Files in dcgerard/updog
Flexible Genotyping for Polyploids

.Rbuildignore
.github/.gitignore
.github/ISSUE_TEMPLATE/Bug_report.md
.github/workflows/R-CMD-check.yaml
.gitignore
CONDUCT.md
DESCRIPTION
NAMESPACE
NEWS.md R/RcppExports.R R/ashdog.R R/data.R R/multidog.R R/oracle.R R/plot_geno.R R/pp.R R/rflexdog.R R/updog.R README.Rmd README.md
_pkgdown.yml
data/snpdat.RData
data/uitdewilligen.RData
docs/404.html
docs/CONDUCT.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/index.html
docs/articles/multidog.html
docs/articles/multidog_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/multidog_files/figure-html/unnamed-chunk-6-1.png
docs/articles/multidog_files/figure-html/unnamed-chunk-6-2.png
docs/articles/multidog_files/figure-html/unnamed-chunk-6-3.png
docs/articles/multidog_files/figure-html/unnamed-chunk-8-1.png
docs/articles/multidog_files/figure-html/unnamed-chunk-8-2.png
docs/articles/multidog_files/figure-html/unnamed-chunk-8-3.png
docs/articles/multidog_files/header-attrs-2.11/header-attrs.js
docs/articles/multidog_files/header-attrs-2.6/header-attrs.js
docs/articles/oracle_calculations.html
docs/articles/oracle_calculations_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/oracle_calculations_files/figure-html/unnamed-chunk-3-1.png
docs/articles/oracle_calculations_files/figure-html/unnamed-chunk-5-1.png
docs/articles/oracle_calculations_files/header-attrs-2.11/header-attrs.js
docs/articles/oracle_calculations_files/header-attrs-2.6/header-attrs.js
docs/articles/simulate_ngs.html
docs/articles/simulate_ngs_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/simulate_ngs_files/figure-html/unnamed-chunk-4-1.png
docs/articles/simulate_ngs_files/figure-html/unnamed-chunk-6-1.png
docs/articles/simulate_ngs_files/figure-html/unnamed-chunk-7-1.png
docs/articles/simulate_ngs_files/header-attrs-2.11/header-attrs.js
docs/articles/simulate_ngs_files/header-attrs-2.6/header-attrs.js
docs/articles/smells_like_updog.html
docs/articles/smells_like_updog_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/smells_like_updog_files/figure-html/unnamed-chunk-4-1.png
docs/articles/smells_like_updog_files/figure-html/unnamed-chunk-6-1.png
docs/articles/smells_like_updog_files/header-attrs-2.11/header-attrs.js
docs/articles/smells_like_updog_files/header-attrs-2.6/header-attrs.js
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js
docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.1.3/bootstrap.min.css
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.2.2/bootstrap.min.css
docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js
docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.3.1/bootstrap.min.css
docs/deps/bootstrap-5.3.1/font.css
docs/deps/bootstrap-5.3.1/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVs9pbCIPrc.woff
docs/deps/bootstrap-5.3.1/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVvaorCIPrc.woff
docs/deps/bootstrap-5.3.1/fonts/1adeadb2fe618c5ed46221f15e12b9c8.woff
docs/deps/bootstrap-5.3.1/fonts/4iCs6KVjbNBYlgo6ew.woff
docs/deps/bootstrap-5.3.1/fonts/4iCs6KVjbNBYlgoKfw7w.woff
docs/deps/bootstrap-5.3.1/fonts/4iCv6KVjbNBYlgoCxCvTtA.woff
docs/deps/bootstrap-5.3.1/fonts/4iCv6KVjbNBYlgoCxCvjsGyL.woff
docs/deps/bootstrap-5.3.1/fonts/6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7nsDQ.woff
docs/deps/bootstrap-5.3.1/fonts/6xK1dSBYKcSV-LCoeQqfX1RYOo3qPa7j.woff
docs/deps/bootstrap-5.3.1/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3aPA.woff
docs/deps/bootstrap-5.3.1/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3qOK7j.woff
docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3i54rAkw.woff
docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vAkw.woff
docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlxdo.woff
docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zAkw.woff
docs/deps/bootstrap-5.3.1/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlxdo.woff
docs/deps/bootstrap-5.3.1/fonts/CSR54z1Qlv-GDxkbKVQ_dFsvWNRevw.woff
docs/deps/bootstrap-5.3.1/fonts/CSR54z1Qlv-GDxkbKVQ_dFsvaNA.woff
docs/deps/bootstrap-5.3.1/fonts/CSR64z1Qlv-GDxkbKVQ_TOQ.woff
docs/deps/bootstrap-5.3.1/fonts/CSR64z1Qlv-GDxkbKVQ_fOAKSw.woff
docs/deps/bootstrap-5.3.1/fonts/HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DBKXhM0.woff
docs/deps/bootstrap-5.3.1/fonts/HI_diYsKILxRpg3hIP6sJ7fM7PqPMcMnZFqUwX28DMyQhM0.woff
docs/deps/bootstrap-5.3.1/fonts/HI_jiYsKILxRpg3hIP6sJ7fM7PqlOPHYvDP_W9O7GQTTbI1rSg.woff
docs/deps/bootstrap-5.3.1/fonts/HI_jiYsKILxRpg3hIP6sJ7fM7PqlOPHYvDP_W9O7GQTTsoprSg.woff
docs/deps/bootstrap-5.3.1/fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtZ6Ew9.woff
docs/deps/bootstrap-5.3.1/fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCtr6Ew9.woff
docs/deps/bootstrap-5.3.1/fonts/JTUHjIg1_i6t8kCHKm4532VJOt5-QNFgpCuM70w9.woff
docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmEU9fBBc-.woff
docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmEU9vAA.woff
docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmSU5fBBc-.woff
docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmSU5vAA.woff
docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmWUlfBBc-.woff
docs/deps/bootstrap-5.3.1/fonts/KFOlCnqEu92Fr1MmWUlvAA.woff
docs/deps/bootstrap-5.3.1/fonts/KFOmCnqEu92Fr1Me5g.woff
docs/deps/bootstrap-5.3.1/fonts/KFOmCnqEu92Fr1Mu4mxM.woff
docs/deps/bootstrap-5.3.1/fonts/QGYpz_kZZAGCONcK2A4bGOj8mNhL.woff
docs/deps/bootstrap-5.3.1/fonts/S6u8w4BMUTPHjxsAXC-s.woff
docs/deps/bootstrap-5.3.1/fonts/S6u8w4BMUTPHjxswWA.woff
docs/deps/bootstrap-5.3.1/fonts/S6u9w4BMUTPHh6UVSwiPHw.woff
docs/deps/bootstrap-5.3.1/fonts/S6u9w4BMUTPHh6UVeww.woff
docs/deps/bootstrap-5.3.1/fonts/S6u9w4BMUTPHh7USSwiPHw.woff
docs/deps/bootstrap-5.3.1/fonts/S6u9w4BMUTPHh7USeww.woff
docs/deps/bootstrap-5.3.1/fonts/S6uyw4BMUTPHjx4wWA.woff
docs/deps/bootstrap-5.3.1/fonts/S6uyw4BMUTPHvxo.woff
docs/deps/bootstrap-5.3.1/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuFuYMZs.woff
docs/deps/bootstrap-5.3.1/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuI6fMZs.woff
docs/deps/bootstrap-5.3.1/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuLyfMZs.woff
docs/deps/bootstrap-5.3.1/fonts/XRXI3I6Li01BKofiOc5wtlZ2di8HDFwmRTA.woff
docs/deps/bootstrap-5.3.1/fonts/XRXI3I6Li01BKofiOc5wtlZ2di8HDGUmRTA.woff
docs/deps/bootstrap-5.3.1/fonts/XRXI3I6Li01BKofiOc5wtlZ2di8HDLshRTA.woff
docs/deps/bootstrap-5.3.1/fonts/a98f7a7574819ba83bec6279a2cecd95.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk0ZjaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk_RkaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkxhjaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff
docs/deps/bootstrap-5.3.1/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsgH1y4k.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgshZ1y4k.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff
docs/deps/bootstrap-5.3.1/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjr0C4k.woff
docs/deps/bootstrap-5.3.1/fonts/q5uGsou0JOdh94bfvQlr.woff
docs/deps/data-deps.txt
docs/deps/jquery-3.6.0/jquery-3.6.0.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.map
docs/docsearch.css
docs/docsearch.js
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/betabinom.html
docs/reference/figures/logo.png
docs/reference/filter_snp.html
docs/reference/flexdog-1.png
docs/reference/flexdog-2.png
docs/reference/flexdog.html
docs/reference/flexdog_full-1.png
docs/reference/flexdog_full.html
docs/reference/format_multidog.html
docs/reference/get_q_array.html
docs/reference/index.html
docs/reference/is.flexdog.html
docs/reference/is.multidog.html
docs/reference/log_sum_exp.html
docs/reference/log_sum_exp_2.html
docs/reference/multidog.html
docs/reference/oracle_cor.html
docs/reference/oracle_cor_from_joint.html
docs/reference/oracle_joint.html
docs/reference/oracle_mis.html
docs/reference/oracle_mis_from_joint.html
docs/reference/oracle_mis_vec.html
docs/reference/oracle_mis_vec_from_joint.html
docs/reference/oracle_plot-1.png
docs/reference/oracle_plot.html
docs/reference/plot.flexdog.html
docs/reference/plot.multidog.html
docs/reference/plot_geno-1.png
docs/reference/plot_geno.html
docs/reference/rflexdog-1.png
docs/reference/rflexdog.html
docs/reference/rgeno.html
docs/reference/snpdat.html
docs/reference/uitdewilligen.html
docs/reference/updog-package.html
docs/reference/wem.html
docs/search.json
docs/sitemap.xml
inst/CITATION
inst/include/updog.h
inst/include/updog_RcppExports.h
man/betabinom.Rd
man/figures/logo.png
man/filter_snp.Rd man/flexdog.Rd man/flexdog_full.Rd man/format_multidog.Rd man/get_q_array.Rd man/is.flexdog.Rd man/is.multidog.Rd man/log_sum_exp.Rd man/log_sum_exp_2.Rd man/multidog.Rd man/oracle_cor.Rd man/oracle_cor_from_joint.Rd man/oracle_joint.Rd man/oracle_mis.Rd man/oracle_mis_from_joint.Rd man/oracle_mis_vec.Rd man/oracle_mis_vec_from_joint.Rd man/oracle_plot.Rd man/plot.flexdog.Rd man/plot.multidog.Rd man/plot_geno.Rd man/rflexdog.Rd man/rgeno.Rd man/snpdat.Rd man/uitdewilligen.Rd man/updog-package.Rd man/wem.Rd
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
src/.gitignore
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/betabinom.cpp
src/em.cpp
src/flexdog.cpp
src/gradients.cpp
src/mupdog.h
src/objective.cpp
src/oracle.cpp
src/util_funs.cpp
tests/testthat.R
tests/testthat/cvx_prob.RDS
tests/testthat/out_err.RData
tests/testthat/test_dbetabinom.R tests/testthat/test_f1_genotyping.R tests/testthat/test_flexdog.R tests/testthat/test_gradients.R tests/testthat/test_objectives.R tests/testthat/test_oracle.R tests/testthat/test_rflexdog.R tests/testthat/test_utils.R tests/testthat/test_wikmat.R
tests/testthat/testdat.RData
vignettes/.gitignore
vignettes/multidog.Rmd vignettes/oracle_calculations.Rmd vignettes/simulate_ngs.Rmd vignettes/smells_like_updog.Rmd
dcgerard/updog documentation built on Jan. 4, 2024, 1:08 p.m.