├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── DESCRIPTION ├── MAPpoly.Rproj ├── MAPpoly_workflow.png ├── NAMESPACE ├── NEWS.md ├── R ├── RcppExports.R ├── add_drop.R ├── build_map_by_steps.R ├── cache_twopts.R ├── calc_genoprob.R ├── calc_genoprob_dist.R ├── calc_genoprob_error.R ├── calc_genoprob_single_parent.R ├── check_phase_configurations.R ├── cross_simulate.R ├── data.R ├── eliminate_redundant.R ├── est_map_hmm.R ├── export_map_list.R ├── export_qtlpoly.R ├── filters.R ├── find_blocks.R ├── get_counts.R ├── get_counts_from_web.R ├── get_submap.R ├── group.R ├── haplotype_map_utils.R ├── homolog_probs.R ├── import_from_polymapR.R ├── import_from_updog.R ├── loglike_hmm.R ├── make_mat.R ├── make_pairs.R ├── make_seq.R ├── marker_info.R ├── mds.R ├── merge_maps.R ├── pairwise_rf.R ├── plot_genome_vs_map.R ├── plot_map_list.R ├── plot_progeny_dosage_change.R ├── preferential_pairing.R ├── prior_dist_hmm.R ├── read_fitpoly.R ├── read_mappoly.R ├── read_mappoly_csv.R ├── read_mappoly_prob.R ├── read_mappoly_vcf.R ├── reest_map_error.R ├── reestimate_map.R ├── rf_list_to_matrix.R ├── segreg_poly.R ├── sim_homologous.R ├── simulation_utils.R ├── single_map_hmm.R ├── single_paprent_single_phase_hmm.R ├── split_and_rephase.R ├── sysdata.rda ├── utils.R └── zzz.R ├── README.md ├── _config.yml ├── appveyor.yml ├── cran-comments.md ├── data ├── datalist └── example_data.rda ├── hex.png ├── inst ├── CITATION └── extdata │ └── potato_example.csv ├── man ├── add_marker.Rd ├── add_md_markers.Rd ├── add_mrk_at_tail_ph_list.Rd ├── aggregate_matrix.Rd ├── cache_counts_twopt.Rd ├── calc_genoprob.Rd ├── calc_genoprob_dist.Rd ├── calc_genoprob_error.Rd ├── calc_genoprob_haplo.Rd ├── calc_genoprob_single_parent.Rd ├── calc_homologprob.Rd ├── calc_prefpair_profiles.Rd ├── cat_phase.Rd ├── check_data_dist_sanity.Rd ├── check_data_dose_sanity.Rd ├── check_data_sanity.Rd ├── check_if_rf_is_possible.Rd ├── check_ls_phase.Rd ├── check_pairwise.Rd ├── compare_haplotypes.Rd ├── compare_maps.Rd ├── concatenate_new_marker.Rd ├── concatenate_ph_list.Rd ├── create_map.Rd ├── cross_simulate.Rd ├── detect_info_par.Rd ├── dist_prob_to_class.Rd ├── draw_cross.Rd ├── draw_phases.Rd ├── drop_marker.Rd ├── edit_order.Rd ├── elim_conf_using_two_pts.Rd ├── elim_equiv.Rd ├── elim_redundant.Rd ├── est_full_hmm_with_global_error.Rd ├── est_full_hmm_with_prior_prob.Rd ├── est_haplo_hmm.Rd ├── est_map_haplo_given_genoprob.Rd ├── est_pairwise_rf.Rd ├── est_pairwise_rf2.Rd ├── est_rf_hmm.Rd ├── est_rf_hmm_sequential.Rd ├── est_rf_hmm_single_phase.Rd ├── est_rf_hmm_single_phase_single_parent.Rd ├── export_data_to_polymapR.Rd ├── export_map_list.Rd ├── export_qtlpoly.Rd ├── extract_map.Rd ├── filter_aneuploid.Rd ├── filter_individuals.Rd ├── filter_map_at_hmm_thres.Rd ├── filter_missing.Rd ├── filter_missing_ind.Rd ├── filter_missing_mrk.Rd ├── filter_non_conforming_classes.Rd ├── filter_segregation.Rd ├── find_blocks.Rd ├── format_rf.Rd ├── framework_map.Rd ├── generate_all_link_phase_elim_equivalent.Rd ├── generate_all_link_phases_elim_equivalent_haplo.Rd ├── genetic-mapping-functions.Rd ├── genotyping_global_error.Rd ├── get_LOD.Rd ├── get_cache_two_pts_from_web.Rd ├── get_counts.Rd ├── get_counts_all_phases.Rd ├── get_counts_single_parent.Rd ├── get_counts_two_parents.Rd ├── get_dosage_type.Rd ├── get_full_info_tail.Rd ├── get_genomic_order.Rd ├── get_ij.Rd ├── get_indices_from_selected_phases.Rd ├── get_ols_map.Rd ├── get_ph_conf_ret_sh.Rd ├── get_ph_list_subset.Rd ├── get_rf_from_list.Rd ├── get_rf_from_mat.Rd ├── get_states_and_emission_single_parent.Rd ├── get_submap.Rd ├── get_tab_mrks.Rd ├── get_w_m.Rd ├── gg_color_hue.Rd ├── group_mappoly.Rd ├── hexafake.Rd ├── hexafake.geno.dist.Rd ├── import_data_from_polymapR.Rd ├── import_from_updog.Rd ├── import_phased_maplist_from_polymapR.Rd ├── is.prob.data.Rd ├── loglike_hmm.Rd ├── ls_linkage_phases.Rd ├── make_mat_mappoly.Rd ├── make_pairs_mappoly.Rd ├── make_seq_mappoly.Rd ├── mappoly-color-palettes.Rd ├── maps.hexafake.Rd ├── mds_mappoly.Rd ├── merge_datasets.Rd ├── merge_maps.Rd ├── merge_parental_maps.Rd ├── mrk_chisq_test.Rd ├── msg.Rd ├── paralell_pairwise_discrete.Rd ├── paralell_pairwise_discrete_rcpp.Rd ├── paralell_pairwise_probability.Rd ├── parallel_block.Rd ├── perm_pars.Rd ├── perm_tot.Rd ├── ph_list_to_matrix.Rd ├── ph_matrix_to_list.Rd ├── plot.mappoly.homoprob.Rd ├── plot.mappoly.prefpair.profiles.Rd ├── plot_GIC.Rd ├── plot_compare_haplotypes.Rd ├── plot_genome_vs_map.Rd ├── plot_map_list.Rd ├── plot_mappoly.map2.Rd ├── plot_mrk_info.Rd ├── plot_one_map.Rd ├── plot_progeny_dosage_change.Rd ├── poly_hmm_est.Rd ├── prepare_map.Rd ├── print_mrk.Rd ├── print_ph.Rd ├── read_fitpoly.Rd ├── read_geno.Rd ├── read_geno_csv.Rd ├── read_geno_prob.Rd ├── read_vcf.Rd ├── reest_rf.Rd ├── rev_map.Rd ├── rf_list_to_matrix.Rd ├── rf_snp_filter.Rd ├── sample_data.Rd ├── segreg_poly.Rd ├── select_rf.Rd ├── sim_cross_one_informative_parent.Rd ├── sim_cross_two_informative_parents.Rd ├── sim_homologous.Rd ├── solcap.dose.map.Rd ├── solcap.err.map.Rd ├── solcap.mds.map.Rd ├── solcap.prior.map.Rd ├── split_and_rephase.Rd ├── split_mappoly.Rd ├── summary_maps.Rd ├── table_to_mappoly.Rd ├── tetra.solcap.Rd ├── tetra.solcap.geno.dist.Rd ├── update_framework_map.Rd ├── update_map.Rd ├── update_missing.Rd ├── update_ph_list_at_hmm_thres.Rd └── v_2_m.Rd ├── mappoly.gif ├── nifa-black-lockup-4x.png ├── nifa-color-lockup-4x.png ├── nifa-color-lockup.png ├── pkgdown.yml ├── revdep ├── .gitignore ├── README.md ├── cran.md ├── email.yml ├── failures.md └── problems.md ├── src ├── Makevars ├── Makevars.win ├── RcppExports.cpp ├── calc_genoprob.cpp ├── calc_genoprob.h ├── calc_genoprob_based_on_phased_marker_blocks.cpp ├── calc_genoprob_based_on_phased_marker_blocks.h ├── calc_loglike_given_map.cpp ├── calc_loglike_given_map.h ├── combinatorial.cpp ├── combinatorial.h ├── 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