Files in eriqande/gscramble
Simulating Admixed Genotypes Without Replacement
.Rbuildignore
.github/.gitignore
.github/workflows/check-standard.yaml
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md
R/check_chrom_lengths.R
R/check_gsp_for_validity_and_saturation.R
R/check_pedigree_for_inbreeding.R
R/check_rec_rates_formatting.R
R/check_reppop.R
R/computeQs_from_segments.R
R/create_GSP.R
R/data.R
R/drop-segs-down-gsp.R
R/gscramble2newhybrids.R
R/gscramble2plink.R
R/gsp2dot.R
R/import.R
R/make_subscript_matrix.R
R/mat_scramble.R
R/perm_gs_by_pops.R
R/plink2gscramble.R
R/plink_map2rec_rates.R
R/plot_simulated_chromosome_segments.R
R/prep_gsp_for_hap_dropping.R
R/rearrange_genos.R
R/recomb_point.R
R/renumber_GSP.R
R/seg2tib.R
R/seg_haps_through_gsp.R
R/segments2markers.R
R/segregate.R
R/sim_level_founder_haplos.R
R/tidy_up_sampled_haplos.R
R/xover.R
README.Rmd
README.md
TODO.md
_pkgdown.yml
cran-comments.md
data/GSP.rda
data/GSP_opts.rda
data/Geno.rda
data/I_meta.rda
data/M_meta.rda
data/RecRates.rda
data/RepPop1.rda
data/RepPop4.rda
data/example_chrom_lengths.rda
data/example_segements.rda
data/gsp3.rda
data/gsp4.rda
development/.gitignore
development/13-member-ped.xlsx
development/bias-inducing-simulation/.gitignore
development/bias-inducing-simulation/bias-inducing-simulation.Rmd
development/dot_drawings/.gitignore
development/dot_drawings/gsp3.dot
development/dot_drawings/gsp3.png
development/dot_drawings/ped13
development/dot_drawings/ped13.dot
development/dot_drawings/ped13.png
development/dot_drawings/ped13_complex.dot
development/dot_drawings/ped13_complex.png
development/make-marker-focused-map.Rmd
development/old_data_and_extdata/data/Geno_Big.rda
development/old_data_and_extdata/data/I_meta_Big.rda
development/old_data_and_extdata/data/M_meta_Big.rda
development/old_data_and_extdata/data/RecRates_Big.rda
development/old_data_and_extdata/data/RepPop1_Big.rda
development/old_data_and_extdata/data/RepPop4_Big.rda
development/old_data_and_extdata/extdata/text_Missouri_329x25165.map.gz
development/old_data_and_extdata/extdata/text_Missouri_329x25165.ped.gz
development/old_vignettes_etc/a-feral-pig-example.Rmd
development/old_vignettes_etc/a-feral-pig-example.nb.html
development/old_vignettes_etc/developer-notes.Rmd
development/old_vignettes_etc/simulating-bx-Qs.Rmd
development/ped-seg-dropping.Rmd
development/pig-stuff.Rmd
development/random-dot-stuff.R
docs/.nothing
gscramble.Rproj
inst/extdata/13-member-ped-with-errors.csv
inst/extdata/13-member-ped.csv
inst/extdata/Torterau_et_al_2012_sus_scrofa_map.txt.gz
inst/extdata/another-ped.csv
inst/extdata/eight_BX2s.csv
inst/extdata/example-plink-with-morgans.map.gz
inst/extdata/example-plink.map.gz
inst/extdata/example-plink.ped.gz
inst/extdata/four_BX1s.csv
inst/extdata/gsp3.csv
inst/extdata/gsp4.csv
inst/extdata/two_F1s.csv
man/GSP.Rd
man/GSP_opts.Rd
man/Geno.Rd
man/I_meta.Rd
man/M_meta.Rd
man/RecRates.Rd
man/RepPop1.Rd
man/RepPop4.Rd
man/check_chrom_lengths.Rd
man/check_gsp_for_validity_and_saturation.Rd
man/check_pedigree_for_inbreeding.Rd
man/check_rec_rates_formatting.Rd
man/check_reppop.Rd
man/computeQs_from_segments.Rd
man/create_GSP.Rd
man/drop_segs_down_gsp.Rd
man/example_chrom_lengths.Rd
man/example_segments.Rd
man/figures/1.svg
man/figures/10.svg
man/figures/11.svg
man/figures/12.svg
man/figures/13-member-ped.svg
man/figures/13.svg
man/figures/14.svg
man/figures/15.svg
man/figures/2.svg
man/figures/3.svg
man/figures/4.svg
man/figures/5.svg
man/figures/6.svg
man/figures/7.svg
man/figures/8.svg
man/figures/9.svg
man/figures/F1-500.png
man/figures/gsp4-700.png
man/gscramble2newhybrids.Rd
man/gscramble2plink.Rd
man/gsp2dot.Rd
man/gsp3.Rd
man/gsp4.Rd
man/make_subscript_matrix.Rd
man/mat_scramble.Rd
man/perm_gs_by_pops.Rd
man/plink2gscramble.Rd
man/plink_map2rec_rates.Rd
man/plot_simulated_chromomsome_segments.Rd
man/prep_gsp_for_hap_dropping.Rd
man/rearrange_genos.Rd
man/recomb_point.Rd
man/renumber_GSP.Rd
man/seg2tib.Rd
man/seg_haps_through_gsp.Rd
man/segments2markers.Rd
man/segregate.Rd
man/sim_level_founder_haplos.Rd
man/tidy_up_sampled_haplos.Rd
man/xover.Rd
vignettes/.gitignore
vignettes/about-createGSP.Rmd
vignettes/gscramble-tutorial.Rmd
vignettes/images/13-member-ped.svg
vignettes/images/13.svg
vignettes/images/F1-500.png
vignettes/images/eight-BX2s-500.png
vignettes/images/four-BX1s-500.png
vignettes/images/gsp3-500.png
vignettes/images/gsp3.png
vignettes/images/gsp4-700.png
vignettes/images/ped13_complex.svg
vignettes/permutation-options.Rmd
