eriqande/CKMRsim
Inference of Pairwise Relationships Using Likelihood Ratios

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Inference of Pairwise Relationships Using Likelihood Ratios

.Rbuildignore
.gitignore
.travis.yml
CKMRsim.Rproj
DESCRIPTION
IDEAS.md
NAMESPACE
NEWS.md R/CKMRsim-package.R R/Qij-class.R R/RcppExports.R R/ckmr-class.R R/ckmr2colony.R R/combine_miscalls_and_dropouts.R R/create_ckmr.R R/create_integer_genotype_matrix.R R/data.R R/extract_logls.R R/find_close_matching_genotypes.R R/flatten-ckmr.R R/ge_model_TGIE.R R/ge_model_microhap1.R R/ge_model_microsat1.R R/geno_err_models.R R/genotypes_and_error.R R/geometric_chromo_lengths.R R/hello.R R/import.R R/mendel-install.R R/mendel-interface.R R/pairwise_kin_logl_ratios.R R/reindex_markers.R R/sample.R R/simulate.R R/simulate_Qij.R R/sprinkle_markers_into_genomes.R R/tag_mendelian_incompatibilities.R README.Rmd README.md
_pkgdown.yml
data/brook_trout_genos.rda
data/example_L_biallelic.rda
data/example_L_microhap.rda
data/example_L_microsat.rda
data/kappas.rda
data/labrador_salar_ngs_msats.rda
data/linked_mhaps.rda
data/long_markers.rda
data/markers40.rda
data/markers_on_map.rda
data/microhaps.rda
data/pedigrees.rda
data/sebastes.rda
deprecated/morgan-interface.R
development/.gitignore
development/R-main/ckmr-do-dev.R development/R-main/devel-high-level.R development/R-main/explore-linked-markers-imp-samp.R development/R-main/linked-markers-main-dev.R development/R-main/unliked-markers-main-dev.R
development/Rmd/.gitignore
development/Rmd/chinook_mhaps.Rmd development/Rmd/compare-linked-and-unlinked-new-pedigrees.Rmd development/Rmd/gtseq_kelp_rockfish_juvies.Rmd development/Rmd/reading-and-formatting-brook-trout-data.Rmd development/Rmd/sebastes_power_1.Rmd development/Rmd/sebastes_power_for_mhap_paper.Rmd development/Rmd/spip-simulate-microhaps.Rmd development/Rmd/splitnose.Rmd
development/Rmd/struct_dat.txt
development/Rmd/tracking-down-gtyp-err-and-linkage-issues.Rmd
development/data/RCU_33_LOCI_OFFSPRING.xlsx
development/data/RCU_33_LOCI_PARENTS.xlsx
development/data/chinook_microhaps_status.xlsx
development/data/chinook_read_data_lightly_filtered.csv
development/data/filtered_haplotype_panel_1.csv.gz
development/data/filtered_haplotype_panel_2.csv.gz
development/data/panel1_status.xlsx
development/data/panel2_status.xlsx
development/data/spip400_geno.txt.gz
development/data/spip400_ped.txt
development/data/spip4K_geno.txt.gz
development/data/spip4K_ped.txt.gz
development/data/splitnose_adults.txt
development/data/splitnose_recruits.txt
development/data/splitnose_recruits_noheader.txt
development/data/test_Qvals.rds
docs/404.html
docs/IDEAS.html
docs/articles/CKMRsim-developer-notes.html
docs/articles/CKMRsim-example-1.html
docs/articles/CKMRsim-example-1_files/figure-html/unnamed-chunk-19-1.png
docs/articles/CKMRsim-example-1_files/figure-html/unnamed-chunk-20-1.png
docs/articles/CKMRsim-example-1_files/figure-html/unnamed-chunk-21-1.png
docs/articles/CKMRsim-example-2-microsatellites.html
docs/articles/CKMRsim-example-2-microsatellites_files/figure-html/unnamed-chunk-11-1.png
docs/articles/CKMRsim-example-2-microsatellites_files/figure-html/unnamed-chunk-12-1.png
docs/articles/CKMRsim-example-2-microsatellites_files/figure-html/unnamed-chunk-18-1.png
docs/articles/CKMRsim-example-2-microsatellites_files/figure-html/unnamed-chunk-22-1.png
docs/articles/CKMRsim-pairwise-relationships.html
docs/articles/CKMRsim-simulating-linked-markers.html
docs/articles/CKMRsim-simulating-linked-markers_files/figure-html/unnamed-chunk-9-1.png
docs/articles/CKMRsim-writing-geno-error-funcs.html
docs/articles/images/AN.png
docs/articles/images/DFC.png
docs/articles/images/DHFC.png
docs/articles/images/FC.png
docs/articles/images/FS.png
docs/articles/images/GP.png
docs/articles/images/HAN.png
docs/articles/images/HFC.png
docs/articles/images/HS.png
docs/articles/images/HSC.png
docs/articles/images/PO.png
docs/articles/images/SC.png
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/CKMRsim.html
docs/reference/Qij_class.html
docs/reference/Rplot001.png
docs/reference/afreq_str.html
docs/reference/brook_trout_genos.html
docs/reference/ckmr2colony.html
docs/reference/ckmr_class.html
docs/reference/ckmr_relats.html
docs/reference/combine_miscalls_and_dropouts.html
docs/reference/comp_ind_pairwise.html
docs/reference/create_ckmr.html
docs/reference/create_integer_genotype_matrix.html
docs/reference/example_L_biallelic.html
docs/reference/example_L_microhap.html
docs/reference/example_L_microsat.html
docs/reference/extract_logls.html
docs/reference/find_close_matching_genotypes.html
docs/reference/flatten_ckmr.html
docs/reference/format.Qij.html
docs/reference/format.ckmr.html
docs/reference/ge_model_TGIE.html
docs/reference/ge_model_microhap1.html
docs/reference/ge_model_microsat1.html
docs/reference/general_allele_based_geno_err_model.html
docs/reference/geometric_chromo_lengths.html
docs/reference/hap_obs_prob.html
docs/reference/id_prepend.html
docs/reference/index.html
docs/reference/index_ab.html
docs/reference/insert_C_l_matrices.html
docs/reference/insert_Y_l_matrices.html
docs/reference/install_mendel.html
docs/reference/kappas.html
docs/reference/labrador_salar_ngs_msats.html
docs/reference/linked_mhaps.html
docs/reference/locus_specific_pairwise.html
docs/reference/loggy_reweight.html
docs/reference/long_markers.html
docs/reference/long_markers_to_X_l_list.html
docs/reference/make_matrix_X_l.html
docs/reference/markers2mendel_def_lines.html
docs/reference/markers2mendel_map_lines.html
docs/reference/markers40.html
docs/reference/markers_on_map.html
docs/reference/mc_sample_simple.html
docs/reference/mendelBin.html
docs/reference/mendel_control_list.html
docs/reference/microhaplotype_geno_err_matrix.html
docs/reference/microhaps.html
docs/reference/pairwise_geno_id.html
docs/reference/pairwise_kin_logl_ratios.html
docs/reference/pedigree2mendel_ped_file.html
docs/reference/pedigrees.html
docs/reference/pipe.html
docs/reference/print.Qij.html
docs/reference/print.ckmr.html
docs/reference/read_mendel_outped.html
docs/reference/reindex_markers.html
docs/reference/run_mendel.html
docs/reference/samp_from_mat.html
docs/reference/sample_linked_genotype_pairs.html
docs/reference/sebastes.html
docs/reference/simulate_Qij.html
docs/reference/simulate_and_calc_Q.html
docs/reference/sprinkle_markers_into_genome.html
docs/reference/tag_mendelian_incompatibilities.html
docs/reference/top_index.html
docs/reference/write_all_mendel_files.html
docs/sitemap.xml
inst/extdata/kelp_adults.rds
inst/extdata/kelp_genos_used_two_col.csv.gz
inst/extdata/kelp_juveniles.rds
inst/script/slurp_outped.sh
man/CKMRsim.Rd man/Qij_class.Rd man/afreq_str.Rd man/brook_trout_genos.Rd man/ckmr2colony.Rd man/ckmr_class.Rd man/ckmr_relats.Rd man/combine_miscalls_and_dropouts.Rd man/comp_ind_pairwise.Rd man/create_ckmr.Rd man/create_integer_genotype_matrix.Rd man/example_L_biallelic.Rd man/example_L_microhap.Rd man/example_L_microsat.Rd man/extract_logls.Rd man/find_close_matching_genotypes.Rd man/flatten_ckmr.Rd man/format.Qij.Rd man/format.ckmr.Rd man/ge_model_TGIE.Rd man/ge_model_microhap1.Rd man/ge_model_microsat1.Rd man/general_allele_based_geno_err_model.Rd man/geometric_chromo_lengths.Rd man/hap_obs_prob.Rd man/id_prepend.Rd man/index_ab.Rd man/insert_C_l_matrices.Rd man/insert_Y_l_matrices.Rd man/install_mendel.Rd man/kappas.Rd man/labrador_salar_ngs_msats.Rd man/linked_mhaps.Rd man/locus_specific_pairwise.Rd man/loggy_reweight.Rd man/long_markers.Rd man/long_markers_to_X_l_list.Rd man/make_matrix_X_l.Rd man/markers2mendel_def_lines.Rd man/markers2mendel_map_lines.Rd man/markers40.Rd man/markers_on_map.Rd man/mc_sample_simple.Rd man/mendelBin.Rd man/mendel_control_list.Rd man/microhaplotype_geno_err_matrix.Rd man/microhaps.Rd man/pairwise_geno_id.Rd man/pairwise_kin_logl_ratios.Rd man/pedigree2mendel_ped_file.Rd man/pedigrees.Rd man/pipe.Rd man/print.Qij.Rd man/print.ckmr.Rd man/read_mendel_outped.Rd man/reindex_markers.Rd man/run_mendel.Rd man/samp_from_mat.Rd man/sample_linked_genotype_pairs.Rd man/sebastes.Rd man/simulate_Qij.Rd man/simulate_and_calc_Q.Rd man/sprinkle_markers_into_genome.Rd man/tag_mendelian_incompatibilities.Rd man/top_index.Rd man/write_all_mendel_files.Rd scratch/create-data.R scratch/geno-indices.R
src/RcppExports.cpp
src/geno_probs.cpp
src/pairwise_comps.cpp
src/read_mendel_output.cpp
src/samp_from_mat.cpp
src/top_index.cpp
vignettes/.gitignore
vignettes/CKMRsim-developer-notes.Rmd vignettes/CKMRsim-example-1.Rmd vignettes/CKMRsim-example-2-microsatellites.Rmd vignettes/CKMRsim-pairwise-relationships.Rmd vignettes/CKMRsim-simulating-linked-markers.Rmd vignettes/CKMRsim-writing-geno-error-funcs.Rmd
vignettes/data/lnl_logls.rds
vignettes/images/AN.png
vignettes/images/DFC.png
vignettes/images/DHFC.png
vignettes/images/FC.png
vignettes/images/FS.png
vignettes/images/GP.png
vignettes/images/HAN.png
vignettes/images/HFC.png
vignettes/images/HS.png
vignettes/images/HSC.png
vignettes/images/PO.png
vignettes/images/SC.png
vignettes/references.bib
eriqande/CKMRsim documentation built on March 1, 2025, 11:59 p.m.

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