Files in dcgerard/updogAlpha

Using Parental Data for Offspring Genotyping

.Rbuildignore

.gitignore

.travis.yml

DESCRIPTION

LICENSE

NAMESPACE

R/RcppExports.R R/bad_updog_ideas.R R/data.R R/diagnostics.R R/est_seq.R R/generics.R R/misc_plot.R R/update_all.R R/updog.R R/updog_bb.R README.Rmd README.md

appveyor.yml

codecov.yml

data/snpdat.rda

docs/.gitignore

docs/LICENSE.html

docs/articles/genobib.bib

docs/articles/index.html

docs/articles/smells_like_updog.html

docs/articles/smells_like_updog_files/figure-html/unnamed-chunk-11-1.png

docs/articles/smells_like_updog_files/figure-html/unnamed-chunk-5-1.png

docs/articles/smells_like_updog_files/figure-html/unnamed-chunk-7-1.png

docs/articles/smells_like_updog_files/figure-html/unnamed-chunk-8-1.png

docs/authors.html

docs/index.html

docs/jquery.sticky-kit.min.js

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/reference/bb_post.html

docs/reference/bb_simple_post.html

docs/reference/bbpost_double.html

docs/reference/bbpost_tot.html

docs/reference/bin_post.html

docs/reference/colSums_cpp.html

docs/reference/dbeta_dd.html

docs/reference/dbeta_deps.html

docs/reference/dbeta_dh.html

docs/reference/dbeta_dl.html

docs/reference/dbeta_dprop.html

docs/reference/dbeta_dr.html

docs/reference/dbeta_dr_ell.html

docs/reference/dbeta_ds.html

docs/reference/dbeta_dtau.html

docs/reference/dbeta_dtau_withxi.html

docs/reference/dbetabinom.html

docs/reference/dbetabinom_cpp.html

docs/reference/dbetabinom_mu_rho.html

docs/reference/dbetabinom_mu_rho_cpp.html

docs/reference/dbetabinom_mu_rho_cpp_double.html

docs/reference/dd_ds.html

docs/reference/deps_dell.html

docs/reference/df_deps.html

docs/reference/dh_dr.html

docs/reference/dh_dtau.html

docs/reference/dhyper_cpp.html

docs/reference/dupdog.html

docs/reference/dxi_dd.html

docs/reference/dxi_df.html

docs/reference/est_seq_error.html

docs/reference/est_seq_post.html

docs/reference/expit.html

docs/reference/fn_cov_mle.html

docs/reference/get_cov_mle.html

docs/reference/get_dimname.html

docs/reference/get_out_prop.html

docs/reference/get_parent_outprop.html

docs/reference/get_prob_geno.html

docs/reference/get_pvec.html

docs/reference/get_q_array.html

docs/reference/get_q_array_cpp.html

docs/reference/get_transition_mat.html

docs/reference/good_bb_obj.html

docs/reference/grad_offspring.html

docs/reference/grad_offspring_mat.html

docs/reference/grad_offspring_mat_original.html

docs/reference/grad_offspring_original.html

docs/reference/grad_offspring_weights.html

docs/reference/grad_offspring_weights_original.html

docs/reference/grad_parent.html

docs/reference/grad_parent_reparam.html

docs/reference/grad_wrapp_all.html

docs/reference/index.html

docs/reference/is.updog.html

docs/reference/logsumexp.html

docs/reference/obj_offspring.html

docs/reference/obj_offspring_reparam.html

docs/reference/obj_offspring_vec.html

docs/reference/obj_offspring_weights.html

docs/reference/obj_offspring_weights_reparam.html

docs/reference/obj_parent.html

docs/reference/obj_parent_reparam.html

docs/reference/obj_wrapp_all.html

docs/reference/out_grad_parent.html

docs/reference/out_grad_wrapp.html

docs/reference/out_obj_wrapp.html

docs/reference/outlier_bb_obj.html

docs/reference/outlier_grad.html

docs/reference/outlier_obj.html

docs/reference/pbias.html

docs/reference/pbias_double.html

docs/reference/plot.updog.html

docs/reference/plot_beta_dist.html

docs/reference/plot_beta_dist_gg.html

docs/reference/plot_geno.html

docs/reference/plot_geno_base.html

docs/reference/plot_problines.html

docs/reference/rbetabinom_mu_rho.html

docs/reference/rupdog.html

docs/reference/screen_oracle.html

docs/reference/snpdat.html

docs/reference/summary.updog.html

docs/reference/up_bb_fix.html

docs/reference/up_bb_obj.html

docs/reference/up_fix.html

docs/reference/up_max_bb.html

docs/reference/up_obj.html

docs/reference/update_good.html

docs/reference/updog-1.png

docs/reference/updog.html

docs/reference/updog_iterate.html

docs/reference/updog_maximize.html

docs/reference/updog_mcmc.html

docs/reference/updog_old.html

docs/reference/updog_update_all.html

docs/reference/updog_vanilla.html

inst/CITATION

man/bb_post.Rd man/bb_simple_post.Rd man/bbpost_double.Rd man/bbpost_tot.Rd man/bin_post.Rd man/colSums_cpp.Rd man/dbeta_dd.Rd man/dbeta_deps.Rd man/dbeta_dh.Rd man/dbeta_dl.Rd man/dbeta_dprop.Rd man/dbeta_dr.Rd man/dbeta_dr_ell.Rd man/dbeta_ds.Rd man/dbeta_dtau.Rd man/dbeta_dtau_withxi.Rd man/dbetabinom.Rd man/dbetabinom_cpp.Rd man/dbetabinom_mu_rho.Rd man/dbetabinom_mu_rho_cpp.Rd man/dbetabinom_mu_rho_cpp_double.Rd man/dd_ds.Rd man/deps_dell.Rd man/df_deps.Rd man/dh_dr.Rd man/dh_dtau.Rd man/dhyper_cpp.Rd man/dupdog.Rd man/dxi_dd.Rd man/dxi_df.Rd man/est_seq_error.Rd man/est_seq_post.Rd man/expit.Rd man/fn_cov_mle.Rd man/get_cov_mle.Rd man/get_dimname.Rd man/get_out_prop.Rd man/get_parent_outprop.Rd man/get_prob_geno.Rd man/get_pvec.Rd man/get_q_array.Rd man/get_q_array_cpp.Rd man/get_transition_mat.Rd man/good_bb_obj.Rd man/grad_offspring.Rd man/grad_offspring_mat.Rd man/grad_offspring_mat_original.Rd man/grad_offspring_original.Rd man/grad_offspring_weights.Rd man/grad_offspring_weights_original.Rd man/grad_parent.Rd man/grad_parent_reparam.Rd man/grad_wrapp_all.Rd man/is.updog.Rd man/logsumexp.Rd man/obj_offspring.Rd man/obj_offspring_reparam.Rd man/obj_offspring_vec.Rd man/obj_offspring_weights.Rd man/obj_offspring_weights_reparam.Rd man/obj_parent.Rd man/obj_parent_reparam.Rd man/obj_wrapp_all.Rd man/out_grad_parent.Rd man/out_grad_wrapp.Rd man/out_obj_wrapp.Rd man/outlier_bb_obj.Rd man/outlier_grad.Rd man/outlier_obj.Rd man/pbias.Rd man/pbias_double.Rd man/plot.updog.Rd man/plot_beta_dist.Rd man/plot_beta_dist_gg.Rd man/plot_geno.Rd man/plot_geno_base.Rd man/plot_problines.Rd man/rbetabinom_mu_rho.Rd man/rupdog.Rd man/screen_oracle.Rd man/snpdat.Rd man/summary.updog.Rd man/up_bb_fix.Rd man/up_bb_obj.Rd man/up_fix.Rd man/up_max_bb.Rd man/up_obj.Rd man/update_good.Rd man/updog.Rd man/updog_iterate.Rd man/updog_maximize.Rd man/updog_mcmc.Rd man/updog_old.Rd man/updog_update_all.Rd man/updog_vanilla.Rd

src/.gitignore

src/RcppExports.cpp

src/bb_post.cpp

src/em.cpp

src/gradients.cpp

src/objectives.cpp

src/out_step.cpp

src/parent_contributions.cpp

src/prob_functions.cpp

src/updog.h

src/utitility.cpp

tests/testthat.R

tests/testthat/alpha_err_dat.RDS

tests/testthat/bad_dat.RDS

tests/testthat/bad_vals.RDS

tests/testthat/dat.RDS

tests/testthat/err_list.RDS

tests/testthat/err_list2

tests/testthat/example_snp.RDS

tests/testthat/new_updog_result.RDS

tests/testthat/non_llike_increase_dat.RDS

tests/testthat/obj_wrapp_all_input.RDS

tests/testthat/old_updog_result.RDS

tests/testthat/problem_params.RDS

tests/testthat/test_alpha_err.R tests/testthat/test_bb.R tests/testthat/test_diagnostics.R tests/testthat/test_gradients.R tests/testthat/test_hw.R tests/testthat/test_hyper.R tests/testthat/test_obj_functions.R tests/testthat/test_outprop.R tests/testthat/test_parents.R tests/testthat/test_plot.R tests/testthat/test_plot_na.R tests/testthat/test_problem_params.R tests/testthat/test_seq.R tests/testthat/test_seq_od_zero.R tests/testthat/test_update.R tests/testthat/test_update_all.R

tests/testthat/updog_class.RDS

tests/testthat/updog_obj.RDS

tests/testthat/warn_dat.RDS

ubib.bib

vignettes/genobib.bib

vignettes/smells_like_updog.Rmd

dcgerard/updogAlpha documentation built on May 14, 2019, 3:10 a.m.