42d9a186df0f7c0738a25f9c38e4f3a5 *DESCRIPTION
482e91b50a6166bc25538d87ff7e65ed *NAMESPACE
13f017bf3d9c9bd8e9ba7e6b090fb109 *R/RcppExports.R
25f25e8fdd3750bbe9cb08e4a35bb8bd *R/cache_twopts.R
bfaaf3f0b51750ec30548e4d78857852 *R/calc_genoprob.R
888d9b7bb5d1902fa5ffe3fba6d7e29b *R/calc_genoprob_dist.R
46f1002e344d2cb8c8e6648b4fd4a365 *R/calc_genoprob_error.R
31c1f90d05c2fa8de2e23e96c84bd162 *R/check_phase_configurations.R
ece8cfc6d8613c89bbb9e064a5e444b4 *R/data.R
1772cb2746b67e5390eb30db7e51d911 *R/eliminate_redundant.R
124519be8e1d745ed8ba72806017cf11 *R/est_map_hmm.R
7bcb698891e612b14ab3d1b8c52571c6 *R/export_map_list.R
6fe1b0fdcc6c0630d6c0283a39f584cb *R/filters.R
db2c68dc836c3dcce6abff0244b11c55 *R/get_counts.R
f80e6d743936aca44cdcc377b6b2ba87 *R/get_counts_from_web.R
8fe8674a410dcf76e4f9a972560fec87 *R/get_submap.R
96a4bef89f7de807a0e132f9bbf7546c *R/group.R
199a9fc7cb2de521e1101ba7970b6626 *R/haplotype_map_utils.R
f52f61b8d4bdad4d5b1b900aa4daa5db *R/homolog_probs.R
39cde6e60582abaf1f377195d1cf8ae2 *R/import_from_polymapR.R
24b7c52621de880ca77972632e0bc7d4 *R/import_from_updog.R
c9c2d81537eeb230e2800441007a00c3 *R/loglike_hmm.R
5af0e41e7a8487ba85a16dbe460631b8 *R/make_mat.R
f270728804450091546a994f97025df4 *R/make_pairs.R
1df5551a46d922ac5cb49394727a3afc *R/make_seq.R
2446ae0ecb987df81c77736a5ef128c8 *R/marker_info.R
a95c5638a84cb20611334effa1155337 *R/mds.R
67ae9e872a3ae50e56d06916cb12a9dd *R/merge_maps.R
7a7fa8a8f79683bef147cfcd8af8a018 *R/pairwise_rf.R
3029f52625ac76c66c33987cf44850f0 *R/plot_genome_vs_map.R
3f7099993609766add366a08a8d1bfb4 *R/plot_map_list.R
72369d859700fd32c8596f171bfc7b3b *R/poly_cross_simulate.R
120ec5dbbb4585dd4730862e3a76783e *R/preferential_pairing.R
7b01ba1e688f750cdac2db1cf84be41d *R/prior_dist_hmm.R
7eb186108edd95ddbb7224c5686dec9c *R/read_mappoly.R
8c70efe1e49468c53b129d3917657dc2 *R/read_mappoly_csv.R
c97c18221faaf52d78a012c3a7daf9b8 *R/read_mappoly_prob.R
18fb8235c2ca046ecdcac5a2d7b2a602 *R/read_mappoly_vcf.R
3d211845be71d4372212a4d319d9a448 *R/reestimate_map.R
97d5095532bde7337185bbccaa8adc80 *R/reestimate_map_with_global_genotypic_error.R
ccfb73ca7fc73e5b08ae21b69e657608 *R/reestimate_map_with_prior_genotypic_probability.R
8a17da46ae29eb5f860f4c12a527361f *R/rf_list_to_matrix.R
537fe88c78da1d563eba7e8e7490fd65 *R/rf_snp_filter.R
49ddc07079ee760348cde0d933f362f5 *R/segreg_poly.R
51877ccfe3daea35c9ba451f29356190 *R/sim_homologous.R
5e3e34ecc8c58551eab0bc1db3e4c2a4 *R/simulation_utils.R
5c403667571d620309cca92139b0fb1c *R/single_map_hmm.R
fc7093daa0b30e02ecc685a55a8db306 *R/split_and_rephase.R
bc21f1ca0dd227c631c14a466ddb80f8 *R/sysdata.rda
2f254655fd0a46db9665e0489566d05d *R/utils.R
9073df9c9f77185ca206d016065ece2d *R/zzz.R
e872de3e839da662570c9179d71e5ed2 *README.md
d6d36b9a3d5ccf1217a6b6b0f0a9513e *data/datalist
44e9989cbbb1399cfecc5b36d7627a06 *data/hexafake.geno.dist.rda
9c571299b39da3425fcec611eb521c2c *data/hexafake.rda
644222bd1bc03491f8a807d7a7668fb0 *data/maps.hexafake.rda
53c9f3f156739522526e9c8a795909af *data/solcap.dose.map.rda
4a90ac47bc48d5568cfa7d76797f0a52 *data/solcap.error.map.rda
4948bc45991dd281b065091b2636ea30 *data/solcap.mds.map.rda
7c99a906550bf3e26461b6d062ebb15a *data/solcap.prior.map.rda
44d2945a38a2e3a7e2c38a2c61641683 *data/tetra.solcap.geno.dist.rda
7042cdfd6f198c67c53df026be5f5cbf *data/tetra.solcap.rda
af13bbf32f082454785efce1918e941c *inst/CITATION
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8e35f3d939f7cea00c329bc40c91846c *man/cache_counts_twopt.Rd
0d2c47d9d0db1098b006807e71b24dce *man/calc_genoprob.Rd
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14ee2915b323a04d2a85ef461b4c4e13 *man/calc_genoprob_error.Rd
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f7b30185757c2323854c1cf081b36e49 *man/calc_prefpair_profiles.Rd
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01b7a67cdb11f6ddea423a91faf50bf3 *man/check_data_sanity.Rd
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90c7dddb0d011a3559bdb126864e62b8 *man/compare_haplotypes.Rd
21cc2e67b02a4c70397b621a90fef004 *man/concatenate_new_marker.Rd
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08f5fdad48ac7d79ac0b7a99968da7a3 *man/create_map.Rd
6765d85ae5be3eee0434d8d4519e8720 *man/dist_prob_to_class.Rd
6a0d1d0b2ea68294191f4952d271c385 *man/draw_cross.Rd
5c3e62c7388afd81dbab3ddc49364422 *man/draw_phases.Rd
b65b6ac548c4aaabb7ed82d74c929215 *man/drop_marker.Rd
bb1dd81f3413baf8866b13aaab376bab *man/elim_conf_using_two_pts.Rd
124a8cff230a06b13aca3f9dab4dfb20 *man/elim_equiv.Rd
de642f8d8c0de32c5903b6d75a4601f6 *man/elim_redundant.Rd
217fe46515b55c64e02b003976bf20e5 *man/est_full_hmm_with_global_error.Rd
1b5480915acad5954de38152f30ce582 *man/est_full_hmm_with_prior_prob.Rd
7e998e3be3a10b967f885b6001e7ba25 *man/est_haplo_hmm.Rd
f2acac67461533ceb2ab52f69f162552 *man/est_map_haplo_given_genoprob.Rd
937a13de5d0e40ac1c04a2ee943d461b *man/est_pairwise_rf.Rd
2c3e7e56d0204ae64c6dafbfae963dce *man/est_rf_hmm.Rd
ffc2962a908151da0c897e271faa9514 *man/est_rf_hmm_sequential.Rd
0339e3bf76057c71ec6756a5808f1b00 *man/est_rf_hmm_single.Rd
e59d516c6a0cc52acf29e830b8eed186 *man/export_data_to_polymapR.Rd
1f49160b409624f2b02f5a08eeaa526f *man/export_map_list.Rd
8f3eaf6c8fffa5e5dcdcfebcefa04da2 *man/extract_map.Rd
aed62955ebfd4b68edf529bc7c6d4827 *man/filter_map_at_hmm_thres.Rd
e8805a46c1bd96bcc63c842b11d7d433 *man/filter_missing.Rd
110a078646a51b89707ccb709cd21bd8 *man/filter_missing_ind.Rd
3f766668aa8a4176a2c2e63eb0320ec1 *man/filter_missing_mrk.Rd
eba91de964e0067f268c54fdec130321 *man/filter_non_conforming_classes.Rd
c72642bb5eae240fbc2da75540d58e35 *man/filter_segregation.Rd
72932ac7454347730e40699b46539e40 *man/format_rf.Rd
981c74f5be157c56efffe2dec6a49950 *man/generate_all_link_phase_elim_equivalent.Rd
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39348fe3098394c7b6806641336a28d4 *man/genotyping_global_error.Rd
da8332ff3970030a4e7f6e51c8530b2b *man/get_LOD.Rd
a329800269f8963cff49f7dd8fbb83ea *man/get_cache_two_pts_from_web.Rd
1c22b8484e292c41b7397faa83b8ca0f *man/get_counts.Rd
8b7dd32aaf64f1b66e5bd215ee295c2c *man/get_counts_all_phases.Rd
d80592b6835431bcd131d65906011ea1 *man/get_counts_one_parent.Rd
1cffdf56c7c7b5f206032e2a8f262743 *man/get_counts_two_parents.Rd
f751603b51cc2e430255527e980e277b *man/get_full_info_tail.Rd
d0cc092deb6dd52ec385c104fdd1e9bc *man/get_genomic_order.Rd
3f37a70dc0a6dc85b041d8c6b50b175f *man/get_ij.Rd
7c1566d8bb4f14df7fba26bc80a84474 *man/get_indices_from_selected_phases.Rd
28bc7d99d9d5c945167d2e036aeb7b9e *man/get_ph_conf_ret_sh.Rd
ba2db71c4be28d1818eeee7a857b213e *man/get_ph_list_subset.Rd
41bcad8ce2cbdaeb21a08ce179a7f81f *man/get_rf_from_list.Rd
6a23b4adcddb38d98aa61293fc766472 *man/get_rf_from_mat.Rd
57928c195ae36602d5c6f6f4e8fe3d29 *man/get_submap.Rd
da08091875bf449fcbf89ada4d776265 *man/get_tab_mrks.Rd
bc0521a51d1b9673888817c7831f71ce *man/get_w_m.Rd
aa3c53a7eb6650a1f0af2d42556d4a6c *man/gg_color_hue.Rd
be57e3415119ea65b0d0ab30344918fc *man/group_mappoly.Rd
550e0a226a90c21e95e093bfb92bedd2 *man/hexafake.Rd
b9911bececccf1e64e2ab9c13964563f *man/hexafake.geno.dist.Rd
bf97cf8efcc075e73269799e83d402af *man/imf_h.Rd
497eb80002f3a6b697ec703bd48041c9 *man/imf_k.Rd
516176ab896cd63a12d7f34f26bf5356 *man/imf_m.Rd
239a021246a95eb0f6fd687c57913a06 *man/import_data_from_polymapR.Rd
579038210b72bf4701188b377e2b1dc1 *man/import_from_updog.Rd
830435a86c0ee12ad2e5e66680f390e4 *man/import_phased_maplist_from_polymapR.Rd
bc68a90440055094fefa2edbbf6477aa *man/is.prob.data.Rd
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967fbc8def73870a0e97101227442e1b *man/ls_linkage_phases.Rd
091ac92f7a2841112710c443a814b335 *man/make_mat_mappoly.Rd
3b8567bd48e3d6e9c01689be9187db1f *man/make_pairs_mappoly.Rd
3543d8522f7ee80f1f1061eafd19d9ba *man/make_seq_mappoly.Rd
99c5a8be5d65aa2d07a12dec008196a7 *man/maps.hexafake.Rd
9d5c0095eb528145834fb3e7035492ff *man/mds_mappoly.Rd
a1e1202a8d1d87200e92fbe5f6b7866a *man/merge_datasets.Rd
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89d5b8492ec5912e9650d7adbe68e5e7 *man/mf_h.Rd
688f2f8e6ecd82ac4722274180eb1264 *man/mf_k.Rd
87597c28fe4525c3450f810320f40b43 *man/mf_m.Rd
0f99679d3e818ec45966cdd4a1214ec8 *man/mrk_chisq_test.Rd
51923f56755ad5a786c8f59f56fd4727 *man/msg.Rd
bf0c1e1545ec06e1d7f3d98c4b9b34ee *man/paralell_pairwise.Rd
45ab972a97cf6e243f3e76d57468c2a6 *man/perm_pars.Rd
c9d8296fdeabaa5b50b3aebd5c0132b5 *man/perm_tot.Rd
c76e03541f3c96fba1526af1fd40b319 *man/ph_list_to_matrix.Rd
ad4a4e263efa9a463ebd2783eb0005d4 *man/ph_matrix_to_list.Rd
5b72c691763037d2ccb9a42c0caa9b63 *man/plot.mappoly.homoprob.Rd
eea71d0651310dc6063bfd6cc0646573 *man/plot.mappoly.prefpair.profiles.Rd
a858b52a0305d5a3902f58bce50f0043 *man/plot_compare_haplotypes.Rd
84719479d588fbe9e3f8a49f1bcc2df2 *man/plot_genome_vs_map.Rd
146dec5e209734af28f1921ea9f909b6 *man/plot_map_list.Rd
9b9dbe8aa0a273f3905c069ec4240421 *man/plot_mrk_info.Rd
a7bf0fd59450944c17bd469ae1801d68 *man/plot_one_map.Rd
7248fd83f20921aec95493f1210aa09b *man/poly_cross_simulate.Rd
46d9bf9b5a51c841e5fe5a2f6b82ba24 *man/poly_hmm_est.Rd
cb8acd7b1ebf777278d4ddfd96ba8de1 *man/pos_twopt_est.Rd
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7b51315057b4045e6b28257148043965 *man/print_mrk.Rd
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2b32b184e6e41a97ee45f8aacc480f8e *man/read_geno.Rd
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12795808932b3d5034bbbef9b4502119 *man/read_geno_prob.Rd
b1b37409618ec4d187801567c17dc9c7 *man/read_vcf.Rd
3a1519c791dab975dee56baef2e5a789 *man/reest_rf.Rd
6dbb02ddf54ca7acb0c76a2fd0708406 *man/rev_map.Rd
55da20fb0b927586b014064603a8f6ad *man/rf_list_to_matrix.Rd
def4988e46194e1efa6bee640a2dd588 *man/rf_snp_filter.Rd
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383d2eff3c2492f9fc83eb54915e9a98 *man/segreg_poly.Rd
fa7b104ca12f2dc11316ce0b480f8326 *man/select_rf.Rd
bd29901cc147987034a7906ac458bd55 *man/sim_cross_one_informative_parent.Rd
6f7c7fc6b63148e97faf7320118c4009 *man/sim_cross_two_informative_parents.Rd
ca837c209fd07e647538b4ec9ad01a5c *man/sim_homologous.Rd
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fb412468df70b2ca859b7b3082e1db58 *man/solcap.mds.map.Rd
5809949ba17404d4df9a2f9f38d216ab *man/solcap.prior.map.Rd
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f50ca1a69de69d7d80800e301a83091e *man/tetra.solcap.geno.dist.Rd
655b3223054b4677f487e82c81288f5f *man/update_map.Rd
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104cfd7bfa00a9df15ff566a1ded9ac1 *man/update_ph_list_at_hmm_thres.Rd
4919b4a430e7df0e01ce182fb18f9059 *src/Makevars.win
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6edfa57652516bef54b06035f5927304 *src/calc_genoprob.h
c6393ea8ecb4d124a348b4981057de09 *src/calc_genoprob_based_on_phased_marker_blocks.cpp
3887bfad52d9b66b0c7bcce5e4e85e26 *src/calc_genoprob_based_on_phased_marker_blocks.h
76b3535ab655d2d8a764a345d0b89f25 *src/calc_loglike_given_map.cpp
ba6fdc8848faf750ae7c42ac9121882e *src/calc_loglike_given_map.h
cb6772fac648c6bda9b947ec9f1e5dcf *src/combinatorial.cpp
612ef9cfd76cc2a3b7979e768637fe70 *src/combinatorial.h
072bf59c885f7410847cc478bf62b83d *src/est_hmm_map_based_on_phased_mrk_blocks.cpp
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60592f0507d38d11d481defe5e7aac6f *src/est_map_hmm_given_dose.h
a7063c9c0e264ccfabb5d6a924ef041e *src/est_map_hmm_given_prior.cpp
3402dcd98a9aafe2e076ed6d582e877e *src/est_map_hmm_given_prior.h
55aca96659c7813ddae0ed34bf878515 *src/genotypic_counts.cpp
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7257d93154fa879f9790aba680ca4bb3 *src/hmm_elements.cpp
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1f051d5425b2c4804e9d339272587e25 *tests/testthat/test-merge_maps.R
38873b9c483545e21dda45ea62db52f4 *tests/testthat/test-preferential_pairing.R
fec7eb414a5c52cef9ab04a49c412d5a *tests/testthat/test-read_data.R
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c9bc258542776e6fda96dddca2beb068 *tests/testthat/test-utility_func.R
