Files in nickbrazeau/polySimIBD
Structured Wright Fisher Simulator for Malaria Genetics
.Rbuildignore
.covrignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/RcppExports.R
R/conversions.R
R/forward_sWF.R
R/get_results.R
R/utils.R
R/zzz.R
README.md
R_ignore/COI distribution in PolySimIBD model.docx
R_ignore/COI_equilibrium.R
R_ignore/images/arg.png
R_ignore/images/cotransmission_superinfxn.png
R_ignore/images/polysimibd_hexbadge.png
R_ignore/images/sWFmodelframework.png
R_ignore/migration_models/migration_mat_models.RDS
_pkgdown.yml
docs/404.html
docs/LICENSE-text.html
docs/articles/index.html
docs/articles/installation.html
docs/articles/installation_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/modframework_dldtstructuredwf.html
docs/articles/modframework_dldtstructuredwf_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/modframework_dldtstructuredwf_files/figure-html/unnamed-chunk-4-1.png
docs/articles/orig_mod_framework.html
docs/articles/orig_mod_framework_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/orig_mod_framework_files/figure-html/unnamed-chunk-4-1.png
docs/articles/simdata.html
docs/articles/simdata_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/spatial_extension.html
docs/articles/spatial_extension_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/spatial_extension_files/figure-html/unnamed-chunk-4-1.png
docs/articles/spatial_extension_files/figure-html/unnamed-chunk-6-1.png
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/extract_haplotype_matrix.html
docs/reference/get_ARG.html
docs/reference/get_effective_coi.html
docs/reference/get_haplotype_matrix.html
docs/reference/get_pairwise_bv_ibd.html
docs/reference/get_pairwise_coi_ibd.html
docs/reference/get_realized_coi.html
docs/reference/get_realized_pairwise_ibd.html
docs/reference/get_within_host_IBD.html
docs/reference/get_within_ibd.html
docs/reference/index.html
docs/reference/layer_mutations_on_ARG.html
docs/reference/pipe.html
docs/reference/plotARG.html
docs/reference/plot_barcodes.html
docs/reference/plot_coalescence_trees.html
docs/reference/polySimIBD.html
docs/reference/rbetabinom.html
docs/reference/rdirichlet.html
docs/reference/sim_biallelic.html
docs/reference/sim_swf.html
docs/reference/subset_bvtree.html
docs/sitemap.xml
index.md
inst/CITATION
man/argraph.Rd
man/bvtree.Rd
man/bvtreeToNewick.Rd
man/get_arg.Rd
man/get_bvibd.Rd
man/get_effective_coi.Rd
man/get_within_ibd.Rd
man/pipe.Rd
man/polySimIBD.Rd
man/sim_swf.Rd
man/subset_bvtree.Rd
man/swfsim.Rd
polySimIBD.Rproj
src/.gitignore
src/Haplotype.cpp
src/Haplotype.h
src/Host.cpp
src/Host.h
src/RcppExports.cpp
src/Sampler_v1.cpp
src/Sampler_v1.h
src/main.cpp
src/main.h
src/misc_v9.cpp
src/misc_v9.h
src/probability_v10.cpp
src/probability_v10.h
tests/testthat.R
tests/testthat/test-IBDwithislandmodel.R
tests/testthat/test-backwards_compat.R
tests/testthat/test-conversion.R
tests/testthat/test-cppIBDcalc.R
tests/testthat/test-getresults.R
tests/testthat/test-inheritCOI1.R
tests/testthat/test-migrationmatrix.R
tests/testthat/test-migrationreduction.R
tests/testthat/test-migrationzero.R
tests/testthat/test-modelruns.R
vignettes/.gitignore
vignettes/installation.Rmd
vignettes/orig_mod_framework.Rmd
vignettes/spatial_extension.Rmd
