From fcbdc8322e19af72dbdd58825debb078ebd909ba Mon Sep 17 00:00:00 2001 From: Linda Nab Date: Mon, 13 Nov 2023 22:52:43 +0000 Subject: [PATCH] decrease dummy data size --- project.yaml | 1850 +++++++++++++++++++++++++------------------------- 1 file changed, 925 insertions(+), 925 deletions(-) diff --git a/project.yaml b/project.yaml index 81d086d..87cedb3 100644 --- a/project.yaml +++ b/project.yaml @@ -1,7 +1,7 @@ version: '3.0' expectations: - population_size: 40000 + population_size: 5000 actions: @@ -243,813 +243,813 @@ actions: csv1: output/data_properties/trt_outcm_same_day.csv csv2: output/data_properties/trt_outcm_same_day_red.csv - ## # # # # # # # # # # # # # # # # # # # - ## # # # # # # # # # # # # # # # # # # # - ## 1 MAIN ANALYSIS - COX - ## # # # # # # # # # # # # # # # # # # # - ## # # # # # # # # # # # # # # # # # # # - - ## # # # # # # # # # # # # # # # # # # # - ## 1.1 CCW Analysis - COX - ## # # # # # # # # # # # # # # # # # # # - - perform_ccw_analysis: - run: r:latest analysis/ccw.R - --period ba1 - needs: [data_process] - outputs: - highly_sensitive: - data: output/data/data_long_all.feather - model01: output/models/cox_cens_control_all.rds - model02: output/models/cox_cens_trt_all.rds - model1: output/models/km_trt_all.rds - model2: output/models/km_control_all.rds - model3: output/models/cox_w_all.rds - model4: output/models/cox_uw_all.rds - moderately_sensitive: - table: output/tables/ccw/ccw_all.csv - basehaz1: output/models/basehaz/basehaz_control_all.csv - basehaz2: output/models/basehaz/basehaz_trt_all.csv + # ## # # # # # # # # # # # # # # # # # # # + # ## # # # # # # # # # # # # # # # # # # # + # ## 1 MAIN ANALYSIS - COX + # ## # # # # # # # # # # # # # # # # # # # + # ## # # # # # # # # # # # # # # # # # # # + + # ## # # # # # # # # # # # # # # # # # # # + # ## 1.1 CCW Analysis - COX + # ## # # # # # # # # # # # # # # # # # # # + + # perform_ccw_analysis: + # run: r:latest analysis/ccw.R + # --period ba1 + # needs: [data_process] + # outputs: + # highly_sensitive: + # data: output/data/data_long_all.feather + # model01: output/models/cox_cens_control_all.rds + # model02: output/models/cox_cens_trt_all.rds + # model1: output/models/km_trt_all.rds + # model2: output/models/km_control_all.rds + # model3: output/models/cox_w_all.rds + # model4: output/models/cox_uw_all.rds + # moderately_sensitive: + # table: output/tables/ccw/ccw_all.csv + # basehaz1: output/models/basehaz/basehaz_control_all.csv + # basehaz2: output/models/basehaz/basehaz_trt_all.csv - perform_ccw_analysis_mol: - run: r:latest analysis/ccw.R - --period ba1 - --contrast molnupiravir - needs: [data_process] - outputs: - highly_sensitive: - data: output/data/data_long_molnupiravir.feather - model01: output/models/cox_cens_control_molnupiravir.rds - model02: output/models/cox_cens_trt_molnupiravir.rds - model1: output/models/km_trt_molnupiravir.rds - model2: output/models/km_control_molnupiravir.rds - model3: output/models/cox_w_molnupiravir.rds - model4: output/models/cox_uw_molnupiravir.rds - moderately_sensitive: - table: output/tables/ccw/ccw_molnupiravir.csv - basehaz1: output/models/basehaz/basehaz_control_molnupiravir.csv - basehaz2: output/models/basehaz/basehaz_trt_molnupiravir.csv - - perform_ccw_analysis_sot: - run: r:latest analysis/ccw.R - --period ba1 - --contrast sotrovimab - needs: [data_process] - outputs: - highly_sensitive: - data: output/data/data_long_sotrovimab.feather - model01: output/models/cox_cens_control_sotrovimab.rds - model02: output/models/cox_cens_trt_sotrovimab.rds - model1: output/models/km_trt_sotrovimab.rds - model2: output/models/km_control_sotrovimab.rds - model3: output/models/cox_w_sotrovimab.rds - model4: output/models/cox_uw_sotrovimab.rds - moderately_sensitive: - table: output/tables/ccw/ccw_sotrovimab.csv - basehaz1: output/models/basehaz/basehaz_control_sotrovimab.csv - basehaz2: output/models/basehaz/basehaz_trt_sotrovimab.csv - - save_coef_weight_models: - run: r:latest analysis/models_ccw/coef_weight_models.R - --period ba1 - needs: [perform_ccw_analysis, perform_ccw_analysis_mol, perform_ccw_analysis_sot] - outputs: - moderately_sensitive: - table: output/models/coefficients/cox_cens_*.csv - - perform_ccw_analysis_ba2: - run: r:latest analysis/ccw.R - --period ba2 - needs: [data_process_ba2] - outputs: - highly_sensitive: - data: output/data/ba2_data_long_all.feather - model01: output/models/ba2_cox_cens_control_all.rds - model02: output/models/ba2_cox_cens_trt_all.rds - model1: output/models/ba2_km_trt_all.rds - model2: output/models/ba2_km_control_all.rds - model3: output/models/ba2_cox_w_all.rds - model4: output/models/ba2_cox_uw_all.rds - moderately_sensitive: - table: output/tables/ccw/ba2_ccw_all.csv - basehaz1: output/models/basehaz/ba2_basehaz_control_all.csv - basehaz2: output/models/basehaz/ba2_basehaz_trt_all.csv + # perform_ccw_analysis_mol: + # run: r:latest analysis/ccw.R + # --period ba1 + # --contrast molnupiravir + # needs: [data_process] + # outputs: + # highly_sensitive: + # data: output/data/data_long_molnupiravir.feather + # model01: output/models/cox_cens_control_molnupiravir.rds + # model02: output/models/cox_cens_trt_molnupiravir.rds + # model1: output/models/km_trt_molnupiravir.rds + # model2: output/models/km_control_molnupiravir.rds + # model3: output/models/cox_w_molnupiravir.rds + # model4: output/models/cox_uw_molnupiravir.rds + # moderately_sensitive: + # table: output/tables/ccw/ccw_molnupiravir.csv + # basehaz1: output/models/basehaz/basehaz_control_molnupiravir.csv + # basehaz2: output/models/basehaz/basehaz_trt_molnupiravir.csv + + # perform_ccw_analysis_sot: + # run: r:latest analysis/ccw.R + # --period ba1 + # --contrast sotrovimab + # needs: [data_process] + # outputs: + # highly_sensitive: + # data: output/data/data_long_sotrovimab.feather + # model01: output/models/cox_cens_control_sotrovimab.rds + # model02: output/models/cox_cens_trt_sotrovimab.rds + # model1: output/models/km_trt_sotrovimab.rds + # model2: output/models/km_control_sotrovimab.rds + # model3: output/models/cox_w_sotrovimab.rds + # model4: output/models/cox_uw_sotrovimab.rds + # moderately_sensitive: + # table: output/tables/ccw/ccw_sotrovimab.csv + # basehaz1: output/models/basehaz/basehaz_control_sotrovimab.csv + # basehaz2: output/models/basehaz/basehaz_trt_sotrovimab.csv + + # save_coef_weight_models: + # run: r:latest analysis/models_ccw/coef_weight_models.R + # --period ba1 + # needs: [perform_ccw_analysis, perform_ccw_analysis_mol, perform_ccw_analysis_sot] + # outputs: + # moderately_sensitive: + # table: output/models/coefficients/cox_cens_*.csv + + # perform_ccw_analysis_ba2: + # run: r:latest analysis/ccw.R + # --period ba2 + # needs: [data_process_ba2] + # outputs: + # highly_sensitive: + # data: output/data/ba2_data_long_all.feather + # model01: output/models/ba2_cox_cens_control_all.rds + # model02: output/models/ba2_cox_cens_trt_all.rds + # model1: output/models/ba2_km_trt_all.rds + # model2: output/models/ba2_km_control_all.rds + # model3: output/models/ba2_cox_w_all.rds + # model4: output/models/ba2_cox_uw_all.rds + # moderately_sensitive: + # table: output/tables/ccw/ba2_ccw_all.csv + # basehaz1: output/models/basehaz/ba2_basehaz_control_all.csv + # basehaz2: output/models/basehaz/ba2_basehaz_trt_all.csv - perform_ccw_analysis_mol_ba2: - run: r:latest analysis/ccw.R - --period ba2 - --contrast molnupiravir - needs: [data_process_ba2] - outputs: - highly_sensitive: - data: output/data/ba2_data_long_molnupiravir.feather - model01: output/models/ba2_cox_cens_control_molnupiravir.rds - model02: output/models/ba2_cox_cens_trt_molnupiravir.rds - model1: output/models/ba2_km_trt_molnupiravir.rds - model2: output/models/ba2_km_control_molnupiravir.rds - model3: output/models/ba2_cox_w_molnupiravir.rds - model4: output/models/ba2_cox_uw_molnupiravir.rds - moderately_sensitive: - table: output/tables/ccw/ba2_ccw_molnupiravir.csv - basehaz1: output/models/basehaz/ba2_basehaz_control_molnupiravir.csv - basehaz2: output/models/basehaz/ba2_basehaz_trt_molnupiravir.csv - - perform_ccw_analysis_sot_ba2: - run: r:latest analysis/ccw.R - --period ba2 - --contrast sotrovimab - needs: [data_process_ba2] - outputs: - highly_sensitive: - data: output/data/ba2_data_long_sotrovimab.feather - model01: output/models/ba2_cox_cens_control_sotrovimab.rds - model02: output/models/ba2_cox_cens_trt_sotrovimab.rds - model1: output/models/ba2_km_trt_sotrovimab.rds - model2: output/models/ba2_km_control_sotrovimab.rds - model3: output/models/ba2_cox_w_sotrovimab.rds - model4: output/models/ba2_cox_uw_sotrovimab.rds - moderately_sensitive: - table: output/tables/ccw/ba2_ccw_sotrovimab.csv - basehaz1: output/models/basehaz/ba2_basehaz_control_sotrovimab.csv - basehaz2: output/models/basehaz/ba2_basehaz_trt_sotrovimab.csv - - save_coef_weight_models_ba2: - run: r:latest analysis/models_ccw/coef_weight_models.R - --period ba2 - needs: [perform_ccw_analysis_ba2, perform_ccw_analysis_mol_ba2, perform_ccw_analysis_sot_ba2] - outputs: - moderately_sensitive: - table: output/models/coefficients/ba2_cox_cens_*.csv + # perform_ccw_analysis_mol_ba2: + # run: r:latest analysis/ccw.R + # --period ba2 + # --contrast molnupiravir + # needs: [data_process_ba2] + # outputs: + # highly_sensitive: + # data: output/data/ba2_data_long_molnupiravir.feather + # model01: output/models/ba2_cox_cens_control_molnupiravir.rds + # model02: output/models/ba2_cox_cens_trt_molnupiravir.rds + # model1: output/models/ba2_km_trt_molnupiravir.rds + # model2: output/models/ba2_km_control_molnupiravir.rds + # model3: output/models/ba2_cox_w_molnupiravir.rds + # model4: output/models/ba2_cox_uw_molnupiravir.rds + # moderately_sensitive: + # table: output/tables/ccw/ba2_ccw_molnupiravir.csv + # basehaz1: output/models/basehaz/ba2_basehaz_control_molnupiravir.csv + # basehaz2: output/models/basehaz/ba2_basehaz_trt_molnupiravir.csv + + # perform_ccw_analysis_sot_ba2: + # run: r:latest analysis/ccw.R + # --period ba2 + # --contrast sotrovimab + # needs: [data_process_ba2] + # outputs: + # highly_sensitive: + # data: output/data/ba2_data_long_sotrovimab.feather + # model01: output/models/ba2_cox_cens_control_sotrovimab.rds + # model02: output/models/ba2_cox_cens_trt_sotrovimab.rds + # model1: output/models/ba2_km_trt_sotrovimab.rds + # model2: output/models/ba2_km_control_sotrovimab.rds + # model3: output/models/ba2_cox_w_sotrovimab.rds + # model4: output/models/ba2_cox_uw_sotrovimab.rds + # moderately_sensitive: + # table: output/tables/ccw/ba2_ccw_sotrovimab.csv + # basehaz1: output/models/basehaz/ba2_basehaz_control_sotrovimab.csv + # basehaz2: output/models/basehaz/ba2_basehaz_trt_sotrovimab.csv + + # save_coef_weight_models_ba2: + # run: r:latest analysis/models_ccw/coef_weight_models.R + # --period ba2 + # needs: [perform_ccw_analysis_ba2, perform_ccw_analysis_mol_ba2, perform_ccw_analysis_sot_ba2] + # outputs: + # moderately_sensitive: + # table: output/models/coefficients/ba2_cox_cens_*.csv - ## # # # # # # # # # # # # # # # # # # # - ## 1.2 CCW Analysis - check balance - COX - ## # # # # # # # # # # # # # # # # # # # - - calc_smd: - run: r:latest analysis/smd.R - --period ba1 - needs: [perform_ccw_analysis] - outputs: - moderately_sensitive: - table: output/tables/ccw/smd_all.csv - - calc_smd_mol: - run: r:latest analysis/smd.R - --period ba1 - --contrast molnupiravir - needs: [perform_ccw_analysis_mol] - outputs: - moderately_sensitive: - table: output/tables/ccw/smd_molnupiravir.csv - - calc_smd_sot: - run: r:latest analysis/smd.R - --period ba1 - --contrast sotrovimab - needs: [perform_ccw_analysis_sot] - outputs: - moderately_sensitive: - table: output/tables/ccw/smd_sotrovimab.csv - - calc_smd_ba2: - run: r:latest analysis/smd.R - --period ba2 - needs: [perform_ccw_analysis_ba2] - outputs: - moderately_sensitive: - table: output/tables/ccw/ba2_smd_all.csv - - calc_smd_mol_ba2: - run: r:latest analysis/smd.R - --period ba2 - --contrast molnupiravir - needs: [perform_ccw_analysis_mol_ba2] - outputs: - moderately_sensitive: - table: output/tables/ccw/ba2_smd_molnupiravir.csv - - calc_smd_sot_ba2: - run: r:latest analysis/smd.R - --period ba2 - --contrast sotrovimab - needs: [perform_ccw_analysis_sot_ba2] - outputs: - moderately_sensitive: - table: output/tables/ccw/ba2_smd_sotrovimab.csv - - ## # # # # # # # # # # # # # # # # # # # - ## 1.3 CCW Analysis - density weights - COX - ## # # # # # # # # # # # # # # # # # # # - - dens_weights: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba1 - needs: [perform_ccw_analysis] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/dens_all.csv - table2: output/data_properties/data_long/q*_all.csv + # ## # # # # # # # # # # # # # # # # # # # + # ## 1.2 CCW Analysis - check balance - COX + # ## # # # # # # # # # # # # # # # # # # # + + # calc_smd: + # run: r:latest analysis/smd.R + # --period ba1 + # needs: [perform_ccw_analysis] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/smd_all.csv + + # calc_smd_mol: + # run: r:latest analysis/smd.R + # --period ba1 + # --contrast molnupiravir + # needs: [perform_ccw_analysis_mol] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/smd_molnupiravir.csv + + # calc_smd_sot: + # run: r:latest analysis/smd.R + # --period ba1 + # --contrast sotrovimab + # needs: [perform_ccw_analysis_sot] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/smd_sotrovimab.csv + + # calc_smd_ba2: + # run: r:latest analysis/smd.R + # --period ba2 + # needs: [perform_ccw_analysis_ba2] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/ba2_smd_all.csv + + # calc_smd_mol_ba2: + # run: r:latest analysis/smd.R + # --period ba2 + # --contrast molnupiravir + # needs: [perform_ccw_analysis_mol_ba2] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/ba2_smd_molnupiravir.csv + + # calc_smd_sot_ba2: + # run: r:latest analysis/smd.R + # --period ba2 + # --contrast sotrovimab + # needs: [perform_ccw_analysis_sot_ba2] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/ba2_smd_sotrovimab.csv + + # ## # # # # # # # # # # # # # # # # # # # + # ## 1.3 CCW Analysis - density weights - COX + # ## # # # # # # # # # # # # # # # # # # # + + # dens_weights: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba1 + # needs: [perform_ccw_analysis] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/dens_all.csv + # table2: output/data_properties/data_long/q*_all.csv - dens_weights_mol: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba1 - --contrast molnupiravir - needs: [perform_ccw_analysis_mol] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/dens_molnupiravir.csv - table2: output/data_properties/data_long/q*_molnupiravir.csv - - dens_weights_sot: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba1 - --contrast sotrovimab - needs: [perform_ccw_analysis_sot] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/dens_sotrovimab.csv - table2: output/data_properties/data_long/q*_sotrovimab.csv - - dens_weights_ba2: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba2 - needs: [perform_ccw_analysis_ba2] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/ba2_dens_all.csv - table2: output/data_properties/data_long/ba2_q*_all.csv - - dens_weights_mol_ba2: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba2 - --contrast molnupiravir - needs: [perform_ccw_analysis_mol_ba2] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/ba2_dens_molnupiravir.csv - table2: output/data_properties/data_long/ba2_q*_molnupiravir.csv - - dens_weights_sot_ba2: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba2 - --contrast sotrovimab - needs: [perform_ccw_analysis_sot_ba2] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/ba2_dens_sotrovimab.csv - table2: output/data_properties/data_long/ba2_q*_sotrovimab.csv - - ## # # # # # # # # # # # # # # # # # # # - ## # # # # # # # # # # # # # # # # # # # - ## 2 SUBGROUP ANALYSIS: HEAM MALIG - COX - ## # # # # # # # # # # # # # # # # # # # - ## # # # # # # # # # # # # # # # # # # # - - ## # # # # # # # # # # # # # # # # # # # - ## 2.1 CCW Analysis - COX - ## # # # # # # # # # # # # # # # # # # # - - perform_ccw_analysis_haem: - run: r:latest analysis/ccw.R - --period ba1 - --subgrp haem - needs: [data_process] - outputs: - highly_sensitive: - data: output/data/haem/data_long_all_haem.feather - model01: output/models/haem/cox_cens_control_all_haem.rds - model02: output/models/haem/cox_cens_trt_all_haem.rds - model1: output/models/haem/km_trt_all_haem.rds - model2: output/models/haem/km_control_all_haem.rds - model3: output/models/haem/cox_w_all_haem.rds - model4: output/models/haem/cox_uw_all_haem.rds - moderately_sensitive: - table: output/tables/ccw/haem/ccw_all_haem.csv - basehaz1: output/models/basehaz/haem/basehaz_control_all_haem.csv - basehaz2: output/models/basehaz/haem/basehaz_trt_all_haem.csv + # dens_weights_mol: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba1 + # --contrast molnupiravir + # needs: [perform_ccw_analysis_mol] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/dens_molnupiravir.csv + # table2: output/data_properties/data_long/q*_molnupiravir.csv + + # dens_weights_sot: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba1 + # --contrast sotrovimab + # needs: [perform_ccw_analysis_sot] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/dens_sotrovimab.csv + # table2: output/data_properties/data_long/q*_sotrovimab.csv + + # dens_weights_ba2: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba2 + # needs: [perform_ccw_analysis_ba2] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/ba2_dens_all.csv + # table2: output/data_properties/data_long/ba2_q*_all.csv + + # dens_weights_mol_ba2: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba2 + # --contrast molnupiravir + # needs: [perform_ccw_analysis_mol_ba2] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/ba2_dens_molnupiravir.csv + # table2: output/data_properties/data_long/ba2_q*_molnupiravir.csv + + # dens_weights_sot_ba2: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba2 + # --contrast sotrovimab + # needs: [perform_ccw_analysis_sot_ba2] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/ba2_dens_sotrovimab.csv + # table2: output/data_properties/data_long/ba2_q*_sotrovimab.csv + + # ## # # # # # # # # # # # # # # # # # # # + # ## # # # # # # # # # # # # # # # # # # # + # ## 2 SUBGROUP ANALYSIS: HEAM MALIG - COX + # ## # # # # # # # # # # # # # # # # # # # + # ## # # # # # # # # # # # # # # # # # # # + + # ## # # # # # # # # # # # # # # # # # # # + # ## 2.1 CCW Analysis - COX + # ## # # # # # # # # # # # # # # # # # # # + + # perform_ccw_analysis_haem: + # run: r:latest analysis/ccw.R + # --period ba1 + # --subgrp haem + # needs: [data_process] + # outputs: + # highly_sensitive: + # data: output/data/haem/data_long_all_haem.feather + # model01: output/models/haem/cox_cens_control_all_haem.rds + # model02: output/models/haem/cox_cens_trt_all_haem.rds + # model1: output/models/haem/km_trt_all_haem.rds + # model2: output/models/haem/km_control_all_haem.rds + # model3: output/models/haem/cox_w_all_haem.rds + # model4: output/models/haem/cox_uw_all_haem.rds + # moderately_sensitive: + # table: output/tables/ccw/haem/ccw_all_haem.csv + # basehaz1: output/models/basehaz/haem/basehaz_control_all_haem.csv + # basehaz2: output/models/basehaz/haem/basehaz_trt_all_haem.csv - perform_ccw_analysis_mol_haem: - run: r:latest analysis/ccw.R - --period ba1 - --contrast molnupiravir - --subgrp haem - needs: [data_process] - outputs: - highly_sensitive: - data: output/data/haem/data_long_molnupiravir_haem.feather - model01: output/models/haem/cox_cens_control_molnupiravir_haem.rds - model02: output/models/haem/cox_cens_trt_molnupiravir_haem.rds - model1: output/models/haem/km_trt_molnupiravir_haem.rds - model2: output/models/haem/km_control_molnupiravir_haem.rds - model3: output/models/haem/cox_w_molnupiravir_haem.rds - model4: output/models/haem/cox_uw_molnupiravir_haem.rds - moderately_sensitive: - table: output/tables/ccw/haem/ccw_molnupiravir_haem.csv - basehaz1: output/models/basehaz/haem/basehaz_control_molnupiravir_haem.csv - basehaz2: output/models/basehaz/haem/basehaz_trt_molnupiravir_haem.csv - - perform_ccw_analysis_sot_haem: - run: r:latest analysis/ccw.R - --period ba1 - --contrast sotrovimab - --subgrp haem - needs: [data_process] - outputs: - highly_sensitive: - data: output/data/haem/data_long_sotrovimab_haem.feather - model01: output/models/haem/cox_cens_control_sotrovimab_haem.rds - model02: output/models/haem/cox_cens_trt_sotrovimab_haem.rds - model1: output/models/haem/km_trt_sotrovimab_haem.rds - model2: output/models/haem/km_control_sotrovimab_haem.rds - model3: output/models/haem/cox_w_sotrovimab_haem.rds - model4: output/models/haem/cox_uw_sotrovimab_haem.rds - moderately_sensitive: - table: output/tables/ccw/haem/ccw_sotrovimab_haem.csv - basehaz1: output/models/basehaz/haem/basehaz_control_sotrovimab_haem.csv - basehaz2: output/models/basehaz/haem/basehaz_trt_sotrovimab_haem.csv - - save_coef_weight_models_haem: - run: r:latest analysis/models_ccw/coef_weight_models.R - --period ba1 - --subgrp haem - needs: [perform_ccw_analysis_haem, perform_ccw_analysis_mol_haem, perform_ccw_analysis_sot_haem] - outputs: - moderately_sensitive: - table: output/models/coefficients/haem/cox_cens_*.csv - - perform_ccw_analysis_haem_ba2: - run: r:latest analysis/ccw.R - --period ba2 - --subgrp haem - needs: [data_process_ba2] - outputs: - highly_sensitive: - data: output/data/haem/ba2_data_long_all_haem.feather - model01: output/models/haem/ba2_cox_cens_control_all_haem.rds - model02: output/models/haem/ba2_cox_cens_trt_all_haem.rds - model1: output/models/haem/ba2_km_trt_all_haem.rds - model2: output/models/haem/ba2_km_control_all_haem.rds - model3: output/models/haem/ba2_cox_w_all_haem.rds - model4: output/models/haem/ba2_cox_uw_all_haem.rds - moderately_sensitive: - table: output/tables/ccw/haem/ba2_ccw_all_haem.csv - basehaz1: output/models/basehaz/haem/ba2_basehaz_control_all_haem.csv - basehaz2: output/models/basehaz/haem/ba2_basehaz_trt_all_haem.csv + # perform_ccw_analysis_mol_haem: + # run: r:latest analysis/ccw.R + # --period ba1 + # --contrast molnupiravir + # --subgrp haem + # needs: [data_process] + # outputs: + # highly_sensitive: + # data: output/data/haem/data_long_molnupiravir_haem.feather + # model01: output/models/haem/cox_cens_control_molnupiravir_haem.rds + # model02: output/models/haem/cox_cens_trt_molnupiravir_haem.rds + # model1: output/models/haem/km_trt_molnupiravir_haem.rds + # model2: output/models/haem/km_control_molnupiravir_haem.rds + # model3: output/models/haem/cox_w_molnupiravir_haem.rds + # model4: output/models/haem/cox_uw_molnupiravir_haem.rds + # moderately_sensitive: + # table: output/tables/ccw/haem/ccw_molnupiravir_haem.csv + # basehaz1: output/models/basehaz/haem/basehaz_control_molnupiravir_haem.csv + # basehaz2: output/models/basehaz/haem/basehaz_trt_molnupiravir_haem.csv + + # perform_ccw_analysis_sot_haem: + # run: r:latest analysis/ccw.R + # --period ba1 + # --contrast sotrovimab + # --subgrp haem + # needs: [data_process] + # outputs: + # highly_sensitive: + # data: output/data/haem/data_long_sotrovimab_haem.feather + # model01: output/models/haem/cox_cens_control_sotrovimab_haem.rds + # model02: output/models/haem/cox_cens_trt_sotrovimab_haem.rds + # model1: output/models/haem/km_trt_sotrovimab_haem.rds + # model2: output/models/haem/km_control_sotrovimab_haem.rds + # model3: output/models/haem/cox_w_sotrovimab_haem.rds + # model4: output/models/haem/cox_uw_sotrovimab_haem.rds + # moderately_sensitive: + # table: output/tables/ccw/haem/ccw_sotrovimab_haem.csv + # basehaz1: output/models/basehaz/haem/basehaz_control_sotrovimab_haem.csv + # basehaz2: output/models/basehaz/haem/basehaz_trt_sotrovimab_haem.csv + + # save_coef_weight_models_haem: + # run: r:latest analysis/models_ccw/coef_weight_models.R + # --period ba1 + # --subgrp haem + # needs: [perform_ccw_analysis_haem, perform_ccw_analysis_mol_haem, perform_ccw_analysis_sot_haem] + # outputs: + # moderately_sensitive: + # table: output/models/coefficients/haem/cox_cens_*.csv + + # perform_ccw_analysis_haem_ba2: + # run: r:latest analysis/ccw.R + # --period ba2 + # --subgrp haem + # needs: [data_process_ba2] + # outputs: + # highly_sensitive: + # data: output/data/haem/ba2_data_long_all_haem.feather + # model01: output/models/haem/ba2_cox_cens_control_all_haem.rds + # model02: output/models/haem/ba2_cox_cens_trt_all_haem.rds + # model1: output/models/haem/ba2_km_trt_all_haem.rds + # model2: output/models/haem/ba2_km_control_all_haem.rds + # model3: output/models/haem/ba2_cox_w_all_haem.rds + # model4: output/models/haem/ba2_cox_uw_all_haem.rds + # moderately_sensitive: + # table: output/tables/ccw/haem/ba2_ccw_all_haem.csv + # basehaz1: output/models/basehaz/haem/ba2_basehaz_control_all_haem.csv + # basehaz2: output/models/basehaz/haem/ba2_basehaz_trt_all_haem.csv - perform_ccw_analysis_mol_haem_ba2: - run: r:latest analysis/ccw.R - --period ba2 - --contrast molnupiravir - --subgrp haem - needs: [data_process_ba2] - outputs: - highly_sensitive: - data: output/data/haem/ba2_data_long_molnupiravir_haem.feather - model01: output/models/haem/ba2_cox_cens_control_molnupiravir_haem.rds - model02: output/models/haem/ba2_cox_cens_trt_molnupiravir_haem.rds - model1: output/models/haem/ba2_km_trt_molnupiravir_haem.rds - model2: output/models/haem/ba2_km_control_molnupiravir_haem.rds - model3: output/models/haem/ba2_cox_w_molnupiravir_haem.rds - model4: output/models/haem/ba2_cox_uw_molnupiravir_haem.rds - moderately_sensitive: - table: output/tables/ccw/haem/ba2_ccw_molnupiravir_haem.csv - basehaz1: output/models/basehaz/haem/ba2_basehaz_control_molnupiravir_haem.csv - basehaz2: output/models/basehaz/haem/ba2_basehaz_trt_molnupiravir_haem.csv - - perform_ccw_analysis_sot_haem_ba2: - run: r:latest analysis/ccw.R - --period ba2 - --contrast sotrovimab - --subgrp haem - needs: [data_process_ba2] - outputs: - highly_sensitive: - data: output/data/haem/ba2_data_long_sotrovimab_haem.feather - model01: output/models/haem/ba2_cox_cens_control_sotrovimab_haem.rds - model02: output/models/haem/ba2_cox_cens_trt_sotrovimab_haem.rds - model1: output/models/haem/ba2_km_trt_sotrovimab_haem.rds - model2: output/models/haem/ba2_km_control_sotrovimab_haem.rds - model3: output/models/haem/ba2_cox_w_sotrovimab_haem.rds - model4: output/models/haem/ba2_cox_uw_sotrovimab_haem.rds - moderately_sensitive: - table: output/tables/ccw/haem/ba2_ccw_sotrovimab_haem.csv - basehaz1: output/models/basehaz/haem/ba2_basehaz_control_sotrovimab_haem.csv - basehaz2: output/models/basehaz/haem/ba2_basehaz_trt_sotrovimab_haem.csv - - save_coef_weight_models_haem_ba2: - run: r:latest analysis/models_ccw/coef_weight_models.R - --period ba2 - --subgrp haem - needs: [perform_ccw_analysis_haem_ba2, perform_ccw_analysis_mol_haem_ba2, perform_ccw_analysis_sot_haem_ba2] - outputs: - moderately_sensitive: - table: output/models/coefficients/haem/ba2_cox_cens_*.csv + # perform_ccw_analysis_mol_haem_ba2: + # run: r:latest analysis/ccw.R + # --period ba2 + # --contrast molnupiravir + # --subgrp haem + # needs: [data_process_ba2] + # outputs: + # highly_sensitive: + # data: output/data/haem/ba2_data_long_molnupiravir_haem.feather + # model01: output/models/haem/ba2_cox_cens_control_molnupiravir_haem.rds + # model02: output/models/haem/ba2_cox_cens_trt_molnupiravir_haem.rds + # model1: output/models/haem/ba2_km_trt_molnupiravir_haem.rds + # model2: output/models/haem/ba2_km_control_molnupiravir_haem.rds + # model3: output/models/haem/ba2_cox_w_molnupiravir_haem.rds + # model4: output/models/haem/ba2_cox_uw_molnupiravir_haem.rds + # moderately_sensitive: + # table: output/tables/ccw/haem/ba2_ccw_molnupiravir_haem.csv + # basehaz1: output/models/basehaz/haem/ba2_basehaz_control_molnupiravir_haem.csv + # basehaz2: output/models/basehaz/haem/ba2_basehaz_trt_molnupiravir_haem.csv + + # perform_ccw_analysis_sot_haem_ba2: + # run: r:latest analysis/ccw.R + # --period ba2 + # --contrast sotrovimab + # --subgrp haem + # needs: [data_process_ba2] + # outputs: + # highly_sensitive: + # data: output/data/haem/ba2_data_long_sotrovimab_haem.feather + # model01: output/models/haem/ba2_cox_cens_control_sotrovimab_haem.rds + # model02: output/models/haem/ba2_cox_cens_trt_sotrovimab_haem.rds + # model1: output/models/haem/ba2_km_trt_sotrovimab_haem.rds + # model2: output/models/haem/ba2_km_control_sotrovimab_haem.rds + # model3: output/models/haem/ba2_cox_w_sotrovimab_haem.rds + # model4: output/models/haem/ba2_cox_uw_sotrovimab_haem.rds + # moderately_sensitive: + # table: output/tables/ccw/haem/ba2_ccw_sotrovimab_haem.csv + # basehaz1: output/models/basehaz/haem/ba2_basehaz_control_sotrovimab_haem.csv + # basehaz2: output/models/basehaz/haem/ba2_basehaz_trt_sotrovimab_haem.csv + + # save_coef_weight_models_haem_ba2: + # run: r:latest analysis/models_ccw/coef_weight_models.R + # --period ba2 + # --subgrp haem + # needs: [perform_ccw_analysis_haem_ba2, perform_ccw_analysis_mol_haem_ba2, perform_ccw_analysis_sot_haem_ba2] + # outputs: + # moderately_sensitive: + # table: output/models/coefficients/haem/ba2_cox_cens_*.csv - ## # # # # # # # # # # # # # # # # # # # - ## 2.2 CCW Analysis - check balance - COX - ## # # # # # # # # # # # # # # # # # # # - - calc_smd_haem: - run: r:latest analysis/smd.R - --period ba1 - --subgrp haem - needs: [perform_ccw_analysis_haem] - outputs: - moderately_sensitive: - table: output/tables/ccw/haem/smd_all_haem.csv - - calc_smd_mol_haem: - run: r:latest analysis/smd.R - --period ba1 - --contrast molnupiravir - --subgrp haem - needs: [perform_ccw_analysis_mol_haem] - outputs: - moderately_sensitive: - table: output/tables/ccw/haem/smd_molnupiravir_haem.csv - - calc_smd_sot_haem: - run: r:latest analysis/smd.R - --period ba1 - --contrast sotrovimab - --subgrp haem - needs: [perform_ccw_analysis_sot_haem] - outputs: - moderately_sensitive: - table: output/tables/ccw/haem/smd_sotrovimab_haem.csv - - calc_smd_haem_ba2: - run: r:latest analysis/smd.R - --period ba2 - --subgrp haem - needs: [perform_ccw_analysis_haem_ba2] - outputs: - moderately_sensitive: - table: output/tables/ccw/haem/ba2_smd_all_haem.csv - - calc_smd_mol_haem_ba2: - run: r:latest analysis/smd.R - --period ba2 - --contrast molnupiravir - --subgrp haem - needs: [perform_ccw_analysis_mol_haem_ba2] - outputs: - moderately_sensitive: - table: output/tables/ccw/haem/ba2_smd_molnupiravir_haem.csv - - calc_smd_sot_haem_ba2: - run: r:latest analysis/smd.R - --period ba2 - --contrast sotrovimab - --subgrp haem - needs: [perform_ccw_analysis_sot_haem_ba2] - outputs: - moderately_sensitive: - table: output/tables/ccw/haem/ba2_smd_sotrovimab_haem.csv - - ## # # # # # # # # # # # # # # # # # # # - ## 2.3 CCW Analysis - density weights - COX - ## # # # # # # # # # # # # # # # # # # # - - dens_weights_haem: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba1 - --subgrp haem - needs: [perform_ccw_analysis_haem] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/haem/dens_all_haem.csv - table2: output/data_properties/data_long/haem/q*_all_haem.csv + # ## # # # # # # # # # # # # # # # # # # # + # ## 2.2 CCW Analysis - check balance - COX + # ## # # # # # # # # # # # # # # # # # # # + + # calc_smd_haem: + # run: r:latest analysis/smd.R + # --period ba1 + # --subgrp haem + # needs: [perform_ccw_analysis_haem] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/haem/smd_all_haem.csv + + # calc_smd_mol_haem: + # run: r:latest analysis/smd.R + # --period ba1 + # --contrast molnupiravir + # --subgrp haem + # needs: [perform_ccw_analysis_mol_haem] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/haem/smd_molnupiravir_haem.csv + + # calc_smd_sot_haem: + # run: r:latest analysis/smd.R + # --period ba1 + # --contrast sotrovimab + # --subgrp haem + # needs: [perform_ccw_analysis_sot_haem] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/haem/smd_sotrovimab_haem.csv + + # calc_smd_haem_ba2: + # run: r:latest analysis/smd.R + # --period ba2 + # --subgrp haem + # needs: [perform_ccw_analysis_haem_ba2] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/haem/ba2_smd_all_haem.csv + + # calc_smd_mol_haem_ba2: + # run: r:latest analysis/smd.R + # --period ba2 + # --contrast molnupiravir + # --subgrp haem + # needs: [perform_ccw_analysis_mol_haem_ba2] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/haem/ba2_smd_molnupiravir_haem.csv + + # calc_smd_sot_haem_ba2: + # run: r:latest analysis/smd.R + # --period ba2 + # --contrast sotrovimab + # --subgrp haem + # needs: [perform_ccw_analysis_sot_haem_ba2] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/haem/ba2_smd_sotrovimab_haem.csv + + # ## # # # # # # # # # # # # # # # # # # # + # ## 2.3 CCW Analysis - density weights - COX + # ## # # # # # # # # # # # # # # # # # # # + + # dens_weights_haem: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba1 + # --subgrp haem + # needs: [perform_ccw_analysis_haem] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/haem/dens_all_haem.csv + # table2: output/data_properties/data_long/haem/q*_all_haem.csv - dens_weights_mol_haem: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba1 - --contrast molnupiravir - --subgrp haem - needs: [perform_ccw_analysis_mol_haem] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/haem/dens_molnupiravir_haem.csv - table2: output/data_properties/data_long/haem/q*_molnupiravir_haem.csv - - dens_weights_sot_haem: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba1 - --contrast sotrovimab - --subgrp haem - needs: [perform_ccw_analysis_sot_haem] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/haem/dens_sotrovimab_haem.csv - table2: output/data_properties/data_long/haem/q*_sotrovimab_haem.csv - - dens_weights_haem_ba2: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba2 - --subgrp haem - needs: [perform_ccw_analysis_haem_ba2] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/haem/ba2_dens_all_haem.csv - table2: output/data_properties/data_long/haem/ba2_q*_all_haem.csv - - dens_weights_mol_haem_ba2: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba2 - --contrast molnupiravir - --subgrp haem - needs: [perform_ccw_analysis_mol_haem_ba2] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/haem/ba2_dens_molnupiravir_haem.csv - table2: output/data_properties/data_long/haem/ba2_q*_molnupiravir_haem.csv - - dens_weights_sot_haem_ba2: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba2 - --contrast sotrovimab - --subgrp haem - needs: [perform_ccw_analysis_sot_haem_ba2] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/haem/ba2_dens_sotrovimab_haem.csv - table2: output/data_properties/data_long/haem/ba2_q*_sotrovimab_haem.csv - - ## # # # # # # # # # # # # # # # # # # # - ## # # # # # # # # # # # # # # # # # # # - ## 3 SUBGROUP ANALYSIS: ORGAN TRNSPLNT - COX - ## # # # # # # # # # # # # # # # # # # # - ## # # # # # # # # # # # # # # # # # # # - - ## # # # # # # # # # # # # # # # # # # # - ## 3.1 CCW Analysis - COX - ## # # # # # # # # # # # # # # # # # # # - - perform_ccw_analysis_transplant: - run: r:latest analysis/ccw.R - --period ba1 - --subgrp transplant - needs: [data_process] - outputs: - highly_sensitive: - data: output/data/transplant/data_long_all_transplant.feather - model01: output/models/transplant/cox_cens_control_all_transplant.rds - model02: output/models/transplant/cox_cens_trt_all_transplant.rds - model1: output/models/transplant/km_trt_all_transplant.rds - model2: output/models/transplant/km_control_all_transplant.rds - model3: output/models/transplant/cox_w_all_transplant.rds - model4: output/models/transplant/cox_uw_all_transplant.rds - moderately_sensitive: - table: output/tables/ccw/transplant/ccw_all_transplant.csv - basehaz1: output/models/basehaz/transplant/basehaz_control_all_transplant.csv - basehaz2: output/models/basehaz/transplant/basehaz_trt_all_transplant.csv + # dens_weights_mol_haem: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba1 + # --contrast molnupiravir + # --subgrp haem + # needs: [perform_ccw_analysis_mol_haem] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/haem/dens_molnupiravir_haem.csv + # table2: output/data_properties/data_long/haem/q*_molnupiravir_haem.csv + + # dens_weights_sot_haem: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba1 + # --contrast sotrovimab + # --subgrp haem + # needs: [perform_ccw_analysis_sot_haem] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/haem/dens_sotrovimab_haem.csv + # table2: output/data_properties/data_long/haem/q*_sotrovimab_haem.csv + + # dens_weights_haem_ba2: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba2 + # --subgrp haem + # needs: [perform_ccw_analysis_haem_ba2] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/haem/ba2_dens_all_haem.csv + # table2: output/data_properties/data_long/haem/ba2_q*_all_haem.csv + + # dens_weights_mol_haem_ba2: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba2 + # --contrast molnupiravir + # --subgrp haem + # needs: [perform_ccw_analysis_mol_haem_ba2] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/haem/ba2_dens_molnupiravir_haem.csv + # table2: output/data_properties/data_long/haem/ba2_q*_molnupiravir_haem.csv + + # dens_weights_sot_haem_ba2: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba2 + # --contrast sotrovimab + # --subgrp haem + # needs: [perform_ccw_analysis_sot_haem_ba2] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/haem/ba2_dens_sotrovimab_haem.csv + # table2: output/data_properties/data_long/haem/ba2_q*_sotrovimab_haem.csv + + # ## # # # # # # # # # # # # # # # # # # # + # ## # # # # # # # # # # # # # # # # # # # + # ## 3 SUBGROUP ANALYSIS: ORGAN TRNSPLNT - COX + # ## # # # # # # # # # # # # # # # # # # # + # ## # # # # # # # # # # # # # # # # # # # + + # ## # # # # # # # # # # # # # # # # # # # + # ## 3.1 CCW Analysis - COX + # ## # # # # # # # # # # # # # # # # # # # + + # perform_ccw_analysis_transplant: + # run: r:latest analysis/ccw.R + # --period ba1 + # --subgrp transplant + # needs: [data_process] + # outputs: + # highly_sensitive: + # data: output/data/transplant/data_long_all_transplant.feather + # model01: output/models/transplant/cox_cens_control_all_transplant.rds + # model02: output/models/transplant/cox_cens_trt_all_transplant.rds + # model1: output/models/transplant/km_trt_all_transplant.rds + # model2: output/models/transplant/km_control_all_transplant.rds + # model3: output/models/transplant/cox_w_all_transplant.rds + # model4: output/models/transplant/cox_uw_all_transplant.rds + # moderately_sensitive: + # table: output/tables/ccw/transplant/ccw_all_transplant.csv + # basehaz1: output/models/basehaz/transplant/basehaz_control_all_transplant.csv + # basehaz2: output/models/basehaz/transplant/basehaz_trt_all_transplant.csv - perform_ccw_analysis_mol_transplant: - run: r:latest analysis/ccw.R - --period ba1 - --contrast molnupiravir - --subgrp transplant - needs: [data_process] - outputs: - highly_sensitive: - data: output/data/transplant/data_long_molnupiravir_transplant.feather - model01: output/models/transplant/cox_cens_control_molnupiravir_transplant.rds - model02: output/models/transplant/cox_cens_trt_molnupiravir_transplant.rds - model1: output/models/transplant/km_trt_molnupiravir_transplant.rds - model2: output/models/transplant/km_control_molnupiravir_transplant.rds - model3: output/models/transplant/cox_w_molnupiravir_transplant.rds - model4: output/models/transplant/cox_uw_molnupiravir_transplant.rds - moderately_sensitive: - table: output/tables/ccw/transplant/ccw_molnupiravir_transplant.csv - basehaz1: output/models/basehaz/transplant/basehaz_control_molnupiravir_transplant.csv - basehaz2: output/models/basehaz/transplant/basehaz_trt_molnupiravir_transplant.csv - - perform_ccw_analysis_sot_transplant: - run: r:latest analysis/ccw.R - --period ba1 - --contrast sotrovimab - --subgrp transplant - needs: [data_process] - outputs: - highly_sensitive: - data: output/data/transplant/data_long_sotrovimab_transplant.feather - model01: output/models/transplant/cox_cens_control_sotrovimab_transplant.rds - model02: output/models/transplant/cox_cens_trt_sotrovimab_transplant.rds - model1: output/models/transplant/km_trt_sotrovimab_transplant.rds - model2: output/models/transplant/km_control_sotrovimab_transplant.rds - model3: output/models/transplant/cox_w_sotrovimab_transplant.rds - model4: output/models/transplant/cox_uw_sotrovimab_transplant.rds - moderately_sensitive: - table: output/tables/ccw/transplant/ccw_sotrovimab_transplant.csv - basehaz1: output/models/basehaz/transplant/basehaz_control_sotrovimab_transplant.csv - basehaz2: output/models/basehaz/transplant/basehaz_trt_sotrovimab_transplant.csv - - save_coef_weight_models_transplant: - run: r:latest analysis/models_ccw/coef_weight_models.R - --period ba1 - --subgrp transplant - needs: [perform_ccw_analysis_transplant, perform_ccw_analysis_mol_transplant, perform_ccw_analysis_sot_transplant] - outputs: - moderately_sensitive: - table: output/models/coefficients/transplant/cox_cens_*.csv - - perform_ccw_analysis_transplant_ba2: - run: r:latest analysis/ccw.R - --period ba2 - --subgrp transplant - needs: [data_process_ba2] - outputs: - highly_sensitive: - data: output/data/transplant/ba2_data_long_all_transplant.feather - model01: output/models/transplant/ba2_cox_cens_control_all_transplant.rds - model02: output/models/transplant/ba2_cox_cens_trt_all_transplant.rds - model1: output/models/transplant/ba2_km_trt_all_transplant.rds - model2: output/models/transplant/ba2_km_control_all_transplant.rds - model3: output/models/transplant/ba2_cox_w_all_transplant.rds - model4: output/models/transplant/ba2_cox_uw_all_transplant.rds - moderately_sensitive: - table: output/tables/ccw/transplant/ba2_ccw_all_transplant.csv - basehaz1: output/models/basehaz/transplant/ba2_basehaz_control_all_transplant.csv - basehaz2: output/models/basehaz/transplant/ba2_basehaz_trt_all_transplant.csv + # perform_ccw_analysis_mol_transplant: + # run: r:latest analysis/ccw.R + # --period ba1 + # --contrast molnupiravir + # --subgrp transplant + # needs: [data_process] + # outputs: + # highly_sensitive: + # data: output/data/transplant/data_long_molnupiravir_transplant.feather + # model01: output/models/transplant/cox_cens_control_molnupiravir_transplant.rds + # model02: output/models/transplant/cox_cens_trt_molnupiravir_transplant.rds + # model1: output/models/transplant/km_trt_molnupiravir_transplant.rds + # model2: output/models/transplant/km_control_molnupiravir_transplant.rds + # model3: output/models/transplant/cox_w_molnupiravir_transplant.rds + # model4: output/models/transplant/cox_uw_molnupiravir_transplant.rds + # moderately_sensitive: + # table: output/tables/ccw/transplant/ccw_molnupiravir_transplant.csv + # basehaz1: output/models/basehaz/transplant/basehaz_control_molnupiravir_transplant.csv + # basehaz2: output/models/basehaz/transplant/basehaz_trt_molnupiravir_transplant.csv + + # perform_ccw_analysis_sot_transplant: + # run: r:latest analysis/ccw.R + # --period ba1 + # --contrast sotrovimab + # --subgrp transplant + # needs: [data_process] + # outputs: + # highly_sensitive: + # data: output/data/transplant/data_long_sotrovimab_transplant.feather + # model01: output/models/transplant/cox_cens_control_sotrovimab_transplant.rds + # model02: output/models/transplant/cox_cens_trt_sotrovimab_transplant.rds + # model1: output/models/transplant/km_trt_sotrovimab_transplant.rds + # model2: output/models/transplant/km_control_sotrovimab_transplant.rds + # model3: output/models/transplant/cox_w_sotrovimab_transplant.rds + # model4: output/models/transplant/cox_uw_sotrovimab_transplant.rds + # moderately_sensitive: + # table: output/tables/ccw/transplant/ccw_sotrovimab_transplant.csv + # basehaz1: output/models/basehaz/transplant/basehaz_control_sotrovimab_transplant.csv + # basehaz2: output/models/basehaz/transplant/basehaz_trt_sotrovimab_transplant.csv + + # save_coef_weight_models_transplant: + # run: r:latest analysis/models_ccw/coef_weight_models.R + # --period ba1 + # --subgrp transplant + # needs: [perform_ccw_analysis_transplant, perform_ccw_analysis_mol_transplant, perform_ccw_analysis_sot_transplant] + # outputs: + # moderately_sensitive: + # table: output/models/coefficients/transplant/cox_cens_*.csv + + # perform_ccw_analysis_transplant_ba2: + # run: r:latest analysis/ccw.R + # --period ba2 + # --subgrp transplant + # needs: [data_process_ba2] + # outputs: + # highly_sensitive: + # data: output/data/transplant/ba2_data_long_all_transplant.feather + # model01: output/models/transplant/ba2_cox_cens_control_all_transplant.rds + # model02: output/models/transplant/ba2_cox_cens_trt_all_transplant.rds + # model1: output/models/transplant/ba2_km_trt_all_transplant.rds + # model2: output/models/transplant/ba2_km_control_all_transplant.rds + # model3: output/models/transplant/ba2_cox_w_all_transplant.rds + # model4: output/models/transplant/ba2_cox_uw_all_transplant.rds + # moderately_sensitive: + # table: output/tables/ccw/transplant/ba2_ccw_all_transplant.csv + # basehaz1: output/models/basehaz/transplant/ba2_basehaz_control_all_transplant.csv + # basehaz2: output/models/basehaz/transplant/ba2_basehaz_trt_all_transplant.csv - perform_ccw_analysis_mol_transplant_ba2: - run: r:latest analysis/ccw.R - --period ba2 - --contrast molnupiravir - --subgrp transplant - needs: [data_process_ba2] - outputs: - highly_sensitive: - data: output/data/transplant/ba2_data_long_molnupiravir_transplant.feather - model01: output/models/transplant/ba2_cox_cens_control_molnupiravir_transplant.rds - model02: output/models/transplant/ba2_cox_cens_trt_molnupiravir_transplant.rds - model1: output/models/transplant/ba2_km_trt_molnupiravir_transplant.rds - model2: output/models/transplant/ba2_km_control_molnupiravir_transplant.rds - model3: output/models/transplant/ba2_cox_w_molnupiravir_transplant.rds - model4: output/models/transplant/ba2_cox_uw_molnupiravir_transplant.rds - moderately_sensitive: - table: output/tables/ccw/transplant/ba2_ccw_molnupiravir_transplant.csv - basehaz1: output/models/basehaz/transplant/ba2_basehaz_control_molnupiravir_transplant.csv - basehaz2: output/models/basehaz/transplant/ba2_basehaz_trt_molnupiravir_transplant.csv - - perform_ccw_analysis_sot_transplant_ba2: - run: r:latest analysis/ccw.R - --period ba2 - --contrast sotrovimab - --subgrp transplant - needs: [data_process_ba2] - outputs: - highly_sensitive: - data: output/data/transplant/ba2_data_long_sotrovimab_transplant.feather - model01: output/models/transplant/ba2_cox_cens_control_sotrovimab_transplant.rds - model02: output/models/transplant/ba2_cox_cens_trt_sotrovimab_transplant.rds - model1: output/models/transplant/ba2_km_trt_sotrovimab_transplant.rds - model2: output/models/transplant/ba2_km_control_sotrovimab_transplant.rds - model3: output/models/transplant/ba2_cox_w_sotrovimab_transplant.rds - model4: output/models/transplant/ba2_cox_uw_sotrovimab_transplant.rds - moderately_sensitive: - table: output/tables/ccw/transplant/ba2_ccw_sotrovimab_transplant.csv - basehaz1: output/models/basehaz/transplant/ba2_basehaz_control_sotrovimab_transplant.csv - basehaz2: output/models/basehaz/transplant/ba2_basehaz_trt_sotrovimab_transplant.csv - - save_coef_weight_models_transplant_ba2: - run: r:latest analysis/models_ccw/coef_weight_models.R - --period ba2 - --subgrp transplant - needs: [perform_ccw_analysis_transplant_ba2, perform_ccw_analysis_mol_transplant_ba2, perform_ccw_analysis_sot_transplant_ba2] - outputs: - moderately_sensitive: - table: output/models/coefficients/transplant/ba2_cox_cens_*.csv + # perform_ccw_analysis_mol_transplant_ba2: + # run: r:latest analysis/ccw.R + # --period ba2 + # --contrast molnupiravir + # --subgrp transplant + # needs: [data_process_ba2] + # outputs: + # highly_sensitive: + # data: output/data/transplant/ba2_data_long_molnupiravir_transplant.feather + # model01: output/models/transplant/ba2_cox_cens_control_molnupiravir_transplant.rds + # model02: output/models/transplant/ba2_cox_cens_trt_molnupiravir_transplant.rds + # model1: output/models/transplant/ba2_km_trt_molnupiravir_transplant.rds + # model2: output/models/transplant/ba2_km_control_molnupiravir_transplant.rds + # model3: output/models/transplant/ba2_cox_w_molnupiravir_transplant.rds + # model4: output/models/transplant/ba2_cox_uw_molnupiravir_transplant.rds + # moderately_sensitive: + # table: output/tables/ccw/transplant/ba2_ccw_molnupiravir_transplant.csv + # basehaz1: output/models/basehaz/transplant/ba2_basehaz_control_molnupiravir_transplant.csv + # basehaz2: output/models/basehaz/transplant/ba2_basehaz_trt_molnupiravir_transplant.csv + + # perform_ccw_analysis_sot_transplant_ba2: + # run: r:latest analysis/ccw.R + # --period ba2 + # --contrast sotrovimab + # --subgrp transplant + # needs: [data_process_ba2] + # outputs: + # highly_sensitive: + # data: output/data/transplant/ba2_data_long_sotrovimab_transplant.feather + # model01: output/models/transplant/ba2_cox_cens_control_sotrovimab_transplant.rds + # model02: output/models/transplant/ba2_cox_cens_trt_sotrovimab_transplant.rds + # model1: output/models/transplant/ba2_km_trt_sotrovimab_transplant.rds + # model2: output/models/transplant/ba2_km_control_sotrovimab_transplant.rds + # model3: output/models/transplant/ba2_cox_w_sotrovimab_transplant.rds + # model4: output/models/transplant/ba2_cox_uw_sotrovimab_transplant.rds + # moderately_sensitive: + # table: output/tables/ccw/transplant/ba2_ccw_sotrovimab_transplant.csv + # basehaz1: output/models/basehaz/transplant/ba2_basehaz_control_sotrovimab_transplant.csv + # basehaz2: output/models/basehaz/transplant/ba2_basehaz_trt_sotrovimab_transplant.csv + + # save_coef_weight_models_transplant_ba2: + # run: r:latest analysis/models_ccw/coef_weight_models.R + # --period ba2 + # --subgrp transplant + # needs: [perform_ccw_analysis_transplant_ba2, perform_ccw_analysis_mol_transplant_ba2, perform_ccw_analysis_sot_transplant_ba2] + # outputs: + # moderately_sensitive: + # table: output/models/coefficients/transplant/ba2_cox_cens_*.csv - ## # # # # # # # # # # # # # # # # # # # - ## 3.2 CCW Analysis - check balance - COX - ## # # # # # # # # # # # # # # # # # # # - - calc_smd_transplant: - run: r:latest analysis/smd.R - --period ba1 - --subgrp transplant - needs: [perform_ccw_analysis_transplant] - outputs: - moderately_sensitive: - table: output/tables/ccw/transplant/smd_all_transplant.csv - - calc_smd_mol_transplant: - run: r:latest analysis/smd.R - --period ba1 - --contrast molnupiravir - --subgrp transplant - needs: [perform_ccw_analysis_mol_transplant] - outputs: - moderately_sensitive: - table: output/tables/ccw/transplant/smd_molnupiravir_transplant.csv - - calc_smd_sot_transplant: - run: r:latest analysis/smd.R - --period ba1 - --contrast sotrovimab - --subgrp transplant - needs: [perform_ccw_analysis_sot_transplant] - outputs: - moderately_sensitive: - table: output/tables/ccw/transplant/smd_sotrovimab_transplant.csv - - calc_smd_transplant_ba2: - run: r:latest analysis/smd.R - --period ba2 - --subgrp transplant - needs: [perform_ccw_analysis_transplant_ba2] - outputs: - moderately_sensitive: - table: output/tables/ccw/transplant/ba2_smd_all_transplant.csv - - calc_smd_mol_transplant_ba2: - run: r:latest analysis/smd.R - --period ba2 - --contrast molnupiravir - --subgrp transplant - needs: [perform_ccw_analysis_mol_transplant_ba2] - outputs: - moderately_sensitive: - table: output/tables/ccw/transplant/ba2_smd_molnupiravir_transplant.csv - - calc_smd_sot_transplant_ba2: - run: r:latest analysis/smd.R - --period ba2 - --contrast sotrovimab - --subgrp transplant - needs: [perform_ccw_analysis_sot_transplant_ba2] - outputs: - moderately_sensitive: - table: output/tables/ccw/transplant/ba2_smd_sotrovimab_transplant.csv - - ## # # # # # # # # # # # # # # # # # # # - ## 3.3 CCW Analysis - density weights - COX - ## # # # # # # # # # # # # # # # # # # # - - dens_weights_transplant: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba1 - --subgrp transplant - needs: [perform_ccw_analysis_transplant] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/transplant/dens_all_transplant.csv - table2: output/data_properties/data_long/transplant/q*_all_transplant.csv + # ## # # # # # # # # # # # # # # # # # # # + # ## 3.2 CCW Analysis - check balance - COX + # ## # # # # # # # # # # # # # # # # # # # + + # calc_smd_transplant: + # run: r:latest analysis/smd.R + # --period ba1 + # --subgrp transplant + # needs: [perform_ccw_analysis_transplant] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/transplant/smd_all_transplant.csv + + # calc_smd_mol_transplant: + # run: r:latest analysis/smd.R + # --period ba1 + # --contrast molnupiravir + # --subgrp transplant + # needs: [perform_ccw_analysis_mol_transplant] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/transplant/smd_molnupiravir_transplant.csv + + # calc_smd_sot_transplant: + # run: r:latest analysis/smd.R + # --period ba1 + # --contrast sotrovimab + # --subgrp transplant + # needs: [perform_ccw_analysis_sot_transplant] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/transplant/smd_sotrovimab_transplant.csv + + # calc_smd_transplant_ba2: + # run: r:latest analysis/smd.R + # --period ba2 + # --subgrp transplant + # needs: [perform_ccw_analysis_transplant_ba2] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/transplant/ba2_smd_all_transplant.csv + + # calc_smd_mol_transplant_ba2: + # run: r:latest analysis/smd.R + # --period ba2 + # --contrast molnupiravir + # --subgrp transplant + # needs: [perform_ccw_analysis_mol_transplant_ba2] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/transplant/ba2_smd_molnupiravir_transplant.csv + + # calc_smd_sot_transplant_ba2: + # run: r:latest analysis/smd.R + # --period ba2 + # --contrast sotrovimab + # --subgrp transplant + # needs: [perform_ccw_analysis_sot_transplant_ba2] + # outputs: + # moderately_sensitive: + # table: output/tables/ccw/transplant/ba2_smd_sotrovimab_transplant.csv + + # ## # # # # # # # # # # # # # # # # # # # + # ## 3.3 CCW Analysis - density weights - COX + # ## # # # # # # # # # # # # # # # # # # # + + # dens_weights_transplant: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba1 + # --subgrp transplant + # needs: [perform_ccw_analysis_transplant] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/transplant/dens_all_transplant.csv + # table2: output/data_properties/data_long/transplant/q*_all_transplant.csv - dens_weights_mol_transplant: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba1 - --contrast molnupiravir - --subgrp transplant - needs: [perform_ccw_analysis_mol_transplant] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/transplant/dens_molnupiravir_transplant.csv - table2: output/data_properties/data_long/transplant/q*_molnupiravir_transplant.csv - - dens_weights_sot_transplant: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba1 - --contrast sotrovimab - --subgrp transplant - needs: [perform_ccw_analysis_sot_transplant] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/transplant/dens_sotrovimab_transplant.csv - table2: output/data_properties/data_long/transplant/q*_sotrovimab_transplant.csv - - dens_weights_transplant_ba2: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba2 - --subgrp transplant - needs: [perform_ccw_analysis_transplant_ba2] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/transplant/ba2_dens_all_transplant.csv - table2: output/data_properties/data_long/transplant/ba2_q*_all_transplant.csv - - dens_weights_mol_transplant_ba2: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba2 - --contrast molnupiravir - --subgrp transplant - needs: [perform_ccw_analysis_mol_transplant_ba2] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/transplant/ba2_dens_molnupiravir_transplant.csv - table2: output/data_properties/data_long/transplant/ba2_q*_molnupiravir_transplant.csv - - dens_weights_sot_transplant_ba2: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba2 - --contrast sotrovimab - --subgrp transplant - needs: [perform_ccw_analysis_sot_transplant_ba2] - outputs: - moderately_sensitive: - table1: output/data_properties/data_long/transplant/ba2_dens_sotrovimab_transplant.csv - table2: output/data_properties/data_long/transplant/ba2_q*_sotrovimab_transplant.csv + # dens_weights_mol_transplant: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba1 + # --contrast molnupiravir + # --subgrp transplant + # needs: [perform_ccw_analysis_mol_transplant] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/transplant/dens_molnupiravir_transplant.csv + # table2: output/data_properties/data_long/transplant/q*_molnupiravir_transplant.csv + + # dens_weights_sot_transplant: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba1 + # --contrast sotrovimab + # --subgrp transplant + # needs: [perform_ccw_analysis_sot_transplant] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/transplant/dens_sotrovimab_transplant.csv + # table2: output/data_properties/data_long/transplant/q*_sotrovimab_transplant.csv + + # dens_weights_transplant_ba2: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba2 + # --subgrp transplant + # needs: [perform_ccw_analysis_transplant_ba2] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/transplant/ba2_dens_all_transplant.csv + # table2: output/data_properties/data_long/transplant/ba2_q*_all_transplant.csv + + # dens_weights_mol_transplant_ba2: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba2 + # --contrast molnupiravir + # --subgrp transplant + # needs: [perform_ccw_analysis_mol_transplant_ba2] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/transplant/ba2_dens_molnupiravir_transplant.csv + # table2: output/data_properties/data_long/transplant/ba2_q*_molnupiravir_transplant.csv + + # dens_weights_sot_transplant_ba2: + # run: r:latest analysis/data_ccw/dens_weights.R + # --period ba2 + # --contrast sotrovimab + # --subgrp transplant + # needs: [perform_ccw_analysis_sot_transplant_ba2] + # outputs: + # moderately_sensitive: + # table1: output/data_properties/data_long/transplant/ba2_dens_sotrovimab_transplant.csv + # table2: output/data_properties/data_long/transplant/ba2_q*_sotrovimab_transplant.csv ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # @@ -2724,85 +2724,85 @@ actions: ## KM curves ## # # # # # # # # # # # # # # # # # # # - # COX - plot_km: - run: r:latest analysis/km.R - --plot TRUE - needs: [perform_ccw_analysis] - outputs: - highly_sensitive: - feather: output/figures/km_estimates/km_estimates.feather - moderately_sensitive: - csv: output/figures/km_estimates/km_estimates.csv - plot1: output/figures/km_estimates/km_estimates.png - plot2: output/figures/km_estimates/km_estimates_red.png - - plot_km_mol: - run: r:latest analysis/km.R - --df_input output/data/data_long_molnupiravir.feather - --contrast molnupiravir - --plot TRUE - needs: [perform_ccw_analysis_mol] - outputs: - highly_sensitive: - feather: output/figures/km_estimates/km_estimates_molnupiravir.feather - moderately_sensitive: - csv: output/figures/km_estimates/km_estimates_molnupiravir.csv - plot: output/figures/km_estimates/km_estimates_molnupiravir.png + # # COX + # plot_km: + # run: r:latest analysis/km.R + # --plot TRUE + # needs: [perform_ccw_analysis] + # outputs: + # highly_sensitive: + # feather: output/figures/km_estimates/km_estimates.feather + # moderately_sensitive: + # csv: output/figures/km_estimates/km_estimates.csv + # plot1: output/figures/km_estimates/km_estimates.png + # plot2: output/figures/km_estimates/km_estimates_red.png + + # plot_km_mol: + # run: r:latest analysis/km.R + # --df_input output/data/data_long_molnupiravir.feather + # --contrast molnupiravir + # --plot TRUE + # needs: [perform_ccw_analysis_mol] + # outputs: + # highly_sensitive: + # feather: output/figures/km_estimates/km_estimates_molnupiravir.feather + # moderately_sensitive: + # csv: output/figures/km_estimates/km_estimates_molnupiravir.csv + # plot: output/figures/km_estimates/km_estimates_molnupiravir.png - plot_km_sot: - run: r:latest analysis/km.R - --df_input output/data/data_long_sotrovimab.feather - --contrast sotrovimab - --plot TRUE - needs: [perform_ccw_analysis_sot] - outputs: - highly_sensitive: - feather: output/figures/km_estimates/km_estimates_sotrovimab.feather - moderately_sensitive: - csv: output/figures/km_estimates/km_estimates_sotrovimab.csv - plot: output/figures/km_estimates/km_estimates_sotrovimab.png - - plot_km_ba2: - run: r:latest analysis/km.R - --df_input output/data/ba2_data_long_all.feather - --period ba2 - --plot TRUE - needs: [perform_ccw_analysis_ba2] - outputs: - highly_sensitive: - feather: output/figures/km_estimates/ba2_km_estimates.feather - moderately_sensitive: - csv: output/figures/km_estimates/ba2_km_estimates.csv - plot: output/figures/km_estimates/ba2_km_estimates.png - - plot_km_mol_ba2: - run: r:latest analysis/km.R - --df_input output/data/ba2_data_long_molnupiravir.feather - --period ba2 - --contrast molnupiravir - --plot TRUE - needs: [perform_ccw_analysis_mol_ba2] - outputs: - highly_sensitive: - feather: output/figures/km_estimates/ba2_km_estimates_molnupiravir.feather - moderately_sensitive: - csv: output/figures/km_estimates/ba2_km_estimates_molnupiravir.csv - plot: output/figures/km_estimates/ba2_km_estimates_molnupiravir.png + # plot_km_sot: + # run: r:latest analysis/km.R + # --df_input output/data/data_long_sotrovimab.feather + # --contrast sotrovimab + # --plot TRUE + # needs: [perform_ccw_analysis_sot] + # outputs: + # highly_sensitive: + # feather: output/figures/km_estimates/km_estimates_sotrovimab.feather + # moderately_sensitive: + # csv: output/figures/km_estimates/km_estimates_sotrovimab.csv + # plot: output/figures/km_estimates/km_estimates_sotrovimab.png + + # plot_km_ba2: + # run: r:latest analysis/km.R + # --df_input output/data/ba2_data_long_all.feather + # --period ba2 + # --plot TRUE + # needs: [perform_ccw_analysis_ba2] + # outputs: + # highly_sensitive: + # feather: output/figures/km_estimates/ba2_km_estimates.feather + # moderately_sensitive: + # csv: output/figures/km_estimates/ba2_km_estimates.csv + # plot: output/figures/km_estimates/ba2_km_estimates.png + + # plot_km_mol_ba2: + # run: r:latest analysis/km.R + # --df_input output/data/ba2_data_long_molnupiravir.feather + # --period ba2 + # --contrast molnupiravir + # --plot TRUE + # needs: [perform_ccw_analysis_mol_ba2] + # outputs: + # highly_sensitive: + # feather: output/figures/km_estimates/ba2_km_estimates_molnupiravir.feather + # moderately_sensitive: + # csv: output/figures/km_estimates/ba2_km_estimates_molnupiravir.csv + # plot: output/figures/km_estimates/ba2_km_estimates_molnupiravir.png - plot_km_sot_ba2: - run: r:latest analysis/km.R - --df_input output/data/ba2_data_long_sotrovimab.feather - --period ba2 - --contrast sotrovimab - --plot TRUE - needs: [perform_ccw_analysis_sot_ba2] - outputs: - highly_sensitive: - feather: output/figures/km_estimates/ba2_km_estimates_sotrovimab.feather - moderately_sensitive: - csv: output/figures/km_estimates/ba2_km_estimates_sotrovimab.csv - plot: output/figures/km_estimates/ba2_km_estimates_sotrovimab.png + # plot_km_sot_ba2: + # run: r:latest analysis/km.R + # --df_input output/data/ba2_data_long_sotrovimab.feather + # --period ba2 + # --contrast sotrovimab + # --plot TRUE + # needs: [perform_ccw_analysis_sot_ba2] + # outputs: + # highly_sensitive: + # feather: output/figures/km_estimates/ba2_km_estimates_sotrovimab.feather + # moderately_sensitive: + # csv: output/figures/km_estimates/ba2_km_estimates_sotrovimab.csv + # plot: output/figures/km_estimates/ba2_km_estimates_sotrovimab.png # PLR plot_km_plr: @@ -2885,7 +2885,7 @@ actions: plot1: output/plr/figures/km_estimates/ba2_km_estimates_molnupiravir.png plot2: output/plr/figures/km_estimates/ba2_km_estimates_molnupiravir_red.png - plot_km_sot_plr_ba2: + plot_km_sot_plr_ba2: run: r:latest analysis/km.R --df_input output/plr/data/ba2_data_long_sotrovimab_plr.feather --dir_output output/plr/figures/km_estimates @@ -2964,57 +2964,57 @@ actions: html1: output/tables/transplant/ba2_table1_redacted_transplant.html html2: output/tables/transplant/ba2_table1_unredacted_transplant.html - create_table_ccw: - run: r:latest analysis/table_ccw.R - --period ba1 - needs: [perform_ccw_analysis, perform_ccw_analysis_mol, perform_ccw_analysis_sot] - outputs: - moderately_sensitive: - html: output/tables/table_ccw.html - - create_table_ccw_ba2: - run: r:latest analysis/table_ccw.R - --period ba2 - needs: [perform_ccw_analysis_ba2, perform_ccw_analysis_mol_ba2, perform_ccw_analysis_sot_ba2] - outputs: - moderately_sensitive: - html: output/tables/ba2_table_ccw.html - - create_table_ccw_haem: - run: r:latest analysis/table_ccw.R - --period ba1 - --subgrp haem - needs: [perform_ccw_analysis_haem, perform_ccw_analysis_mol_haem, perform_ccw_analysis_sot_haem] - outputs: - moderately_sensitive: - html: output/tables/haem/table_ccw_haem.html - - create_table_ccw_haem_ba2: - run: r:latest analysis/table_ccw.R - --period ba2 - --subgrp haem - needs: [perform_ccw_analysis_haem_ba2, perform_ccw_analysis_mol_haem_ba2, perform_ccw_analysis_sot_haem_ba2] - outputs: - moderately_sensitive: - html: output/tables/haem/ba2_table_ccw_haem.html - - create_table_ccw_transplant: - run: r:latest analysis/table_ccw.R - --period ba1 - --subgrp transplant - needs: [perform_ccw_analysis_transplant, perform_ccw_analysis_mol_transplant, perform_ccw_analysis_sot_transplant] - outputs: - moderately_sensitive: - html: output/tables/transplant/table_ccw_transplant.html - - create_table_ccw_transplant_ba2: - run: r:latest analysis/table_ccw.R - --period ba2 - --subgrp transplant - needs: [perform_ccw_analysis_transplant_ba2, perform_ccw_analysis_mol_transplant_ba2, perform_ccw_analysis_sot_transplant_ba2] - outputs: - moderately_sensitive: - html: output/tables/transplant/ba2_table_ccw_transplant.html + # create_table_ccw: + # run: r:latest analysis/table_ccw.R + # --period ba1 + # needs: [perform_ccw_analysis, perform_ccw_analysis_mol, perform_ccw_analysis_sot] + # outputs: + # moderately_sensitive: + # html: output/tables/table_ccw.html + + # create_table_ccw_ba2: + # run: r:latest analysis/table_ccw.R + # --period ba2 + # needs: [perform_ccw_analysis_ba2, perform_ccw_analysis_mol_ba2, perform_ccw_analysis_sot_ba2] + # outputs: + # moderately_sensitive: + # html: output/tables/ba2_table_ccw.html + + # create_table_ccw_haem: + # run: r:latest analysis/table_ccw.R + # --period ba1 + # --subgrp haem + # needs: [perform_ccw_analysis_haem, perform_ccw_analysis_mol_haem, perform_ccw_analysis_sot_haem] + # outputs: + # moderately_sensitive: + # html: output/tables/haem/table_ccw_haem.html + + # create_table_ccw_haem_ba2: + # run: r:latest analysis/table_ccw.R + # --period ba2 + # --subgrp haem + # needs: [perform_ccw_analysis_haem_ba2, perform_ccw_analysis_mol_haem_ba2, perform_ccw_analysis_sot_haem_ba2] + # outputs: + # moderately_sensitive: + # html: output/tables/haem/ba2_table_ccw_haem.html + + # create_table_ccw_transplant: + # run: r:latest analysis/table_ccw.R + # --period ba1 + # --subgrp transplant + # needs: [perform_ccw_analysis_transplant, perform_ccw_analysis_mol_transplant, perform_ccw_analysis_sot_transplant] + # outputs: + # moderately_sensitive: + # html: output/tables/transplant/table_ccw_transplant.html + + # create_table_ccw_transplant_ba2: + # run: r:latest analysis/table_ccw.R + # --period ba2 + # --subgrp transplant + # needs: [perform_ccw_analysis_transplant_ba2, perform_ccw_analysis_mol_transplant_ba2, perform_ccw_analysis_sot_transplant_ba2] + # outputs: + # moderately_sensitive: + # html: output/tables/transplant/ba2_table_ccw_transplant.html create_table_ccw_plr: run: r:latest analysis/table_ccw.R