e *inst/doc/seg-vignette.html
0ea6e449f7675894e6252d4744ac9ec6 *inst/extdata/Chr1.phased
622c8d50e200a74f538f1cc3a25f610c *inst/extdata/Chr2.phased
6aa3dee74c97119764e01be0688b74a6 *man/Cattle.Rd
c16062ca4c6d3206c4c3567aca546baa *man/Chr1.phased.Rd
ac7d45f2605d40401d4d60bb39e4c27e *man/Chr2.phased.Rd
23f7c0196fa43992cd08fc3f3f394261 *man/ExamplePed.Rd
0e81cda49c52d1e8cfe7de672fd752aa *man/Kin.Rd
040ff6a22ea4345868baf4791e8b6169 *man/PedigWithErrors.Rd
78a32e19900880cad0594fcf5efeb07b *man/Phen.Rd
8c1a7023bf911395f59dd5f807e52a7f *man/completeness.Rd
bb9b51b31aeccdc15731c9a1c2d91b70 *man/conttac.Rd
299eb24197e820a14fdddf621247786f *man/freqlist.Rd
cf81d9c7e18e0305a52103a343da58cb *man/genecont.Rd
9b985378f58a7d540587d1c96a23ba28 *man/haplofreq.Rd
dd1f5a87789bdb67fda6470f5d229a77 *man/help.opticont.Rd
14842b0711f64080b473f86131adf849 *man/help.opticont4mb.Rd
135a6197ef812675275738eada5b126e *man/kinlist.Rd
0c580d9440b721c5b15cc2fdeefb80d0 *man/kinwac.Rd
847e17fe77e417ff25c4774b69b8078e *man/makeA.Rd
708b70f7515e6be9b87876b2f827f356 *man/map.Rd
a5fc955052ee24cc1f5e0090edcb9515 *man/matings.Rd
5c7c45d2f1dc3af5581f2b2f8c7456d8 *man/noffspring.Rd
8daccccb07c2ce8892c370bdb8946531 *man/optiSel-package.Rd
21b467ab10521530b4a9000fe39352bb *man/opticomp.Rd
4ca3c90df93aefe039070ecedd04db78 *man/opticont.Rd
33d7dbbb443a749f457bba3be73dab7f *man/opticont4mb.Rd
11ae313392a979d8d2458759a06bb972 *man/pedBreedComp.Rd
610a0b8f54483b1bc888821b7228e7c7 *man/pedIBD.Rd
77ebdfa99444a2dea00e16001e1a38f2 *man/pedIBDatN.Rd
f8f21b62a2e391cc06a30fb58bfc0d59 *man/pedIBDorM.Rd
86f187596ea715c606afdd69184063b6 *man/pedInbreeding.Rd
ffcaa394388ebe87fe4542fa4d60da52 *man/pedplot.Rd
0cdfba2e5f41e314949c7e618d806bdf *man/plot.HaploFreq.Rd
1ace2174c73ac5524f5b2c03c068707d *man/prePed.Rd
db4492c7b5192bb1e6e2606391774d64 *man/read.indiv.Rd
fd6fb3218028f4aa5b2ef832a31c659c *man/sampleIndiv.Rd
f9a8f1650fd687ba69a35e35d030da9e *man/segBreedComp.Rd
5326012ac477568586e52754902eecfa *man/segIBD.Rd
cc82c6fbcdc0bc08ea79aff914d61305 *man/segIBDandN.Rd
4c8fac2f2f2e0d358449332e9b62fdda *man/segIBDatN.Rd
31d2c317cc386bd7b339a3148941de19 *man/segInbreeding.Rd
d035569fc3607bc9c1d3dd56c8c774d6 *man/segN.Rd
249510fcbd267e036746ad22d67230a7 *man/sim2dis.Rd
78a929196b25857841ee839ae3cd49bc *man/subPed.Rd
7552b9f3f4d4a2eae2f52ae8dd1a7314 *man/summary.Pedig.Rd
04597ca0f4b21232db73e9dc7b1022fa *man/summary.kinMatrices.Rd
7858e0e5cb07f7e5dbcc90adc89f703c *man/summary.opticont.Rd
a1e86627020c43852446a8e2c2141b3f *src/Makevars
027279118ece0dbdfc3646fbd05078ed *src/Makevars.win
d0405b876f6689461d8e76a5020d4712 *src/RcppExports.cpp
2db6ee49d2eb32553f3329d320df9ac6 *src/init.c
86ae53ee0932d63b6c01f0623e05f189 *src/rcpp_completeness.cpp
6e859b6b5fe18306770077c7af762b7a *src/rcpp_genecont.cpp
7a88d7811c63dd2f314a609d35e5f4ac *src/rcpp_haplofreq.cpp
10a26a4a84b3ff18999edfb656264795 *src/rcpp_makeA.cpp
1e895e36e0f72e44286941c23a036b80 *src/rcpp_makeA_lowMem.cpp
fc35055952882daa9c35875dcd953cfc *src/rcpp_nativecont.cpp
61184c6e8e8ac936bb2eb8d4ec858224 *src/rcpp_segBreedComp.cpp
d37e857555631decb106d47da4ad980e *src/rcpp_segIBD.cpp
8f1165bbb8f2243d421c30cadcf6ec1e *src/rcpp_segIBDandN.cpp
40e59841f7758c21bfed5841fda0610d *src/rcpp_segIBDandNVersion2.cpp
7fc6f2cbf1a94c257567d2636f4838ab *src/rcpp_segInbreeding.cpp
3e44336a967f3f4c5351568bfe94d931 *src/rcpp_segN.cpp
03fc934aee18757a8bff602bb4bec201 *vignettes/HaplotypeEval/freq.Angler.Chr1.in.others.txt
21e84f70bac057ee28eb8b5cbf219705 *vignettes/HaplotypeEval/freq.Angler.Chr2.in.others.txt
5a6c57c46b2c53f4ac692b4f8934b273 *vignettes/HaplotypeEval/match.Angler.Chr1.in.others.txt
832fa1aa53d7172558e4aad81fb948b2 *vignettes/HaplotypeEval/match.Angler.Chr2.in.others.txt
eae142b3e83fd8acc9860c551beecf1d *vignettes/ocs-vignette.Rmd
a61ab0de1ccb4a5c8f5333c27b246a16 *vignettes/ped-vignette.Rmd
b15e67df11855355faff29b7ad31d299 *vignettes/references.bib
4e7b390aa7157ac941a6114bcd03dec2 *vignettes/seg-vignette.Rmd
