Files in JacobHelwig/covdepGE
Covariate Dependent Graph Estimation

.Rbuildignore

.github/.gitignore

.github/ISSUE_TEMPLATE/bug-report-for-covdepge.md .github/ISSUE_TEMPLATE/feature-request-for-covdepge.md

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

.github/workflows/test-coverage.yaml

.gitignore

DESCRIPTION

LICENSE.md

NAMESPACE

R/RcppExports.R R/cavi.R R/covdepGE_package.R R/data.R R/main.R R/plots.R R/weights.R README.Rmd README.md

TOMS_submission/.RData

TOMS_submission/Algorithm_final/docs.pdf TOMS_submission/Algorithm_final/example_driver/example.R TOMS_submission/Algorithm_final/example_driver/example.Rmd TOMS_submission/Algorithm_final/example_driver/example.pdf

TOMS_submission/Algorithm_final/latex_manual/Rd.sty

TOMS_submission/Algorithm_final/latex_manual/Rd2.tex

TOMS_submission/Algorithm_final/simulation_study/analysis.R TOMS_submission/Algorithm_final/simulation_study/data.R

TOMS_submission/Algorithm_final/simulation_study/experiments/cont_4_cov_dep.sh

TOMS_submission/Algorithm_final/simulation_study/experiments/cont_cov_dep.sh

TOMS_submission/Algorithm_final/simulation_study/experiments/cont_cov_dep_hp.sh

TOMS_submission/Algorithm_final/simulation_study/experiments/cont_cov_dep_hp_full.sh

TOMS_submission/Algorithm_final/simulation_study/experiments/cont_cov_dep_seq.sh

TOMS_submission/Algorithm_final/simulation_study/experiments/cont_cov_dep_sine.sh

TOMS_submission/Algorithm_final/simulation_study/experiments/cont_multi_cov_dep.sh

TOMS_submission/Algorithm_final/simulation_study/main.R TOMS_submission/Algorithm_final/simulation_study/models.R TOMS_submission/Algorithm_final/simulation_study/utils.R

TOMS_submission/Algorithm_final/source/.Rbuildignore

TOMS_submission/Algorithm_final/source/DESCRIPTION

TOMS_submission/Algorithm_final/source/NAMESPACE

TOMS_submission/Algorithm_final/source/R/RcppExports.R TOMS_submission/Algorithm_final/source/R/cavi.R TOMS_submission/Algorithm_final/source/R/covdepGE_package.R TOMS_submission/Algorithm_final/source/R/data.R TOMS_submission/Algorithm_final/source/R/main.R TOMS_submission/Algorithm_final/source/R/plots.R TOMS_submission/Algorithm_final/source/R/weights.R

TOMS_submission/Algorithm_final/source/makefile

TOMS_submission/Algorithm_final/source/man/covdepGE-package.Rd TOMS_submission/Algorithm_final/source/man/covdepGE.Rd TOMS_submission/Algorithm_final/source/man/generateData.Rd TOMS_submission/Algorithm_final/source/man/inclusionCurve.Rd TOMS_submission/Algorithm_final/source/man/matViz.Rd TOMS_submission/Algorithm_final/source/man/plot.covdepGE.Rd

TOMS_submission/Algorithm_final/source/src/.gitignore

TOMS_submission/Algorithm_final/source/src/Makevars

TOMS_submission/Algorithm_final/source/src/Makevars.win

TOMS_submission/Algorithm_final/source/src/RcppExports.cpp

TOMS_submission/Algorithm_final/source/src/code.cpp

TOMS_submission/Algorithm_final/source/src/covdepGE_c.cpp

TOMS_submission/Algorithm_final/testing_material/test.R

TOMS_submission/Algorithm_final/testing_material/test_n225_p10_ntrials5_ubuntu.Rout

TOMS_submission/Algorithm_final/testing_material/test_n225_p10_ntrials5_windows.Rout

TOMS_submission/Algorithm_final/testing_material/test_n225_p25_ntrials5_ubuntu.Rout

TOMS_submission/Algorithm_final/testing_material/test_n225_p25_ntrials5_windows.Rout

TOMS_submission/algorithm_covdepGE.pdf TOMS_submission/algorithm_covdepGE_31723.pdf TOMS_submission/archive/simulation_study/analysis.R TOMS_submission/archive/simulation_study/data.R

TOMS_submission/archive/simulation_study/experiments/cont_cov_dep.sh

TOMS_submission/archive/simulation_study/experiments/cont_cov_dep_hp.sh

TOMS_submission/archive/simulation_study/experiments/cont_cov_dep_hp_full.sh

TOMS_submission/archive/simulation_study/experiments/cont_cov_dep_sine.sh

TOMS_submission/archive/simulation_study/experiments/cont_multi_cov_dep.sh

TOMS_submission/sim_study/.R.Rout

TOMS_submission/sim_study/analysis.R TOMS_submission/sim_study/data.R TOMS_submission/sim_study/dev.R

TOMS_submission/sim_study/experiments/cont_4_cov_dep.sh

TOMS_submission/sim_study/experiments/cont_cov_dep.sh

TOMS_submission/sim_study/experiments/cont_cov_dep_hp.sh

TOMS_submission/sim_study/experiments/cont_cov_dep_hp_full.sh

TOMS_submission/sim_study/experiments/cont_cov_dep_seq.sh

TOMS_submission/sim_study/experiments/cont_cov_dep_sine.sh

TOMS_submission/sim_study/experiments/cont_multi_cov_dep.sh

TOMS_submission/sim_study/experiments/z1/cont_cov_dep_ntrials50_p100_n1_75_n2_75_n3_75_2023-02-03_00-12.Rout

TOMS_submission/sim_study/experiments/z1/cont_cov_dep_ntrials50_p10_n1_75_n2_75_n3_75_2023-02-02_18-15.Rout

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TOMS_submission/sim_study/experiments/z1/cont_cov_dep_ntrials50_p50_n1_75_n2_75_n3_75_2023-02-02_20-23.Rout

TOMS_submission/sim_study/experiments/z1/loggle/cont_cov_dep_ntrials50_p100_n1_75_n2_75_n3_75_2023-12-21_16-30.Rout

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TOMS_submission/sim_study/experiments/z1_hp/cont_cov_dep_grid_search_ntrials50_p100_n1_75_n2_75_n3_75_2023-02-02_19-12.Rout

TOMS_submission/sim_study/experiments/z1_hp/cont_cov_dep_grid_search_ntrials50_p10_n1_75_n2_75_n3_75_2023-02-02_18-14.Rout

TOMS_submission/sim_study/experiments/z1_hp/cont_cov_dep_grid_search_ntrials50_p25_n1_75_n2_75_n3_75_2023-02-02_18-19.Rout

TOMS_submission/sim_study/experiments/z1_hp/cont_cov_dep_grid_search_ntrials50_p50_n1_75_n2_75_n3_75_2023-02-02_18-31.Rout

TOMS_submission/sim_study/experiments/z1_hp/cont_cov_dep_model_average_ntrials50_p100_n1_75_n2_75_n3_75_2023-02-03_02-15.Rout

TOMS_submission/sim_study/experiments/z1_hp/cont_cov_dep_model_average_ntrials50_p10_n1_75_n2_75_n3_75_2023-02-02_22-39.Rout

TOMS_submission/sim_study/experiments/z1_hp/cont_cov_dep_model_average_ntrials50_p25_n1_75_n2_75_n3_75_2023-02-02_22-57.Rout

TOMS_submission/sim_study/experiments/z1_hp/cont_cov_dep_model_average_ntrials50_p50_n1_75_n2_75_n3_75_2023-02-02_23-52.Rout

TOMS_submission/sim_study/experiments/z1_hp_full/cont_cov_dep_grid_search_ntrials50_p100_n1_75_n2_75_n3_75_2023-02-02_21-49.Rout

TOMS_submission/sim_study/experiments/z1_hp_full/cont_cov_dep_grid_search_ntrials50_p10_n1_75_n2_75_n3_75_2023-02-02_18-12.Rout

TOMS_submission/sim_study/experiments/z1_hp_full/cont_cov_dep_grid_search_ntrials50_p25_n1_75_n2_75_n3_75_2023-02-02_18-28.Rout

TOMS_submission/sim_study/experiments/z1_hp_full/cont_cov_dep_grid_search_ntrials50_p50_n1_75_n2_75_n3_75_2023-02-02_19-20.Rout

TOMS_submission/sim_study/experiments/z1_hp_full/cont_cov_dep_hybrid_ntrials50_p100_n1_75_n2_75_n3_75_2023-02-03_15-27.Rout

TOMS_submission/sim_study/experiments/z1_hp_full/cont_cov_dep_hybrid_ntrials50_p10_n1_75_n2_75_n3_75_2023-02-03_11-49.Rout

TOMS_submission/sim_study/experiments/z1_hp_full/cont_cov_dep_hybrid_ntrials50_p25_n1_75_n2_75_n3_75_2023-02-03_12-05.Rout

TOMS_submission/sim_study/experiments/z1_hp_full/cont_cov_dep_hybrid_ntrials50_p50_n1_75_n2_75_n3_75_2023-02-03_12-58.Rout

TOMS_submission/sim_study/experiments/z1_seq/cont_cov_dep_seq_ntrials50_p100_n1_75_n2_75_n3_75_2023-09-13_02-28.Rout

TOMS_submission/sim_study/experiments/z1_seq/cont_cov_dep_seq_ntrials50_p10_n1_75_n2_75_n3_75_2023-09-12_23-56.Rout

TOMS_submission/sim_study/experiments/z1_seq/cont_cov_dep_seq_ntrials50_p25_n1_75_n2_75_n3_75_2023-09-13_00-03.Rout

TOMS_submission/sim_study/experiments/z1_seq/cont_cov_dep_seq_ntrials50_p50_n1_75_n2_75_n3_75_2023-09-13_00-32.Rout

TOMS_submission/sim_study/experiments/z1_sine/cont_cov_dep_sine_ntrials50_p100_n1_75_n2_75_n3_75_2023-09-12_19-42.Rout

TOMS_submission/sim_study/experiments/z1_sine/cont_cov_dep_sine_ntrials50_p10_n1_75_n2_75_n3_75_2023-09-12_13-38.Rout

TOMS_submission/sim_study/experiments/z1_sine/cont_cov_dep_sine_ntrials50_p25_n1_75_n2_75_n3_75_2023-09-12_14-13.Rout

TOMS_submission/sim_study/experiments/z1_sine/cont_cov_dep_sine_ntrials50_p50_n1_75_n2_75_n3_75_2023-09-12_15-43.Rout

TOMS_submission/sim_study/experiments/z1_sine/loggle/cont_cov_dep_sine_ntrials50_p100_n1_75_n2_75_n3_75_2023-12-17_22-56.Rout

TOMS_submission/sim_study/experiments/z1_sine/loggle/cont_cov_dep_sine_ntrials50_p10_n1_75_n2_75_n3_75_2023-12-26_17-24.Rout

TOMS_submission/sim_study/experiments/z1_sine/loggle/cont_cov_dep_sine_ntrials50_p25_n1_75_n2_75_n3_75_2023-12-26_20-27.Rout

TOMS_submission/sim_study/experiments/z1_sine/loggle/cont_cov_dep_sine_ntrials50_p50_n1_75_n2_75_n3_75_2023-12-27_03-10.Rout

TOMS_submission/sim_study/experiments/z2/cont_multi_cov_dep_ntrials50_p100_n_25_2023-02-03_17-07.Rout

TOMS_submission/sim_study/experiments/z2/cont_multi_cov_dep_ntrials50_p100_n_25_2023-02-04_13-15.Rout

TOMS_submission/sim_study/experiments/z2/cont_multi_cov_dep_ntrials50_p10_n_25_2023-02-03_10-15.Rout

TOMS_submission/sim_study/experiments/z2/cont_multi_cov_dep_ntrials50_p25_n_25_2023-02-03_10-56.Rout

TOMS_submission/sim_study/experiments/z2/cont_multi_cov_dep_ntrials50_p50_n_25_2023-02-03_12-43.Rout

TOMS_submission/sim_study/experiments/z2/loggle/cont_multi_cov_dep_ntrials50_p100_n_25_2023-12-21_16-31.Rout

TOMS_submission/sim_study/experiments/z2/loggle/cont_multi_cov_dep_ntrials50_p10_n_25_2023-12-25_00-40.Rout

TOMS_submission/sim_study/experiments/z2/loggle/cont_multi_cov_dep_ntrials50_p25_n_25_2023-12-25_03-51.Rout

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TOMS_submission/sim_study/experiments/z4/cont_4_cov_dep_ntrials50_p100_n_225_2023-10-07_04-52.Rout

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TOMS_submission/sim_study/experiments/z4_archive/cont_4_cov_dep_ntrials50_p100_n_225_2023-10-01_00-44.Rout

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TOMS_submission/sim_study/experiments/z4_archive/cont_4_cov_dep_ntrials50_p50_n_225_2023-09-30_19-47.Rout

TOMS_submission/source/.Rbuildignore

TOMS_submission/source/DESCRIPTION

TOMS_submission/source/NAMESPACE

TOMS_submission/source/R/RcppExports.R TOMS_submission/source/R/cavi.R TOMS_submission/source/R/covdepGE_package.R TOMS_submission/source/R/data.R TOMS_submission/source/R/main.R TOMS_submission/source/R/plots.R TOMS_submission/source/R/weights.R

TOMS_submission/source/makefile

TOMS_submission/source/man/covdepGE-package.Rd TOMS_submission/source/man/covdepGE.Rd TOMS_submission/source/man/generateData.Rd TOMS_submission/source/man/inclusionCurve.Rd TOMS_submission/source/man/matViz.Rd TOMS_submission/source/man/plot.covdepGE.Rd

TOMS_submission/source/src/.gitignore

TOMS_submission/source/src/Makevars

TOMS_submission/source/src/Makevars.win

TOMS_submission/source/src/RcppExports.cpp

TOMS_submission/source/src/code.cpp

TOMS_submission/source/src/covdepGE_c.cpp

TOMS_submission/supplemental/Graph_learning.pdf TOMS_submission/supplemental/Graph_learning_supplemental.pdf TOMS_submission/supplemental/README.pdf TOMS_submission/supplemental/portability.pdf TOMS_submission/supplemental_final/Graph_learning.pdf TOMS_submission/supplemental_final/README.pdf TOMS_submission/supplemental_final/portability.pdf TOMS_submission/testing_material/test.R

TOMS_submission/testing_material/test_n225_p10_ntrials5_ubuntu.Rout

TOMS_submission/testing_material/test_n225_p10_ntrials5_windows.Rout

TOMS_submission/testing_material/test_n225_p25_ntrials5_ubuntu.Rout

TOMS_submission/testing_material/test_n225_p25_ntrials5_windows.Rout

TOMS_submission/unix_install.sh

codecov.yml

covdepGE.Rproj

dev/.c

dev/hp_spec_exper.R examples/TCGA_analysis.Rmd examples/TCGA_analysis.md

examples/TCGA_analysis_files/figure-gfm/unnamed-chunk-1-1.png

examples/example.Rmd examples/example.pdf graph_learning_simulation_study/analysis.R graph_learning_simulation_study/data.R

graph_learning_simulation_study/experiments/continuous/cont_cov_dep.sh

graph_learning_simulation_study/experiments/continuous/cont_multi_cov_dep.sh

graph_learning_simulation_study/experiments/discrete/disc_cov_dep_cdge.sh

graph_learning_simulation_study/experiments/discrete/disc_cov_dep_lambda15_n1_50_n2_50.sh

graph_learning_simulation_study/experiments/discrete/disc_cov_dep_lambda15_n1_80_n2_20.sh

graph_learning_simulation_study/experiments/discrete/disc_cov_dep_lambda3_n1_50_n2_50.sh

graph_learning_simulation_study/experiments/discrete/disc_cov_dep_lambda3_n1_80_n2_20.sh

graph_learning_simulation_study/experiments/discrete/disc_cov_dep_p101_n1_30_n2_20.sh

graph_learning_simulation_study/experiments/discrete/disc_cov_dep_p51_n1_40_n2_10.sh

graph_learning_simulation_study/experiments/discrete/disc_cov_free_p11.sh

graph_learning_simulation_study/experiments/discrete/disc_cov_indep_p11.sh

graph_learning_simulation_study/experiments/test.R

graph_learning_simulation_study/experiments/test.sh

graph_learning_simulation_study/main.R graph_learning_simulation_study/models.R graph_learning_simulation_study/utils.R

inst/WORDLIST

latex_manual/Rd.sty

latex_manual/Rd2.tex

makefile

man/covdepGE-package.Rd man/covdepGE.Rd

man/figures/README-example-1.png

man/figures/README-example-10.png

man/figures/README-example-11.png

man/figures/README-example-2.png

man/figures/README-example-3.png

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man/figures/README-example-6.png

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man/figures/README-example-8.png

man/figures/README-example-9.png

man/generateData.Rd man/inclusionCurve.Rd man/matViz.Rd man/plot.covdepGE.Rd simulation_study/analyses/analysis_lite.R simulation_study/analyses/simulation_study_analysis.R simulation_study/mgm_gaussian_example/examples_tvmgm.R simulation_study/misc exps/multi_exp.R simulation_study/misc exps/narrow_exp.R simulation_study/misc exps/tanh_exp.R simulation_study/p100_n300/simulation_study_p100_n300_JGL_mgm.R

simulation_study/p100_n300/simulation_study_p100_n300_JGL_mgm.Rout

simulation_study/p100_n300/simulation_study_p100_n300_covdepGE.R

simulation_study/p100_n300/simulation_study_p100_n300_covdepGE.Rout

simulation_study/p15_n90/simulation_study_p15_n90_JGL_mgm.R

simulation_study/p15_n90/simulation_study_p15_n90_JGL_mgm.Rout

simulation_study/p15_n90/simulation_study_p15_n90_covdepGE.R

simulation_study/p15_n90/simulation_study_p15_n90_covdepGE.Rout

simulation_study/p25_n150/simulation_study_p25_n150_JGL_mgm.R

simulation_study/p25_n150/simulation_study_p25_n150_JGL_mgm.Rout

simulation_study/p25_n150/simulation_study_p25_n150_covdepGE.R

simulation_study/p25_n150/simulation_study_p25_n150_covdepGE.Rout

simulation_study/p50_n150/simulation_study_p50_n150_JGL_mgm.R

simulation_study/p50_n150/simulation_study_p50_n150_JGL_mgm.Rout

simulation_study/p50_n150/simulation_study_p50_n150_covdepGE.R

simulation_study/p50_n150/simulation_study_p50_n150_covdepGE.Rout

simulation_study/p5_n90/simulation_study_p5_n90_JGL_mgm.R

simulation_study/p5_n90/simulation_study_p5_n90_JGL_mgm.Rout

simulation_study/p5_n90/simulation_study_p5_n90_covdepGE.R

simulation_study/p5_n90/simulation_study_p5_n90_covdepGE.Rout

simulation_study/plots/ground_truth_CDS.R simulation_study/plots/ground_truth_CDS.pdf

src/.gitignore

src/Makevars

src/Makevars.win

src/RcppExports.cpp

src/code.cpp

src/covdepGE_c.cpp

tests/testthat.R tests/testthat/test-covdepGE.R

JacobHelwig/covdepGE documentation built on April 11, 2024, 7:22 a.m.

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JacobHelwig/covdepGE
Covariate Dependent Graph Estimation

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JacobHelwig/covdepGE Covariate Dependent Graph Estimation

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JacobHelwig/covdepGE
Covariate Dependent Graph Estimation

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Covariate Dependent Graph Estimation