Files in dcgerard/vicar

Various Ideas for Confounder Adjustment in Regression

.Rbuildignore

.github/.gitignore

.github/workflows/R-CMD-check.yaml

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/RcppExports.R R/ash_wrap.R R/backwash.R R/caw.R R/clean_my_p.R R/data.R R/em_miss.R R/fa_tester.R R/mouthwash.R R/mouthwash_normal_em.R R/mouthwash_uniform_coordinate.R R/mouthwash_uniform_em.R R/plot_methods.R R/ruv2.R R/ruv2_fa.R R/ruv3.R R/ruv4.R R/ruvb.R R/ruvimpute.R R/vicar.R README.Rmd README.md

data/sim_gtex.rda

docs/articles/customFA.html

docs/articles/customFA_files/figure-html/unnamed-chunk-4-1.png

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

docs/articles/customFA_files/header-attrs-2.7/header-attrs.js

docs/articles/customFA_files/header-attrs-2.9/header-attrs.js

docs/articles/custom_prior.html

docs/articles/custom_prior_files/header-attrs-2.7/header-attrs.js

docs/articles/custom_prior_files/header-attrs-2.9/header-attrs.js

docs/articles/index.html

docs/articles/sample_analysis.html

docs/articles/sample_analysis_files/figure-html/unnamed-chunk-10-1.png

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

docs/articles/sample_analysis_files/header-attrs-2.7/header-attrs.js

docs/articles/sample_analysis_files/header-attrs-2.9/header-attrs.js

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Rplot001.png

docs/reference/Rplot002.png

docs/reference/Rplot003.png

docs/reference/Rplot004.png

docs/reference/Rplot005.png

docs/reference/Rplot006.png

docs/reference/adjust_by_t.html

docs/reference/ash_ruv2.html

docs/reference/ash_ruv4.html

docs/reference/ash_wrap.html

docs/reference/back_elbo.html

docs/reference/back_fix.html

docs/reference/back_obj.html

docs/reference/back_update_phi.html

docs/reference/back_update_pi.html

docs/reference/back_update_qbeta.html

docs/reference/back_update_v.html

docs/reference/back_update_xi.html

docs/reference/backwash-1.png

docs/reference/backwash-2.png

docs/reference/backwash-3.png

docs/reference/backwash.html

docs/reference/backwash_second_step.html

docs/reference/bfa_gd_gibbs.html

docs/reference/bfa_gs.html

docs/reference/bfa_gs_linked.html

docs/reference/bfa_gs_linked_gibbs.html

docs/reference/bfa_gs_linked_gibbs_r.html

docs/reference/bfa_wrapper.html

docs/reference/bfl.html

docs/reference/brent_obj_norm.html

docs/reference/bsvd.html

docs/reference/calc_lfsr.html

docs/reference/calc_lfsr_g.html

docs/reference/calc_mean_g.html

docs/reference/calc_quantiles_g.html

docs/reference/caw.html

docs/reference/clean_my_p.html

docs/reference/clean_my_stats.html

docs/reference/cruv4.html

docs/reference/cruv4_multicov.html

docs/reference/dnormalmix.html

docs/reference/dt_wrap.html

docs/reference/em_miss.html

docs/reference/em_miss_fix.html

docs/reference/em_miss_fix_fast.html

docs/reference/em_miss_obj.html

docs/reference/em_miss_obj_fast.html

docs/reference/fa_ml.html

docs/reference/fa_out_test.html

docs/reference/fa_tester.html

docs/reference/fa_tester_ruvb.html

docs/reference/fix_caw.html

docs/reference/fix_caw_wrapper.html

docs/reference/gdfa.html

docs/reference/get_grid_var.html

docs/reference/hard_impute.html

docs/reference/hier_fun.html

docs/reference/impute_block.html

docs/reference/impute_ruv_reproduce.html

docs/reference/index.html

docs/reference/initialize_mixing_prop.html

docs/reference/knn_wrapper.html

docs/reference/missforest_wrapper.html

docs/reference/mouthwash-1.png

docs/reference/mouthwash-2.png

docs/reference/mouthwash-3.png

docs/reference/mouthwash.html

docs/reference/mouthwash_coordinate.html

docs/reference/mouthwash_second_step.html

docs/reference/mouthwash_z_grad.html

docs/reference/normal_mix_fix.html

docs/reference/normal_mix_fix_wrapper.html

docs/reference/normal_mix_llike.html

docs/reference/normal_mix_llike_wrapper.html

docs/reference/normal_prior.html

docs/reference/pca_2step.html

docs/reference/pca_naive.html

docs/reference/pca_ruv2.html

docs/reference/pcaruv2_fix.html

docs/reference/pcaruv2_obj.html

docs/reference/plot.backwash.html

docs/reference/plot.mouthwash.html

docs/reference/plot.ruvb.html

docs/reference/prior_fun_wrapper.html

docs/reference/pt_wrap.html

docs/reference/ptdiff.html

docs/reference/ptdiff_mat.html

docs/reference/ptdiff_mat_log.html

docs/reference/qmle_obj.html

docs/reference/qmle_obj_basic.html

docs/reference/qmle_ruv2.html

docs/reference/qmle_ruv2_lambda_grid.html

docs/reference/qr_ident.html

docs/reference/rmixnorm.html

docs/reference/rnormalmix.html

docs/reference/rotate_model.html

docs/reference/rubin_copy.html

docs/reference/ruv3-1.png

docs/reference/ruv3.html

docs/reference/ruvb-1.png

docs/reference/ruvb.html

docs/reference/ruvem.html

docs/reference/ruvimpute.html

docs/reference/sim_gtex.html

docs/reference/smell_my_p.html

docs/reference/smell_my_stats.html

docs/reference/softimpute_wrapper.html

docs/reference/tregress_em.html

docs/reference/tregress_fix.html

docs/reference/tregress_obj.html

docs/reference/tregress_obj_wrapper.html

docs/reference/unif_int_grad.html

docs/reference/unif_int_obj.html

docs/reference/uniform_mix_fix.html

docs/reference/uniform_mix_fix_wrapper.html

docs/reference/uniform_mix_llike.html

docs/reference/uniform_mix_llike_wrapper.html

docs/reference/update_f.html

docs/reference/update_lambda.html

docs/reference/update_sig_alpha.html

docs/reference/update_sig_alpha_basic.html

docs/reference/vicar.html

docs/reference/vruv2.html

docs/reference/vruv2_old.html

docs/reference/vruv4-1.png

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docs/reference/vruv4.html

docs/reference/vruvinv.html

inst/CITATION

man/adjust_by_t.Rd man/ash_ruv2.Rd man/ash_ruv4.Rd man/ash_wrap.Rd man/back_elbo.Rd man/back_fix.Rd man/back_obj.Rd man/back_update_phi.Rd man/back_update_pi.Rd man/back_update_qbeta.Rd man/back_update_v.Rd man/back_update_xi.Rd man/backwash.Rd man/backwash_second_step.Rd man/bfa_gd_gibbs.Rd man/bfa_gs.Rd man/bfa_gs_linked.Rd man/bfa_gs_linked_gibbs.Rd man/bfa_gs_linked_gibbs_r.Rd man/bfa_wrapper.Rd man/bfl.Rd man/brent_obj_norm.Rd man/bsvd.Rd man/calc_lfsr.Rd man/calc_lfsr_g.Rd man/calc_mean_g.Rd man/calc_quantiles_g.Rd man/caw.Rd man/clean_my_p.Rd man/clean_my_stats.Rd man/cruv4.Rd man/cruv4_multicov.Rd man/dnormalmix.Rd man/dt_wrap.Rd man/em_miss.Rd man/em_miss_fix.Rd man/em_miss_fix_fast.Rd man/em_miss_obj.Rd man/em_miss_obj_fast.Rd man/fa_ml.Rd man/fa_out_test.Rd man/fa_tester.Rd man/fa_tester_ruvb.Rd man/fix_caw.Rd man/fix_caw_wrapper.Rd man/gdfa.Rd man/get_grid_var.Rd man/hard_impute.Rd man/hier_fun.Rd man/impute_block.Rd man/impute_ruv_reproduce.Rd man/initialize_mixing_prop.Rd man/knn_wrapper.Rd man/missforest_wrapper.Rd man/mouthwash.Rd man/mouthwash_coordinate.Rd man/mouthwash_second_step.Rd man/mouthwash_z_grad.Rd man/normal_mix_fix.Rd man/normal_mix_fix_wrapper.Rd man/normal_mix_llike.Rd man/normal_mix_llike_wrapper.Rd man/normal_prior.Rd man/pca_2step.Rd man/pca_naive.Rd man/pca_ruv2.Rd man/pcaruv2_fix.Rd man/pcaruv2_obj.Rd man/plot.backwash.Rd man/plot.mouthwash.Rd man/plot.ruvb.Rd man/prior_fun_wrapper.Rd man/pt_wrap.Rd man/ptdiff.Rd man/ptdiff_mat.Rd man/ptdiff_mat_log.Rd man/qmle_obj.Rd man/qmle_obj_basic.Rd man/qmle_ruv2.Rd man/qmle_ruv2_lambda_grid.Rd man/qr_ident.Rd man/rmixnorm.Rd man/rnormalmix.Rd man/rotate_model.Rd man/rubin_copy.Rd man/ruv3.Rd man/ruvb.Rd man/ruvem.Rd man/ruvimpute.Rd man/sim_gtex.Rd man/smell_my_p.Rd man/smell_my_stats.Rd man/softimpute_wrapper.Rd man/tregress_em.Rd man/tregress_fix.Rd man/tregress_obj.Rd man/tregress_obj_wrapper.Rd man/unif_int_grad.Rd man/unif_int_obj.Rd man/uniform_mix_fix.Rd man/uniform_mix_fix_wrapper.Rd man/uniform_mix_llike.Rd man/uniform_mix_llike_wrapper.Rd man/update_f.Rd man/update_lambda.Rd man/update_sig_alpha.Rd man/update_sig_alpha_basic.Rd man/vicar.Rd man/vruv2.Rd man/vruv2_old.Rd man/vruv4.Rd man/vruvinv.Rd revdep/check.R

src/Makevars

src/RcppExports.cpp

src/gibbs.cpp

tests/testthat.R

tests/testthat/bfa_gd_examp.Rds

tests/testthat/bfa_gd_examp2.Rds

tests/testthat/bout.RDS

tests/testthat/eg.Rdata

tests/testthat/norm_mout.RDS

tests/testthat/normal_mix_fix_wrapper_err_dat.RDS

tests/testthat/old_mouth.Rds

tests/testthat/outlist.Rd

tests/testthat/ruvbout.RDS

tests/testthat/test_ash.R tests/testthat/test_backwash.R tests/testthat/test_caw.R tests/testthat/test_clean.R tests/testthat/test_em_miss.R tests/testthat/test_hierarchical.R tests/testthat/test_impute.R tests/testthat/test_mouthwash.R tests/testthat/test_normal_mix_fix_wrapper.R tests/testthat/test_plots.R tests/testthat/test_rotate.R tests/testthat/test_ruv2.R tests/testthat/test_ruv3.R tests/testthat/test_ruvb.R tests/testthat/test_subsample.R

tests/testthat/testlist.Rd

tests/testthat/unif_mout.RDS

vignettes/customFA.Rmd vignettes/custom_prior.Rmd vignettes/sample_analysis.Rmd

vignettes/vicar.bib

dcgerard/vicar documentation built on July 7, 2021, 1:08 p.m.