Files in dcgerard/updog
Flexible Genotyping for Polyploids

.Rbuildignore
.github/ISSUE_TEMPLATE/Bug_report.md
.gitignore
.travis.yml
CONDUCT.md
DESCRIPTION
NAMESPACE
R/RcppExports.R R/ashdog.R R/data.R R/double_red.R R/oracle.R R/plot_mupdog.R R/pref.R R/rflexdog.R R/updog.R R/vem.R README.Rmd README.md
appveyor.yml
codecov.yml
data/mupout.RData
data/snpdat.RData
data/uitdewilligen.RData
docs/.gitignore
docs/CONDUCT.html
docs/articles/index.html
docs/articles/oracle_calculations.html
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/parallel_computing.html
docs/articles/parallel_computing_files/figure-html/unnamed-chunk-6-1.png
docs/articles/simulate_ngs.html
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/smells_like_updog.html
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/authors.html
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/ashpen_fun.html
docs/reference/betabinom.html
docs/reference/compute_all_log_bb.html
docs/reference/compute_all_phifk.html
docs/reference/compute_all_post_prob.html
docs/reference/convolve.html
docs/reference/dbernbinom.html
docs/reference/dbetabinom_alpha_beta_double.html
docs/reference/dbetabinom_double.html
docs/reference/dc_dtau.html
docs/reference/df_deps.html
docs/reference/dlbeta_dc.html
docs/reference/dlbeta_deps.html
docs/reference/dlbeta_dh.html
docs/reference/dlbeta_dtau.html
docs/reference/dlbeta_dxi.html
docs/reference/doutdist.html
docs/reference/dpen_deps.html
docs/reference/dpen_dh.html
docs/reference/dr_pen.html
docs/reference/dxi_df.html
docs/reference/dxi_dh.html
docs/reference/elbo.html
docs/reference/eta_double.html
docs/reference/eta_fun.html
docs/reference/expit.html
docs/reference/f1_obj.html
docs/reference/flex_update_pivec.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/flexdog_obj.html
docs/reference/flexdog_obj_out.html
docs/reference/get_bivalent_probs.html
docs/reference/get_bivalent_probs_dr.html
docs/reference/get_conv_inner_weights.html
docs/reference/get_dimname.html
docs/reference/get_hyper_weights.html
docs/reference/get_inner_weights.html
docs/reference/get_probk_vec.html
docs/reference/get_q_array.html
docs/reference/get_uni_rep.html
docs/reference/get_wik_mat.html
docs/reference/get_wik_mat_out.html
docs/reference/grad_for_eps.html
docs/reference/grad_for_mu_sigma2.html
docs/reference/grad_for_mu_sigma2_wrapper.html
docs/reference/grad_for_weighted_lbb.html
docs/reference/grad_for_weighted_lnorm.html
docs/reference/index.html
docs/reference/initialize_pivec.html
docs/reference/is.flexdog.html
docs/reference/is.mupdog.html
docs/reference/log_sum_exp.html
docs/reference/log_sum_exp_2.html
docs/reference/logit.html
docs/reference/mupdog-1.png
docs/reference/mupdog-2.png
docs/reference/mupdog-3.png
docs/reference/mupdog-4.png
docs/reference/mupdog-5.png
docs/reference/mupdog-6.png
docs/reference/mupdog-7.png
docs/reference/mupdog.html
docs/reference/mupout.html
docs/reference/obj_for_alpha.html
docs/reference/obj_for_eps.html
docs/reference/obj_for_mu_sigma2.html
docs/reference/obj_for_mu_sigma2_wrapper.html
docs/reference/obj_for_rho.html
docs/reference/obj_for_weighted_lbb.html
docs/reference/obj_for_weighted_lnorm.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/pbetabinom_double.html
docs/reference/pen_bias.html
docs/reference/pen_seq_error.html
docs/reference/pivec_from_segmats.html
docs/reference/plot.flexdog.html
docs/reference/plot.mupdog-1.png
docs/reference/plot.mupdog.html
docs/reference/plot_geno-1.png
docs/reference/plot_geno.html
docs/reference/post_prob.html
docs/reference/pp_brent_obj.html
docs/reference/qbetabinom_double.html
docs/reference/rbetabinom_int.html
docs/reference/rflexdog-1.png
docs/reference/rflexdog.html
docs/reference/rgeno.html
docs/reference/snpdat.html
docs/reference/summary.mupdog-1.png
docs/reference/summary.mupdog.html
docs/reference/uitdewilligen.html
docs/reference/uni_em.html
docs/reference/uni_em_const.html
docs/reference/uni_obj.html
docs/reference/uni_obj_const.html
docs/reference/update_R.html
docs/reference/update_dr.html
docs/reference/update_pp_f1.html
docs/reference/update_pp_s1.html
docs/reference/updog.html
docs/reference/wem.html
docs/reference/xi_double.html
docs/reference/xi_fun.html
inst/CITATION
inst/NEWS.md
inst/include/updog.h
inst/include/updog_RcppExports.h
man/ashpen_fun.Rd man/betabinom.Rd man/compute_all_log_bb.Rd man/compute_all_phifk.Rd man/compute_all_post_prob.Rd man/convolve.Rd man/dbernbinom.Rd man/dbetabinom_alpha_beta_double.Rd man/dbetabinom_double.Rd man/dc_dtau.Rd man/df_deps.Rd man/dlbeta_dc.Rd man/dlbeta_deps.Rd man/dlbeta_dh.Rd man/dlbeta_dtau.Rd man/dlbeta_dxi.Rd man/doutdist.Rd man/dpen_deps.Rd man/dpen_dh.Rd man/dr_pen.Rd man/dxi_df.Rd man/dxi_dh.Rd man/elbo.Rd man/eta_double.Rd man/eta_fun.Rd man/expit.Rd man/f1_obj.Rd man/flex_update_pivec.Rd man/flexdog.Rd man/flexdog_full.Rd man/flexdog_obj.Rd man/flexdog_obj_out.Rd man/get_bivalent_probs.Rd man/get_bivalent_probs_dr.Rd man/get_conv_inner_weights.Rd man/get_dimname.Rd man/get_hyper_weights.Rd man/get_inner_weights.Rd man/get_probk_vec.Rd man/get_q_array.Rd man/get_uni_rep.Rd man/get_wik_mat.Rd man/get_wik_mat_out.Rd man/grad_for_eps.Rd man/grad_for_mu_sigma2.Rd man/grad_for_mu_sigma2_wrapper.Rd man/grad_for_weighted_lbb.Rd man/grad_for_weighted_lnorm.Rd man/initialize_pivec.Rd man/is.flexdog.Rd man/is.mupdog.Rd man/log_sum_exp.Rd man/log_sum_exp_2.Rd man/logit.Rd man/mupdog.Rd man/mupout.Rd man/obj_for_alpha.Rd man/obj_for_eps.Rd man/obj_for_mu_sigma2.Rd man/obj_for_mu_sigma2_wrapper.Rd man/obj_for_rho.Rd man/obj_for_weighted_lbb.Rd man/obj_for_weighted_lnorm.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/pbetabinom_double.Rd man/pen_bias.Rd man/pen_seq_error.Rd man/pivec_from_segmats.Rd man/plot.flexdog.Rd man/plot.mupdog.Rd man/plot_geno.Rd man/post_prob.Rd man/pp_brent_obj.Rd man/qbetabinom_double.Rd man/rbetabinom_int.Rd man/rflexdog.Rd man/rgeno.Rd man/snpdat.Rd man/summary.mupdog.Rd man/uitdewilligen.Rd man/uni_em.Rd man/uni_em_const.Rd man/uni_obj.Rd man/uni_obj_const.Rd man/update_R.Rd man/update_dr.Rd man/update_pp_f1.Rd man/update_pp_s1.Rd man/updog.Rd man/wem.Rd man/xi_double.Rd man/xi_fun.Rd
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/outlier_fns.cpp
src/pref.cpp
src/util_funs.cpp
src/weighted_em_const.cpp
tests/testthat.R
tests/testthat/cvx_prob.RDS
tests/testthat/out_err.RData
tests/testthat/test_cvxr.R tests/testthat/test_dbetabinom.R tests/testthat/test_dr.R tests/testthat/test_f1_genotyping.R tests/testthat/test_flexdog.R tests/testthat/test_generics.R tests/testthat/test_gradients.R tests/testthat/test_mupdog.R tests/testthat/test_objectives.R tests/testthat/test_oracle.R tests/testthat/test_pref.R tests/testthat/test_rflexdog.R tests/testthat/test_uni_gem.R tests/testthat/test_utils.R
tests/testthat/testdat.RData
vignettes/genobib.bib
vignettes/oracle_calculations.Rmd vignettes/parallel_computing.Rmd vignettes/simulate_ngs.Rmd vignettes/smells_like_updog.Rmd
dcgerard/updog documentation built on Aug. 19, 2018, 11:33 p.m.