46ba66be80711240060f2316963b9c72 *DESCRIPTION
a3be5243a96b6322f0f3e12b50b7f0bc *LICENSE
6cf5bdb203b4b0cee2480345b50db35f *NAMESPACE
06be08d317f01a8ebe098632ca428c91 *R/compute_ss.R
09739566e042d74b3751017ac9153b0f *R/data.R
66de9387436da126035171198c0d3ec6 *R/elbo.R
1f8e6e822ed400f480e1b9619bd24bfc *R/elbo_rss.R
b43d4f306fb1cfe6eff7faee0544c239 *R/elbo_ss.R
1596835bbfbd49fa531267a27cacd25d *R/estimate_residual_variance.R
9c51561a2841796f7dd541677a17b587 *R/initialize.R
91c7e3f97510ea62e05091fcb47f161b *R/initialize_rss.R
df6d433909cc86f2c2647b26d386b2b0 *R/predict.susie.R
aae0c804172aa5aeaf66f970107abf0b *R/remove_null_effects.R
99ea33d5c27ff438aa5d6408bb6d0ae6 *R/set_R_attributes.R
06f836dbed4b91b0f67645a0538ab757 *R/set_X_attributes.R
d9a5825c6c1be6bf5ae7a5427f37a127 *R/single_effect_regression.R
2d5d9b6ea1e706321d2c7a8bb47b92fe *R/single_effect_regression_rss.R
c9a04a1b9d80830802906d9bc3a8f1de *R/single_effect_regression_ss.R
f9718ca4b152f6a1d4d3d0ea71247f24 *R/sparse_multiplication.R
5fb69a54bc552f32672b95155d2f563d *R/summary.susie.R
d82ce1ad467b2a85c4d8ceade84726f8 *R/susie.R
e0ef681901465d24f47f9139cb2c086a *R/susieR-package.R
d27fbda5b06f87333e617d52d0be0b25 *R/susie_plot_changepoint.R
173a09862e3284872dc4c715253609e1 *R/susie_plots.R
4834606d59a625a0f72f5da637b6512d *R/susie_rss.R
8b6fdb9ddacaae7cc82e6819cd1e3b40 *R/susie_ss.R
25ef9bc05025a082bb667a11839edfc2 *R/susie_trendfilter.R
ed13f227e0bbb81002358315f78f147f *R/susie_utils.R
ea4488808dba40828ee77e5b679a6001 *R/susie_zzz_auto.R
7f10f37aaaed6dbfe4a473e7ba2f2cc7 *R/trend_filtering_multiplication.R
d909b04c45682cf71d7b4ab483806f23 *R/univariate_regression.R
65a37dc085ffd0988f7aa10f75ee315a *R/update_each_effect.R
33b8522a20dfd18abf1826b09ab973b6 *R/update_each_effect_rss.R
88d31baf0f9b67e8b71af983da35eeaf *R/update_each_effect_ss.R
51034df4e2ee40aba421c2c35e1606ff *README.md
870506b7d952085aa88384b8d60c1f6a *build/partial.rdb
9488d0f209aeb0ca8dc17e6a406c6a4d *build/vignette.rds
6f94bc2019fd6794a159a32c0c90ee44 *data/FinemappingConvergence.RData
61376f255dd2f40420a96191c04f8aa2 *data/N2finemapping.RData
96362a90fc55f3497c82b2df8238d5b0 *data/N3finemapping.RData
8bda8428d1ec33c6532164061a2418fb *data/SummaryConsistency.RData
4ffe4de2b91dd08c42acd8621707990d *inst/CITATION
055877603aa7eb964c256198acebf53e *inst/analysis/optimize.Rmd
abe7af4381abc51da356118e308f5642 *inst/analysis/test_susie_auto.Rmd
5aaee5b393ac8af120d65092042ab6cb *inst/analysis/testing.Rmd
c734e74dd9fd1bf669701c5aaf747a7c *inst/code/caviar.R
58b5976fa2773a46e2b380aa6fa94f99 *inst/code/dap-g.py
0c68bb7496e0781bdee112427f04fd46 *inst/code/finemap.R
c940915206e96508fb8ef34af4142fe3 *inst/code/gen_original_results.R
2eaafa198851004938f32bf2a6817d31 *inst/datafiles/N3finemapping.CAVIAR.RData
270949bf51a2c3fe6069901152d68360 *inst/datafiles/N3finemapping.DAP.RData
0a8062f7f5435e89fcc7f629d0f3a332 *inst/datafiles/N3finemapping.FINEMAP.RData
6b5aa0233bdb8b42b53e068b06a0529f *inst/doc/finemapping.R
fec23052ac0dcf572ad2c82025756b10 *inst/doc/finemapping.Rmd
bca44c2e64f9b57923ef6931100e56d8 *inst/doc/finemapping.html
a63d416570972cdb6772b369ad26c966 *inst/doc/finemapping_summary_statistics.R
fa15052d215f2f5556b026a05cc5efa0 *inst/doc/finemapping_summary_statistics.Rmd
bab2113138e710a85cff786ce54bc377 *inst/doc/finemapping_summary_statistics.html
57611455618bd6180cfc2c23aaf4d286 *inst/doc/l0_initialization.R
5cc4f68e16d9a9b2dadc1d6b1158e0c1 *inst/doc/l0_initialization.Rmd
610c5c4c02fae1c86f7841c72be5a0bb *inst/doc/l0_initialization.html
847f3d38c652363bfefafb6b41dd33b8 *inst/doc/mwe.R
dd4899d3f6c1d8771df2df2ec82e9281 *inst/doc/mwe.Rmd
8e8471cf1a97445aa7852c53630266ac *inst/doc/mwe.html
9e43fd3c04a2afdcb2b4722bb3629145 *inst/doc/sparse_matrix_strategy.R
740085e45b6b363a3e6dafa40049217b *inst/doc/sparse_matrix_strategy.Rmd
0d1bbca61970befce886606c080bfd2c *inst/doc/sparse_matrix_strategy.html
b2479c2657e4c4fb2c9ea8ac2bb54d12 *inst/doc/sparse_susie_eval.R
c207a8c9000f7b33ddfb15902112636b *inst/doc/sparse_susie_eval.Rmd
31259dc301dc4a05fb74853873f07537 *inst/doc/sparse_susie_eval.html
74cad49a1e9566d35a1f356a861d2f75 *inst/doc/susie_refine.R
1fb5c2e7e18da9ffae9ec6c05ec11774 *inst/doc/susie_refine.Rmd
984e764eeb1ada37e77308b2832e085c *inst/doc/susie_refine.html
2ae269b358457096e0bbff85ad69f6ac *inst/doc/susierss_diagnostic.R
66ff75eb63b8caa710b38b498c47bbc8 *inst/doc/susierss_diagnostic.Rmd
5ce9fd7d46ab1e35ccbd0242a9b1dd32 *inst/doc/susierss_diagnostic.html
f6843e7ba9577a8944441986dbdaf6ee *inst/doc/trend_filtering.R
e44146ea74e39426234769df27b777da *inst/doc/trend_filtering.Rmd
94c76d230385954a9b6014db8405f91f *inst/doc/trend_filtering.html
9798c9e4714beec667ed3e254b146401 *inst/doc/trendfiltering_derivations.Rnw
df41f9cc3202b8d0f087d59b28a96133 *inst/doc/trendfiltering_derivations.pdf
5ef7ec32160a728a8e0421664a22884a *inst/misc/post-commit.sh
2db00a6441f8de02698d0a6aede1f6c9 *inst/misc/pre-commit.sh
4f5b52001a426816a1962b6b71f77422 *man/FinemappingConvergence.Rd
e763f77c72fa6944f1c2bb6bce6ed2b6 *man/N2finemapping.Rd
d1c21b3999b672ba1e9663f7b2434920 *man/N3finemapping.Rd
48bc5d6f9a08fc55c8b9ba63e8ac92aa *man/SummaryConsistency.Rd
b85fc88bd1e6f7346601bf954f32d388 *man/coef.susie.Rd
9244037f4de7f2995a8133f6a108e76c *man/compute_ss.Rd
654c21a0db37d1ea582e2bc3ae259d23 *man/compute_suff_stat.Rd
0263103422b1fd58011efdb3af17ab2a *man/estimate_s_rss.Rd
7363d7fb09ff3185c9fcd7296ccb72d5 *man/get_cs_correlation.Rd
81d454615393c27a32f6452747e887f2 *man/kriging_rss.Rd
9b76bea17819c05458c65d8357744e0f *man/predict.susie.Rd
df3259511ae91d3f022331a4252e7df0 *man/single_effect_regression.Rd
38fcf364c50e011ab8996b9d495670e6 *man/summary.susie.Rd
7dd1dfb58ba9a2d064191a1cb94d688f *man/susie.Rd
cb8675f9dc9bb3eb9f25efe64d408858 *man/susieR-package.Rd
6685782d373ee0516221d0972f5e0e5f *man/susie_auto.Rd
a2d3fca492422c7bd7295b2e833f191a *man/susie_get_methods.Rd
c7ea1c7808d619acd070840f622eae2c *man/susie_init_coef.Rd
2ec9ee36c9eb5edca737de1d42f5ee8a *man/susie_plot_changepoint.Rd
a2143177260a97bf973554e3c9b719ca *man/susie_plots.Rd
241f943d3703cb10b60b967af1ac9b13 *man/susie_rss.Rd
75576ac542ebc86504162c114da8b39d *man/susie_trendfilter.Rd
979d2121e527a5bb587e9a6df64e4fdf *man/univariate_regression.Rd
0feb689a4008d1303d5e38f641332584 *tests/README.md
9e57750da8ea08e98bb12218b20dc650 *tests/testthat.R
641aa8e6bbf5a81243c7c25f08f4ebd8 *tests/testthat/ER2_original_res.rds
db86460c48caeb98522a147915ab6d56 *tests/testthat/ER2_rss_lambda0_res.rds
bb4e54e9abf6f40e0cb5ce8ba700380b *tests/testthat/ER2_rss_lambda1_res.rds
ceec7a57ce1ffa3bb0c22b2ce3ad2d13 *tests/testthat/Eloglik_original_res.rds
58f8aba120e11d59a3eca0ae427ac244 *tests/testthat/Eloglik_rss_lambda0_res.rds
156ba213386cd4cfa87e03ccee0dfd6a *tests/testthat/Eloglik_rss_lambda1_res.rds
52f91743306a8660179e4d0ca51ad2e8 *tests/testthat/SER_original_res.rds
57ec0e4dbbf13b7e5fbebc3cc7e82653 *tests/testthat/SER_rss_lambda0_res.rds
376b6e71bcab1844978ddc7a784aaab2 *tests/testthat/SER_rss_lambda1_res.rds
589846a8b3ce89afbc0709dc9eb90d1f *tests/testthat/est_V_debug.rds
2d93b6da744c033d59762c59fde3b0c8 *tests/testthat/helper_testthat.R
e345bb717196a7d27aa5200bec69bd76 *tests/testthat/objective_original_res.rds
266ae5b06d135c242f507d5aa995d32e *tests/testthat/objective_rss_lambda0_res.rds
6d17fda36436dde063f7b6e53f6965e5 *tests/testthat/objective_rss_lambda1_res.rds
f5f2da9ad0b2a1a90e8380fbfb8aea64 *tests/testthat/singleReg_original_res.rds
e36128656466eca93f2c80005d888429 *tests/testthat/singleReg_rss_lambda0_res.rds
0cd6165f3d8ae6388a10526b9be2b023 *tests/testthat/singleReg_rss_lambda1_res.rds
ccb9582205e0480715230135ce6a3455 *tests/testthat/susiefit_original_res.rds
f6b82c192b1c4ff50a1a6c4e3418868e *tests/testthat/susiefit_original_res2.rds
e9ae6aeaa424d458e4c29c2d48ba448d *tests/testthat/susiefit_original_res3.rds
2e7d1f9dd1029e389a2b0e71de0dd5f3 *tests/testthat/susiefit_original_res4.rds
fd0afe6277489e0cbaa2dd2d74adedcc *tests/testthat/susierssfit_lambda0_res.rds
b776e42c6e5fde08590a1af865803f97 *tests/testthat/susierssfit_lambda1_res.rds
57fb271cf938e53ba9a8f7ec1342a567 *tests/testthat/test_Eloglik.R
a001e268d4692558718b83aa58dd7c70 *tests/testthat/test_Eloglik_rss.R
e9e23b1315a03ab3fcc92c62d2c02116 *tests/testthat/test_SER_posterior_e_loglik.R
c0c0e0550017e6f6ccf29c5616ad44d8 *tests/testthat/test_SER_posterior_e_loglik_rss.R
936ba383fad03cb0a1b6be32256ba788 *tests/testthat/test_comput_tf.R
96f99c788755ca3a08da70153036c8ad *tests/testthat/test_est_V.R
055030628a94d4ee6f24ebf3331defc6 *tests/testthat/test_get_ER2.R
23ed62870e2277c8b1241aae0e6757f6 *tests/testthat/test_get_ER2_rss.R
343ce829dd2c36d490d2a107c544f6c2 *tests/testthat/test_get_pip.R
97b24194021c1fa1aba8e3b773f66db9 *tests/testthat/test_get_samples.R
b2f7e254e44e9b3078ceea178ed43870 *tests/testthat/test_init.R
89ab77ee6bbeeafd7e569ff1a76fb977 *tests/testthat/test_intercept_standardize.R
8af8e92161cd582ffec3960372f0cca2 *tests/testthat/test_null_weight.R
4b61b24766e891bceb62dcee70a0bcf7 *tests/testthat/test_prior_weights.R
280c6f97da37f8fd5ddd08c70616e870 *tests/testthat/test_single_effect_regression.R
7ad0a407abae6fc4271dcc63849b3457 *tests/testthat/test_single_effect_regression_rss.R
c4c71d7aac11155b4fed7b71bf785364 *tests/testthat/test_small_resid.R
e283347cf2cd88f25517948438fbd104 *tests/testthat/test_sparse_multiplication.R
4c2b5e312098bd3fcaa900ff22d830d8 *tests/testthat/test_sparse_safe_colScale.R
f4d591cb4aafc25b18c4251f6fb335bf *tests/testthat/test_susie.R
e992ff1dc628ac614ce8a7d6f9757805 *tests/testthat/test_susie_XtX_Xty.R
154845e77ed5405e11d7595b34190d2f *tests/testthat/test_susie_beta_se.R
8a9e21ea28eb17602a67eca3b70581f2 *tests/testthat/test_susie_get_objective.R
38f3520026081f89bf763683babd2fd7 *tests/testthat/test_susie_rss.R
7fbf7a163ae3f7c15dc1ada50c91c8ad *tests/testthat/test_susie_rss_get_objective.R
f33e5b8afda3a5b60f3f1e0d16c2fd0c *tests/testthat/test_susie_trendfilter.R
06d7cb90bd297b39e24cd32ce04b8be5 *tests/testthat/test_update_each_effect.R
128466df1e91cc350c912581ec186b3b *tests/testthat/test_update_each_effect_rss.R
e326fce5c8e7db5a5cd7fe44c8cf80e9 *tests/testthat/vbupdate_original_res.rds
5c2587d93a66dd84a32e6453e26062a3 *tests/testthat/vbupdate_rss_lambda0_res.rds
348e39186218130a1dce2068fed80a9e *tests/testthat/vbupdate_rss_lambda1_res.rds
fec23052ac0dcf572ad2c82025756b10 *vignettes/finemapping.Rmd
fa15052d215f2f5556b026a05cc5efa0 *vignettes/finemapping_summary_statistics.Rmd
5cc4f68e16d9a9b2dadc1d6b1158e0c1 *vignettes/l0_initialization.Rmd
dd4899d3f6c1d8771df2df2ec82e9281 *vignettes/mwe.Rmd
740085e45b6b363a3e6dafa40049217b *vignettes/sparse_matrix_strategy.Rmd
c207a8c9000f7b33ddfb15902112636b *vignettes/sparse_susie_eval.Rmd
1fb5c2e7e18da9ffae9ec6c05ec11774 *vignettes/susie_refine.Rmd
66ff75eb63b8caa710b38b498c47bbc8 *vignettes/susierss_diagnostic.Rmd
e44146ea74e39426234769df27b777da *vignettes/trend_filtering.Rmd
9798c9e4714beec667ed3e254b146401 *vignettes/trendfiltering_derivations.Rnw
8c9d761847070677be0c9acbeebf3690 *vignettes/trendfiltering_derivations.bib
