├── .github └── workflows │ ├── pdoc-documentation-site.yaml │ └── uv-actions.yml ├── .gitignore ├── .python-version ├── LICENSE ├── README.md ├── dcurves ├── __init__.py ├── data │ ├── df_binary.csv │ ├── df_case_control.csv │ └── df_surv.csv ├── dca.py ├── plot_graphs.py ├── prevalence.py └── risks.py ├── docs ├── CHANGELOG.md └── WORKFLOW.md ├── public └── simple_binary_dca.png ├── pyproject.toml ├── tests ├── .coverage ├── __init__.py ├── benchmark_data │ ├── dca_tut_bin_int_marker_risks.csv │ ├── dca_tut_coxph_pr_failure18_vals.csv │ ├── dca_tut_r_stdca_coxph_df.csv │ ├── dca_tut_r_stdca_coxph_pr_failure18_test_consequences.csv │ ├── df_binary.csv │ ├── df_cancer_dx.csv │ ├── df_cancer_dx2.csv │ ├── df_case_control.csv │ ├── df_surv.csv │ ├── r_case1_results.csv │ ├── r_case2_results.csv │ ├── r_case3_results.csv │ ├── r_dca_famhistory.csv │ ├── r_simple_binary_dca_result_df.csv │ ├── r_simple_surv_dca_result_df.csv │ ├── r_simple_surv_tpfp_calc_df.csv │ ├── shishir_simdata.csv │ └── surv_risk_test_df.csv ├── common_test_utils.py ├── conftest.py ├── load_test_data.py ├── test_actual_dca.py ├── test_binary_consequences.py ├── test_create_initial_df.py ├── test_dca_input_checks.py ├── test_dca_risks.py ├── test_dca_tutorial.py ├── test_harms.py ├── test_net_intervention_avoided.py ├── test_plot_smoothing.py ├── test_plotting_core.py ├── test_plotting_options.py ├── test_prevalence.py └── test_surv_consequences.py └── uv.lock /.github/workflows/pdoc-documentation-site.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/.github/workflows/pdoc-documentation-site.yaml -------------------------------------------------------------------------------- /.github/workflows/uv-actions.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/.github/workflows/uv-actions.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/.gitignore -------------------------------------------------------------------------------- /.python-version: -------------------------------------------------------------------------------- 1 | 3.10 2 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/README.md -------------------------------------------------------------------------------- /dcurves/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/dcurves/__init__.py -------------------------------------------------------------------------------- /dcurves/data/df_binary.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/dcurves/data/df_binary.csv -------------------------------------------------------------------------------- /dcurves/data/df_case_control.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/dcurves/data/df_case_control.csv -------------------------------------------------------------------------------- /dcurves/data/df_surv.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/dcurves/data/df_surv.csv -------------------------------------------------------------------------------- /dcurves/dca.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/dcurves/dca.py -------------------------------------------------------------------------------- /dcurves/plot_graphs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/dcurves/plot_graphs.py -------------------------------------------------------------------------------- /dcurves/prevalence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/dcurves/prevalence.py -------------------------------------------------------------------------------- /dcurves/risks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/dcurves/risks.py -------------------------------------------------------------------------------- /docs/CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/docs/CHANGELOG.md -------------------------------------------------------------------------------- /docs/WORKFLOW.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/docs/WORKFLOW.md -------------------------------------------------------------------------------- /public/simple_binary_dca.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/public/simple_binary_dca.png -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/pyproject.toml -------------------------------------------------------------------------------- /tests/.coverage: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/.coverage -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/__init__.py -------------------------------------------------------------------------------- /tests/benchmark_data/dca_tut_bin_int_marker_risks.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/dca_tut_bin_int_marker_risks.csv -------------------------------------------------------------------------------- /tests/benchmark_data/dca_tut_coxph_pr_failure18_vals.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/dca_tut_coxph_pr_failure18_vals.csv -------------------------------------------------------------------------------- /tests/benchmark_data/dca_tut_r_stdca_coxph_df.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/dca_tut_r_stdca_coxph_df.csv -------------------------------------------------------------------------------- /tests/benchmark_data/dca_tut_r_stdca_coxph_pr_failure18_test_consequences.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/dca_tut_r_stdca_coxph_pr_failure18_test_consequences.csv -------------------------------------------------------------------------------- /tests/benchmark_data/df_binary.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/df_binary.csv -------------------------------------------------------------------------------- /tests/benchmark_data/df_cancer_dx.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/df_cancer_dx.csv -------------------------------------------------------------------------------- /tests/benchmark_data/df_cancer_dx2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/df_cancer_dx2.csv -------------------------------------------------------------------------------- /tests/benchmark_data/df_case_control.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/df_case_control.csv -------------------------------------------------------------------------------- /tests/benchmark_data/df_surv.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/df_surv.csv -------------------------------------------------------------------------------- /tests/benchmark_data/r_case1_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/r_case1_results.csv -------------------------------------------------------------------------------- /tests/benchmark_data/r_case2_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/r_case2_results.csv -------------------------------------------------------------------------------- /tests/benchmark_data/r_case3_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/r_case3_results.csv -------------------------------------------------------------------------------- /tests/benchmark_data/r_dca_famhistory.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/r_dca_famhistory.csv -------------------------------------------------------------------------------- /tests/benchmark_data/r_simple_binary_dca_result_df.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/r_simple_binary_dca_result_df.csv -------------------------------------------------------------------------------- /tests/benchmark_data/r_simple_surv_dca_result_df.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/r_simple_surv_dca_result_df.csv -------------------------------------------------------------------------------- /tests/benchmark_data/r_simple_surv_tpfp_calc_df.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/r_simple_surv_tpfp_calc_df.csv -------------------------------------------------------------------------------- /tests/benchmark_data/shishir_simdata.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/shishir_simdata.csv -------------------------------------------------------------------------------- /tests/benchmark_data/surv_risk_test_df.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/benchmark_data/surv_risk_test_df.csv -------------------------------------------------------------------------------- /tests/common_test_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/common_test_utils.py -------------------------------------------------------------------------------- /tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/conftest.py -------------------------------------------------------------------------------- /tests/load_test_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/load_test_data.py -------------------------------------------------------------------------------- /tests/test_actual_dca.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/test_actual_dca.py -------------------------------------------------------------------------------- /tests/test_binary_consequences.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/test_binary_consequences.py -------------------------------------------------------------------------------- /tests/test_create_initial_df.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/test_create_initial_df.py -------------------------------------------------------------------------------- /tests/test_dca_input_checks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/test_dca_input_checks.py -------------------------------------------------------------------------------- /tests/test_dca_risks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/test_dca_risks.py -------------------------------------------------------------------------------- /tests/test_dca_tutorial.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/test_dca_tutorial.py -------------------------------------------------------------------------------- /tests/test_harms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/test_harms.py -------------------------------------------------------------------------------- /tests/test_net_intervention_avoided.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/test_net_intervention_avoided.py -------------------------------------------------------------------------------- /tests/test_plot_smoothing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/test_plot_smoothing.py -------------------------------------------------------------------------------- /tests/test_plotting_core.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/test_plotting_core.py -------------------------------------------------------------------------------- /tests/test_plotting_options.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/test_plotting_options.py -------------------------------------------------------------------------------- /tests/test_prevalence.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/test_prevalence.py -------------------------------------------------------------------------------- /tests/test_surv_consequences.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/tests/test_surv_consequences.py -------------------------------------------------------------------------------- /uv.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MSKCC-Epi-Bio/dcurves/HEAD/uv.lock --------------------------------------------------------------------------------