diff --git a/project.yaml b/project.yaml index ceb97db..5243dd5 100644 --- a/project.yaml +++ b/project.yaml @@ -237,822 +237,43 @@ 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 - - # 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 - - # ## # # # # # # # # # # # # # # # # # # # - # ## 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 - - # 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 - - # ## # # # # # # # # # # # # # # # # # # # - # ## 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 - - # 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 - - # ## # # # # # # # # # # # # # # # # # # # - # ## 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 + ## # # # # # # # # # # # # # # # # # # # + ## # # # # # # # # # # # # # # # # # # # + ## Table 1 + ## # # # # # # # # # # # # # # # # # # # + ## # # # # # # # # # # # # # # # # # # # + + create_table1: + run: r:latest analysis/table_1.R + --period ba1 + needs: [data_process] + outputs: + moderately_sensitive: + csv1: output/tables/table1.csv + csv2: output/tables/table1_redacted.csv + csv3: output/tables/table1_redacted_unf.csv + + create_table1_ba2: + run: r:latest analysis/table_1.R + --period ba2 + needs: [data_process_ba2] + outputs: + moderately_sensitive: + csv1: output/tables/ba2_table1.csv + csv2: output/tables/ba2_table1_redacted.csv + csv3: output/tables/ba2_table1_redacted_unf.csv + csv4: output/tables/ba2_table1_full.csv + csv5: output/tables/ba2_table1_full_redacted.csv + csv6: output/tables/ba2_table1_full_redacted_unf.csv ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # - ## 4 MAIN ANALYSIS - PLR + ## 1 MAIN ANALYSIS - PLR ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # - ## 4.1 CCW Analysis - PLR + ## 1.1 CCW Analysis - PLR ## # # # # # # # # # # # # # # # # # # # perform_ccw_analysis_plr: @@ -1180,7 +401,7 @@ actions: table: output/plr/models/coefficients/ba2_plr_cens*.csv ## # # # # # # # # # # # # # # # # # # # - ## 4.2 CCW Analysis - check balance - PLR + ## 1.2 CCW Analysis - check balance - PLR ## # # # # # # # # # # # # # # # # # # # calc_smd_plr: @@ -1242,7 +463,7 @@ actions: table: output/plr/tables/ccw/ba2_smd_sotrovimab_plr.csv ## # # # # # # # # # # # # # # # # # # # - ## 4.3 CCW Analysis - density weights - PLR + ## 1.3 CCW Analysis - density weights - PLR ## # # # # # # # # # # # # # # # # # # # dens_weights_plr: @@ -1310,8 +531,9 @@ actions: table2: output/plr/data_properties/data_long/ba2_q*_sotrovimab_plr.csv ## # # # # # # # # # # # # # # # # # # # - ## 4.4 CCW Analysis - flow data - PLR + ## 1.4 CCW Analysis - flow data - PLR ## # # # # # # # # # # # # # # # # # # # + describe_flow_data_long_plr: run: r:latest analysis/data_properties/describe_flow_data_long.R --model plr @@ -1375,12 +597,12 @@ actions: ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # - ## 5 TRUNCATED WEIGHTS - PLR + ## 2 TRUNCATED WEIGHTS - PLR ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # - ## 5.1 CCW Analysis - TRUNC x PLR + ## 2.1 CCW Analysis - TRUNC x PLR ## # # # # # # # # # # # # # # # # # # # perform_ccw_analysis_plr_truncated: @@ -1496,7 +718,7 @@ actions: table: output/plr/tables/ccw/truncated/ba2_ccw_sotrovimab_plr_truncated.csv ## # # # # # # # # # # # # # # # # # # # - ## 5.3 CCW Analysis - density weights - TRUNC x PLR + ## 2.3 CCW Analysis - density weights - TRUNC x PLR ## # # # # # # # # # # # # # # # # # # # dens_weights_plr_truncated: @@ -1571,12 +793,12 @@ actions: ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # - ## 6 GRACE 4 - PLR + ## 3 GRACE 4 - PLR ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # - ## 6.1 CCW Analysis - GRACE4 x PLR + ## 3.1 CCW Analysis - GRACE4 x PLR ## # # # # # # # # # # # # # # # # # # # perform_ccw_analysis_plr_grace4: @@ -1712,7 +934,7 @@ actions: table: output/plr/models/coefficients/grace4/ba2_plr_cens_*.csv ## # # # # # # # # # # # # # # # # # # # - ## 6.2 CCW Analysis - check balance - GRACE4 x PLR + ## 3.2 CCW Analysis - check balance - GRACE4 x PLR ## # # # # # # # # # # # # # # # # # # # calc_smd_plr_grace4: @@ -1780,7 +1002,7 @@ actions: table: output/plr/tables/ccw/grace4/ba2_smd_sotrovimab_plr_grace4.csv ## # # # # # # # # # # # # # # # # # # # - ## 6.3 CCW Analysis - density weights - GRACE4 x PLR + ## 3.3 CCW Analysis - density weights - GRACE4 x PLR ## # # # # # # # # # # # # # # # # # # # dens_weights_plr_grace4: @@ -1854,7 +1076,7 @@ actions: table2: output/plr/data_properties/data_long/grace4/ba2_q*_sotrovimab_plr_grace4.csv ## # # # # # # # # # # # # # # # # # # # - ## 6.4 CCW Analysis - flow data - GRACE4 x PLR + ## 3.4 CCW Analysis - flow data - GRACE4 x PLR ## # # # # # # # # # # # # # # # # # # # describe_flow_data_long_plr_grace4: @@ -1880,12 +1102,12 @@ actions: ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # - ## 7 GRACE 3 - PLR + ## 4 GRACE 3 - PLR ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # - ## 7.1 CCW Analysis - GRACE3 x PLR + ## 4.1 CCW Analysis - GRACE3 x PLR ## # # # # # # # # # # # # # # # # # # # perform_ccw_analysis_plr_grace3: @@ -2021,7 +1243,7 @@ actions: table: output/plr/models/coefficients/grace3/ba2_plr_cens_*.csv ## # # # # # # # # # # # # # # # # # # # - ## 7.2 CCW Analysis - check balance - GRACE3 x PLR + ## 4.2 CCW Analysis - check balance - GRACE3 x PLR ## # # # # # # # # # # # # # # # # # # # calc_smd_plr_grace3: @@ -2089,7 +1311,7 @@ actions: table: output/plr/tables/ccw/grace3/ba2_smd_sotrovimab_plr_grace3.csv ## # # # # # # # # # # # # # # # # # # # - ## 7.3 CCW Analysis - density weights - GRACE3 x PLR + ## 4.3 CCW Analysis - density weights - GRACE3 x PLR ## # # # # # # # # # # # # # # # # # # # dens_weights_plr_grace3: @@ -2163,7 +1385,7 @@ actions: table2: output/plr/data_properties/data_long/grace3/ba2_q*_sotrovimab_plr_grace3.csv ## # # # # # # # # # # # # # # # # # # # - ## 7.4 CCW Analysis - flow data - GRACE3 x PLR + ## 4.4 CCW Analysis - flow data - GRACE3 x PLR ## # # # # # # # # # # # # # # # # # # # describe_flow_data_long_plr_grace3: @@ -2187,660 +1409,114 @@ actions: table1: output/plr/data_properties/data_long/grace3/ba2_flow_data_plr_grace3.csv table2: output/plr/data_properties/data_long/grace3/ba2_flow_data_redacted_plr_grace3.csv - ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # - ## 8 SUBGROUP ANALYSIS: HEAM MALIG - PLR + ## 5 PRIMARY OUTCOMES COMBINED - PLR ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # - ## 8.1 CCW Analysis - PLR + ## 5.1 CCW Analysis - PRIMARY_COMBINED x PLR ## # # # # # # # # # # # # # # # # # # # - perform_ccw_analysis_plr_haem: - run: r:latest analysis/ccw.R - --period ba1 - --model plr - --subgrp haem - needs: [data_process] - outputs: - highly_sensitive: - data: output/plr/data/haem/data_long_all_plr_haem.feather - model01: output/plr/models/haem/plr_cens_control_all_plr_haem.rds - model02: output/plr/models/haem/plr_cens_trt_all_plr_haem.rds - model1: output/plr/models/haem/km_trt_all_plr_haem.rds - model2: output/plr/models/haem/km_control_all_plr_haem.rds - model3: output/plr/models/haem/cox_w_all_plr_haem.rds - model4: output/plr/models/haem/cox_uw_all_plr_haem.rds - moderately_sensitive: - table: output/plr/tables/ccw/haem/ccw_all_plr_haem.csv - - perform_ccw_analysis_mol_plr_haem: - run: r:latest analysis/ccw.R - --period ba1 - --contrast molnupiravir - --model plr - --subgrp haem - needs: [data_process] - outputs: - highly_sensitive: - data: output/plr/data/haem/data_long_molnupiravir_plr_haem.feather - model01: output/plr/models/haem/plr_cens_control_molnupiravir_plr_haem.rds - model02: output/plr/models/haem/plr_cens_trt_molnupiravir_plr_haem.rds - model1: output/plr/models/haem/km_trt_molnupiravir_plr_haem.rds - model2: output/plr/models/haem/km_control_molnupiravir_plr_haem.rds - model3: output/plr/models/haem/cox_w_molnupiravir_plr_haem.rds - model4: output/plr/models/haem/cox_uw_molnupiravir_plr_haem.rds - moderately_sensitive: - table: output/plr/tables/ccw/haem/ccw_molnupiravir_plr_haem.csv - - perform_ccw_analysis_sot_plr_haem: + perform_ccw_analysis_primary_combined_plr: run: r:latest analysis/ccw.R --period ba1 - --contrast sotrovimab --model plr - --subgrp haem + --outcome primary_combined needs: [data_process] outputs: highly_sensitive: - data: output/plr/data/haem/data_long_sotrovimab_plr_haem.feather - model01: output/plr/models/haem/plr_cens_control_sotrovimab_plr_haem.rds - model02: output/plr/models/haem/plr_cens_trt_sotrovimab_plr_haem.rds - model1: output/plr/models/haem/km_trt_sotrovimab_plr_haem.rds - model2: output/plr/models/haem/km_control_sotrovimab_plr_haem.rds - model3: output/plr/models/haem/cox_w_sotrovimab_plr_haem.rds - model4: output/plr/models/haem/cox_uw_sotrovimab_plr_haem.rds - moderately_sensitive: - table: output/plr/tables/ccw/haem/ccw_sotrovimab_plr_haem.csv - - save_coef_weight_models_plr_haem: - run: r:latest analysis/models_ccw/coef_weight_models.R - --period ba1 - --model plr - --subgrp haem - needs: [perform_ccw_analysis_plr_haem, perform_ccw_analysis_mol_plr_haem, perform_ccw_analysis_sot_plr_haem] - outputs: - moderately_sensitive: - table: output/plr/models/coefficients/haem/plr_cens_*.csv - - perform_ccw_analysis_plr_haem_ba2: + data: output/plr/data/data_long_all_primary_combined_plr.feather + model01: output/plr/models/plr_cens_control_all_primary_combined_plr.rds + model02: output/plr/models/plr_cens_trt_all_primary_combined_plr.rds + model03: output/plr/models/plr_cens2_trt_all_primary_combined_plr.rds + model1: output/plr/models/km_trt_all_primary_combined_plr.rds + model2: output/plr/models/km_control_all_primary_combined_plr.rds + model3: output/plr/models/cox_w_all_primary_combined_plr.rds + model4: output/plr/models/cox_uw_all_primary_combined_plr.rds + moderately_sensitive: + table: output/plr/tables/ccw/ccw_all_primary_combined_plr.csv + + perform_ccw_analysis_primary_combined_plr_ba2: run: r:latest analysis/ccw.R --period ba2 --model plr - --subgrp haem - needs: [data_process_ba2] - outputs: - highly_sensitive: - data: output/plr/data/haem/ba2_data_long_all_plr_haem.feather - model01: output/plr/models/haem/ba2_plr_cens_control_all_plr_haem.rds - model02: output/plr/models/haem/ba2_plr_cens_trt_all_plr_haem.rds - model1: output/plr/models/haem/ba2_km_trt_all_plr_haem.rds - model2: output/plr/models/haem/ba2_km_control_all_plr_haem.rds - model3: output/plr/models/haem/ba2_cox_w_all_plr_haem.rds - model4: output/plr/models/haem/ba2_cox_uw_all_plr_haem.rds - moderately_sensitive: - table: output/plr/tables/ccw/haem/ba2_ccw_all_plr_haem.csv - - perform_ccw_analysis_mol_plr_haem_ba2: - run: r:latest analysis/ccw.R - --period ba2 - --contrast molnupiravir - --model plr - --subgrp haem + --outcome primary_combined needs: [data_process_ba2] outputs: highly_sensitive: - data: output/plr/data/haem/ba2_data_long_molnupiravir_plr_haem.feather - model01: output/plr/models/haem/ba2_plr_cens_control_molnupiravir_plr_haem.rds - model02: output/plr/models/haem/ba2_plr_cens_trt_molnupiravir_plr_haem.rds - model1: output/plr/models/haem/ba2_km_trt_molnupiravir_plr_haem.rds - model2: output/plr/models/haem/ba2_km_control_molnupiravir_plr_haem.rds - model3: output/plr/models/haem/ba2_cox_w_molnupiravir_plr_haem.rds - model4: output/plr/models/haem/ba2_cox_uw_molnupiravir_plr_haem.rds + data: output/plr/data/ba2_data_long_all_primary_combined_plr.feather + model01: output/plr/models/ba2_plr_cens_control_all_primary_combined_plr.rds + model02: output/plr/models/ba2_plr_cens_trt_all_primary_combined_plr.rds + model03: output/plr/models/ba2_plr_cens2_trt_all_primary_combined_plr.rds + model1: output/plr/models/ba2_km_trt_all_primary_combined_plr.rds + model2: output/plr/models/ba2_km_control_all_primary_combined_plr.rds + model3: output/plr/models/ba2_cox_w_all_primary_combined_plr.rds + model4: output/plr/models/ba2_cox_uw_all_primary_combined_plr.rds moderately_sensitive: - table: output/plr/tables/ccw/haem/ba2_ccw_molnupiravir_plr_haem.csv + table: output/plr/tables/ccw/ba2_ccw_all_primary_combined_plr.csv - perform_ccw_analysis_sot_plr_haem_ba2: - run: r:latest analysis/ccw.R - --period ba2 - --contrast sotrovimab - --model plr - --subgrp haem - needs: [data_process_ba2] - outputs: - highly_sensitive: - data: output/plr/data/haem/ba2_data_long_sotrovimab_plr_haem.feather - model01: output/plr/models/haem/ba2_plr_cens_control_sotrovimab_plr_haem.rds - model02: output/plr/models/haem/ba2_plr_cens_trt_sotrovimab_plr_haem.rds - model1: output/plr/models/haem/ba2_km_trt_sotrovimab_plr_haem.rds - model2: output/plr/models/haem/ba2_km_control_sotrovimab_plr_haem.rds - model3: output/plr/models/haem/ba2_cox_w_sotrovimab_plr_haem.rds - model4: output/plr/models/haem/ba2_cox_uw_sotrovimab_plr_haem.rds - moderately_sensitive: - table: output/plr/tables/ccw/haem/ba2_ccw_sotrovimab_plr_haem.csv - - save_coef_weight_models_plr_haem_ba2: - run: r:latest analysis/models_ccw/coef_weight_models.R - --period ba2 - --model plr - --subgrp haem - needs: [perform_ccw_analysis_plr_haem_ba2, perform_ccw_analysis_mol_plr_haem_ba2, perform_ccw_analysis_sot_plr_haem_ba2] - outputs: - moderately_sensitive: - table: output/plr/models/coefficients/haem/ba2_plr_cens_*.csv - ## # # # # # # # # # # # # # # # # # # # - ## 8.2 CCW Analysis - check balance - PLR + ## 5.2 CCW Analysis - check balance - PRIMARY_COMBINED x PLR ## # # # # # # # # # # # # # # # # # # # - calc_smd_plr_haem: - run: r:latest analysis/smd.R - --period ba1 - --model plr - --subgrp haem - needs: [perform_ccw_analysis_plr_haem] - outputs: - moderately_sensitive: - table: output/plr/tables/ccw/haem/smd_all_plr_haem.csv - - calc_smd_mol_plr_haem: + calc_smd_primary_combined_plr: run: r:latest analysis/smd.R --period ba1 - --contrast molnupiravir --model plr - --subgrp haem - needs: [perform_ccw_analysis_mol_plr_haem] + --outcome primary_combined + needs: [perform_ccw_analysis_primary_combined_plr] outputs: moderately_sensitive: - table: output/plr/tables/ccw/haem/smd_molnupiravir_plr_haem.csv + table: output/plr/tables/ccw/smd_all_primary_combined_plr.csv - calc_smd_sot_plr_haem: - run: r:latest analysis/smd.R - --period ba1 - --contrast sotrovimab - --model plr - --subgrp haem - needs: [perform_ccw_analysis_sot_plr_haem] - outputs: - moderately_sensitive: - table: output/plr/tables/ccw/haem/smd_sotrovimab_plr_haem.csv - - calc_smd_plr_haem_ba2: + calc_smd_primary_combined_plr_ba2: run: r:latest analysis/smd.R --period ba2 --model plr - --subgrp haem - needs: [perform_ccw_analysis_plr_haem_ba2] + --outcome primary_combined + needs: [perform_ccw_analysis_primary_combined_plr_ba2] outputs: moderately_sensitive: - table: output/plr/tables/ccw/haem/ba2_smd_all_plr_haem.csv - - calc_smd_mol_plr_haem_ba2: - run: r:latest analysis/smd.R - --period ba2 - --contrast molnupiravir - --model plr - --subgrp haem - needs: [perform_ccw_analysis_mol_plr_haem_ba2] - outputs: - moderately_sensitive: - table: output/plr/tables/ccw/haem/ba2_smd_molnupiravir_plr_haem.csv - - calc_smd_sot_plr_haem_ba2: - run: r:latest analysis/smd.R - --period ba2 - --contrast sotrovimab - --model plr - --subgrp haem - needs: [perform_ccw_analysis_sot_plr_haem_ba2] - outputs: - moderately_sensitive: - table: output/plr/tables/ccw/haem/ba2_smd_sotrovimab_plr_haem.csv + table: output/plr/tables/ccw/ba2_smd_all_primary_combined_plr.csv ## # # # # # # # # # # # # # # # # # # # - ## 8.3 CCW Analysis - density weights - PLR + ## 5.3 CCW Analysis - density weights - PRIMARY_COMBINED x PLR ## # # # # # # # # # # # # # # # # # # # - dens_weights_plr_haem: + dens_weights_primary_combined_plr: run: r:latest analysis/data_ccw/dens_weights.R --period ba1 --model plr - --subgrp haem - needs: [perform_ccw_analysis_plr_haem] + --outcome primary_combined + needs: [perform_ccw_analysis_primary_combined_plr] outputs: moderately_sensitive: - table1: output/plr/data_properties/data_long/haem/dens_all_plr_haem.csv - table2: output/plr/data_properties/data_long/haem/q*_all_plr_haem.csv - - dens_weights_mol_plr_haem: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba1 - --contrast molnupiravir - --model plr - --subgrp haem - needs: [perform_ccw_analysis_mol_plr_haem] - outputs: - moderately_sensitive: - table1: output/plr/data_properties/data_long/haem/dens_molnupiravir_plr_haem.csv - table2: output/plr/data_properties/data_long/haem/q*_molnupiravir_plr_haem.csv - - dens_weights_sot_plr_haem: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba1 - --contrast sotrovimab - --model plr - --subgrp haem - needs: [perform_ccw_analysis_sot_plr_haem] - outputs: - moderately_sensitive: - table1: output/plr/data_properties/data_long/haem/dens_sotrovimab_plr_haem.csv - table2: output/plr/data_properties/data_long/haem/q*_sotrovimab_plr_haem.csv + table1: output/plr/data_properties/data_long/dens_all_primary_combined_plr.csv + table2: output/plr/data_properties/data_long/q*_all_primary_combined_plr.csv - dens_weights_plr_haem_ba2: + dens_weights_primary_combined_plr_ba2: run: r:latest analysis/data_ccw/dens_weights.R --period ba2 --model plr - --subgrp haem - needs: [perform_ccw_analysis_plr_haem_ba2] + --outcome primary_combined + needs: [perform_ccw_analysis_primary_combined_plr_ba2] outputs: moderately_sensitive: - table1: output/plr/data_properties/data_long/haem/ba2_dens_all_plr_haem.csv - table2: output/plr/data_properties/data_long/haem/ba2_q*_all_plr_haem.csv + table1: output/plr/data_properties/data_long/ba2_dens_all_primary_combined_plr.csv + table2: output/plr/data_properties/data_long/ba2_q*_all_primary_combined_plr.csv - dens_weights_mol_plr_haem_ba2: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba2 - --contrast molnupiravir - --model plr - --subgrp haem - needs: [perform_ccw_analysis_mol_plr_haem_ba2] - outputs: - moderately_sensitive: - table1: output/plr/data_properties/data_long/haem/ba2_dens_molnupiravir_plr_haem.csv - table2: output/plr/data_properties/data_long/haem/ba2_q*_molnupiravir_plr_haem.csv - - dens_weights_sot_plr_haem_ba2: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba2 - --contrast sotrovimab - --model plr - --subgrp haem - needs: [perform_ccw_analysis_sot_plr_haem_ba2] - outputs: - moderately_sensitive: - table1: output/plr/data_properties/data_long/haem/ba2_dens_sotrovimab_plr_haem.csv - table2: output/plr/data_properties/data_long/haem/ba2_q*_sotrovimab_plr_haem.csv - - ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # - ## 9 SUBGROUP ANALYSIS: ORGAN TRNSPLNT - PLR ## # # # # # # # # # # # # # # # # # # # + ## 6 KM curves ## # # # # # # # # # # # # # # # # # # # - - ## # # # # # # # # # # # # # # # # # # # - ## 9.1 CCW Analysis - PLR - ## # # # # # # # # # # # # # # # # # # # - - perform_ccw_analysis_plr_transplant: - run: r:latest analysis/ccw.R - --period ba1 - --model plr - --subgrp transplant - needs: [data_process] - outputs: - highly_sensitive: - data: output/plr/data/transplant/data_long_all_plr_transplant.feather - model01: output/plr/models/transplant/plr_cens_control_all_plr_transplant.rds - model02: output/plr/models/transplant/plr_cens_trt_all_plr_transplant.rds - model1: output/plr/models/transplant/km_trt_all_plr_transplant.rds - model2: output/plr/models/transplant/km_control_all_plr_transplant.rds - model3: output/plr/models/transplant/cox_w_all_plr_transplant.rds - model4: output/plr/models/transplant/cox_uw_all_plr_transplant.rds - moderately_sensitive: - table: output/plr/tables/ccw/transplant/ccw_all_plr_transplant.csv - - perform_ccw_analysis_mol_plr_transplant: - run: r:latest analysis/ccw.R - --period ba1 - --contrast molnupiravir - --model plr - --subgrp transplant - needs: [data_process] - outputs: - highly_sensitive: - data: output/plr/data/transplant/data_long_molnupiravir_plr_transplant.feather - model01: output/plr/models/transplant/plr_cens_control_molnupiravir_plr_transplant.rds - model02: output/plr/models/transplant/plr_cens_trt_molnupiravir_plr_transplant.rds - model1: output/plr/models/transplant/km_trt_molnupiravir_plr_transplant.rds - model2: output/plr/models/transplant/km_control_molnupiravir_plr_transplant.rds - model3: output/plr/models/transplant/cox_w_molnupiravir_plr_transplant.rds - model4: output/plr/models/transplant/cox_uw_molnupiravir_plr_transplant.rds - moderately_sensitive: - table: output/plr/tables/ccw/transplant/ccw_molnupiravir_plr_transplant.csv - - perform_ccw_analysis_sot_plr_transplant: - run: r:latest analysis/ccw.R - --period ba1 - --contrast sotrovimab - --model plr - --subgrp transplant - needs: [data_process] - outputs: - highly_sensitive: - data: output/plr/data/transplant/data_long_sotrovimab_plr_transplant.feather - model01: output/plr/models/transplant/plr_cens_control_sotrovimab_plr_transplant.rds - model02: output/plr/models/transplant/plr_cens_trt_sotrovimab_plr_transplant.rds - model1: output/plr/models/transplant/km_trt_sotrovimab_plr_transplant.rds - model2: output/plr/models/transplant/km_control_sotrovimab_plr_transplant.rds - model3: output/plr/models/transplant/cox_w_sotrovimab_plr_transplant.rds - model4: output/plr/models/transplant/cox_uw_sotrovimab_plr_transplant.rds - moderately_sensitive: - table: output/plr/tables/ccw/transplant/ccw_sotrovimab_plr_transplant.csv - - save_coef_weight_models_plr_transplant: - run: r:latest analysis/models_ccw/coef_weight_models.R - --period ba1 - --model plr - --subgrp transplant - needs: [perform_ccw_analysis_plr_transplant, perform_ccw_analysis_mol_plr_transplant, perform_ccw_analysis_sot_plr_transplant] - outputs: - moderately_sensitive: - table: output/plr/models/coefficients/transplant/plr_cens_*.csv - - perform_ccw_analysis_plr_transplant_ba2: - run: r:latest analysis/ccw.R - --period ba2 - --model plr - --subgrp transplant - needs: [data_process_ba2] - outputs: - highly_sensitive: - data: output/plr/data/transplant/ba2_data_long_all_plr_transplant.feather - model01: output/plr/models/transplant/ba2_plr_cens_control_all_plr_transplant.rds - model02: output/plr/models/transplant/ba2_plr_cens_trt_all_plr_transplant.rds - model1: output/plr/models/transplant/ba2_km_trt_all_plr_transplant.rds - model2: output/plr/models/transplant/ba2_km_control_all_plr_transplant.rds - model3: output/plr/models/transplant/ba2_cox_w_all_plr_transplant.rds - model4: output/plr/models/transplant/ba2_cox_uw_all_plr_transplant.rds - moderately_sensitive: - table: output/plr/tables/ccw/transplant/ba2_ccw_all_plr_transplant.csv - - perform_ccw_analysis_mol_plr_transplant_ba2: - run: r:latest analysis/ccw.R - --period ba2 - --contrast molnupiravir - --model plr - --subgrp transplant - needs: [data_process_ba2] - outputs: - highly_sensitive: - data: output/plr/data/transplant/ba2_data_long_molnupiravir_plr_transplant.feather - model01: output/plr/models/transplant/ba2_plr_cens_control_molnupiravir_plr_transplant.rds - model02: output/plr/models/transplant/ba2_plr_cens_trt_molnupiravir_plr_transplant.rds - model1: output/plr/models/transplant/ba2_km_trt_molnupiravir_plr_transplant.rds - model2: output/plr/models/transplant/ba2_km_control_molnupiravir_plr_transplant.rds - model3: output/plr/models/transplant/ba2_cox_w_molnupiravir_plr_transplant.rds - model4: output/plr/models/transplant/ba2_cox_uw_molnupiravir_plr_transplant.rds - moderately_sensitive: - table: output/plr/tables/ccw/transplant/ba2_ccw_molnupiravir_plr_transplant.csv - - perform_ccw_analysis_sot_plr_transplant_ba2: - run: r:latest analysis/ccw.R - --period ba2 - --contrast sotrovimab - --model plr - --subgrp transplant - needs: [data_process_ba2] - outputs: - highly_sensitive: - data: output/plr/data/transplant/ba2_data_long_sotrovimab_plr_transplant.feather - model01: output/plr/models/transplant/ba2_plr_cens_control_sotrovimab_plr_transplant.rds - model02: output/plr/models/transplant/ba2_plr_cens_trt_sotrovimab_plr_transplant.rds - model1: output/plr/models/transplant/ba2_km_trt_sotrovimab_plr_transplant.rds - model2: output/plr/models/transplant/ba2_km_control_sotrovimab_plr_transplant.rds - model3: output/plr/models/transplant/ba2_cox_w_sotrovimab_plr_transplant.rds - model4: output/plr/models/transplant/ba2_cox_uw_sotrovimab_plr_transplant.rds - moderately_sensitive: - table: output/plr/tables/ccw/transplant/ba2_ccw_sotrovimab_plr_transplant.csv - - save_coef_weight_models_plr_transplant_ba2: - run: r:latest analysis/models_ccw/coef_weight_models.R - --period ba2 - --model plr - --subgrp transplant - needs: [perform_ccw_analysis_plr_transplant_ba2, perform_ccw_analysis_mol_plr_transplant_ba2, perform_ccw_analysis_sot_plr_transplant_ba2] - outputs: - moderately_sensitive: - table: output/plr/models/coefficients/transplant/ba2_plr_cens_*.csv - ## # # # # # # # # # # # # # # # # # # # - ## 9.2 CCW Analysis - check balance - PLR - ## # # # # # # # # # # # # # # # # # # # - - calc_smd_plr_transplant: - run: r:latest analysis/smd.R - --period ba1 - --model plr - --subgrp transplant - needs: [perform_ccw_analysis_plr_transplant] - outputs: - moderately_sensitive: - table: output/plr/tables/ccw/transplant/smd_all_plr_transplant.csv - - calc_smd_mol_plr_transplant: - run: r:latest analysis/smd.R - --period ba1 - --contrast molnupiravir - --model plr - --subgrp transplant - needs: [perform_ccw_analysis_mol_plr_transplant] - outputs: - moderately_sensitive: - table: output/plr/tables/ccw/transplant/smd_molnupiravir_plr_transplant.csv - - calc_smd_sot_plr_transplant: - run: r:latest analysis/smd.R - --period ba1 - --contrast sotrovimab - --model plr - --subgrp transplant - needs: [perform_ccw_analysis_sot_plr_transplant] - outputs: - moderately_sensitive: - table: output/plr/tables/ccw/transplant/smd_sotrovimab_plr_transplant.csv - - calc_smd_plr_transplant_ba2: - run: r:latest analysis/smd.R - --period ba2 - --model plr - --subgrp transplant - needs: [perform_ccw_analysis_plr_transplant_ba2] - outputs: - moderately_sensitive: - table: output/plr/tables/ccw/transplant/ba2_smd_all_plr_transplant.csv - - calc_smd_mol_plr_transplant_ba2: - run: r:latest analysis/smd.R - --period ba2 - --contrast molnupiravir - --model plr - --subgrp transplant - needs: [perform_ccw_analysis_mol_plr_transplant_ba2] - outputs: - moderately_sensitive: - table: output/plr/tables/ccw/transplant/ba2_smd_molnupiravir_plr_transplant.csv - - calc_smd_sot_plr_transplant_ba2: - run: r:latest analysis/smd.R - --period ba2 - --contrast sotrovimab - --model plr - --subgrp transplant - needs: [perform_ccw_analysis_sot_plr_transplant_ba2] - outputs: - moderately_sensitive: - table: output/plr/tables/ccw/transplant/ba2_smd_sotrovimab_plr_transplant.csv ## # # # # # # # # # # # # # # # # # # # - ## 9.3 CCW Analysis - density weights - PLR + ## 6.1 KM curves - PLR ## # # # # # # # # # # # # # # # # # # # - dens_weights_plr_transplant: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba1 - --model plr - --subgrp transplant - needs: [perform_ccw_analysis_plr_transplant] - outputs: - moderately_sensitive: - table1: output/plr/data_properties/data_long/transplant/dens_all_plr_transplant.csv - table2: output/plr/data_properties/data_long/transplant/q*_all_plr_transplant.csv - - dens_weights_mol_plr_transplant: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba1 - --contrast molnupiravir - --model plr - --subgrp transplant - needs: [perform_ccw_analysis_mol_plr_transplant] - outputs: - moderately_sensitive: - table1: output/plr/data_properties/data_long/transplant/dens_molnupiravir_plr_transplant.csv - table2: output/plr/data_properties/data_long/transplant/q*_molnupiravir_plr_transplant.csv - - dens_weights_sot_plr_transplant: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba1 - --contrast sotrovimab - --model plr - --subgrp transplant - needs: [perform_ccw_analysis_sot_plr_transplant] - outputs: - moderately_sensitive: - table1: output/plr/data_properties/data_long/transplant/dens_sotrovimab_plr_transplant.csv - table2: output/plr/data_properties/data_long/transplant/q*_sotrovimab_plr_transplant.csv - - dens_weights_plr_transplant_ba2: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba2 - --model plr - --subgrp transplant - needs: [perform_ccw_analysis_plr_transplant_ba2] - outputs: - moderately_sensitive: - table1: output/plr/data_properties/data_long/transplant/ba2_dens_all_plr_transplant.csv - table2: output/plr/data_properties/data_long/transplant/ba2_q*_all_plr_transplant.csv - - dens_weights_mol_plr_transplant_ba2: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba2 - --contrast molnupiravir - --model plr - --subgrp transplant - needs: [perform_ccw_analysis_mol_plr_transplant_ba2] - outputs: - moderately_sensitive: - table1: output/plr/data_properties/data_long/transplant/ba2_dens_molnupiravir_plr_transplant.csv - table2: output/plr/data_properties/data_long/transplant/ba2_q*_molnupiravir_plr_transplant.csv - - dens_weights_sot_plr_transplant_ba2: - run: r:latest analysis/data_ccw/dens_weights.R - --period ba2 - --contrast sotrovimab - --model plr - --subgrp transplant - needs: [perform_ccw_analysis_sot_plr_transplant_ba2] - outputs: - moderately_sensitive: - table1: output/plr/data_properties/data_long/transplant/ba2_dens_sotrovimab_plr_transplant.csv - table2: output/plr/data_properties/data_long/transplant/ba2_q*_sotrovimab_plr_transplant.csv - - ## # # # # # # # # # # # # # # # # # # # - ## 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 - - # 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 - - # PLR plot_km_plr: run: r:latest analysis/km.R --df_input output/plr/data/data_long_all_plr.feather @@ -2939,133 +1615,47 @@ actions: plot2: output/plr/figures/km_estimates/ba2_km_estimates_sotrovimab_red.png ## # # # # # # # # # # # # # # # # # # # - ## Tables - ## # # # # # # # # # # # # # # # # # # # - - create_table1: - run: r:latest analysis/table_1.R - --period ba1 - needs: [data_process] - outputs: - moderately_sensitive: - csv1: output/tables/table1.csv - csv2: output/tables/table1_redacted.csv - csv3: output/tables/table1_redacted_unf.csv + ## 6.2 KM curves - PRIMARY_COMBINED x PLR + ## # # # # # # # # # # # # # # # # # # # - create_table1_ba2: - run: r:latest analysis/table_1.R - --period ba2 - needs: [data_process_ba2] - outputs: - moderately_sensitive: - csv1: output/tables/ba2_table1.csv - csv2: output/tables/ba2_table1_redacted.csv - csv3: output/tables/ba2_table1_redacted_unf.csv - csv4: output/tables/ba2_table1_full.csv - csv5: output/tables/ba2_table1_full_redacted.csv - csv6: output/tables/ba2_table1_full_redacted_unf.csv - - create_table1_haem: - run: r:latest analysis/table_1.R - --period ba1 - --subgrp haem - needs: [data_process] + plot_km_primary_combined_plr: + run: r:latest analysis/km.R + --df_input output/plr/data/data_long_all_primary_combined_plr.feather + --dir_output output/plr/figures/km_estimates + --outcome primary_combined + --plot TRUE + needs: [perform_ccw_analysis_primary_combined_plr] outputs: + highly_sensitive: + feather: output/plr/figures/km_estimates/km_estimates_primary_combined.feather moderately_sensitive: - csv1: output/tables/haem/table1.csv - csv2: output/tables/haem/table1_redacted.csv - csv3: output/tables/haem/table1_redacted_unf.csv + csv1: output/plr/figures/km_estimates/km_estimates_primary_combined.csv + csv2: output/plr/figures/km_estimates/km_estimates_primary_combined_red*.csv + plot1: output/plr/figures/km_estimates/km_estimates_primary_combined.png + plot2: output/plr/figures/km_estimates/km_estimates_primary_combined_red.png - create_table1_haem_ba2: - run: r:latest analysis/table_1.R + plot_km_primary_combined_plr_ba2: + run: r:latest analysis/km.R + --df_input output/plr/data/ba2_data_long_all_primary_combined_plr.feather + --dir_output output/plr/figures/km_estimates --period ba2 - --subgrp haem - needs: [data_process_ba2] - outputs: - moderately_sensitive: - csv1: output/tables/haem/ba2_table1.csv - csv2: output/tables/haem/ba2_table1_redacted.csv - csv3: output/tables/haem/ba2_table1_redacted_unf.csv - csv4: output/tables/haem/ba2_table1_full.csv - csv5: output/tables/haem/ba2_table1_full_redacted.csv - csv6: output/tables/haem/ba2_table1_full_redacted_unf.csv - - create_table1_transplant: - run: r:latest analysis/table_1.R - --period ba1 - --subgrp transplant - needs: [data_process] + --outcome primary_combined + --plot TRUE + needs: [perform_ccw_analysis_primary_combined_plr_ba2] outputs: + highly_sensitive: + feather: output/plr/figures/km_estimates/ba2_km_estimates_primary_combined.feather moderately_sensitive: - csv1: output/tables/transplant/table1.csv - csv2: output/tables/transplant/table1_redacted.csv - csv3: output/tables/transplant/table1_redacted_unf.csv + csv1: output/plr/figures/km_estimates/ba2_km_estimates_primary_combined.csv + csv2: output/plr/figures/km_estimates/ba2_km_estimates_primary_combined_red*.csv + plot1: output/plr/figures/km_estimates/ba2_km_estimates_primary_combined.png + plot2: output/plr/figures/km_estimates/ba2_km_estimates_primary_combined_red.png - create_table1_transplant_ba2: - run: r:latest analysis/table_1.R - --period ba2 - --subgrp transplant - needs: [data_process_ba2] - outputs: - moderately_sensitive: - csv1: output/tables/transplant/ba2_table1.csv - csv2: output/tables/transplant/ba2_table1_redacted.csv - csv3: output/tables/transplant/ba2_table1_redacted_unf.csv - csv4: output/tables/transplant/ba2_table1_full.csv - csv5: output/tables/transplant/ba2_table1_full_redacted.csv - csv6: output/tables/transplant/ba2_table1_full_redacted_unf.csv - - # 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 + ## # # # # # # # # # # # # # # # # # # # + ## # # # # # # # # # # # # # # # # # # # + ## 7 COLLATE tables + ## # # # # # # # # # # # # # # # # # # # + ## # # # # # # # # # # # # # # # # # # # create_table_ccw_plr: run: r:latest analysis/table_ccw.R @@ -3143,44 +1733,4 @@ actions: needs: [perform_ccw_analysis_plr_grace3_ba2, perform_ccw_analysis_mol_plr_grace3_ba2, perform_ccw_analysis_sot_plr_grace3_ba2] outputs: moderately_sensitive: - html: output/plr/tables/grace3/ba2_table_ccw_plr_grace3.csv - - create_table_ccw_plr_haem: - run: r:latest analysis/table_ccw.R - --period ba1 - --model plr - --subgrp haem - needs: [perform_ccw_analysis_plr_haem, perform_ccw_analysis_mol_plr_haem, perform_ccw_analysis_sot_plr_haem] - outputs: - moderately_sensitive: - html: output/plr/tables/haem/table_ccw_plr_haem.csv - - create_table_ccw_plr_haem_ba2: - run: r:latest analysis/table_ccw.R - --period ba2 - --model plr - --subgrp haem - needs: [perform_ccw_analysis_plr_haem_ba2, perform_ccw_analysis_mol_plr_haem_ba2, perform_ccw_analysis_sot_plr_haem_ba2] - outputs: - moderately_sensitive: - html: output/plr/tables/haem/ba2_table_ccw_plr_haem.csv - - create_table_ccw_plr_transplant: - run: r:latest analysis/table_ccw.R - --period ba1 - --model plr - --subgrp transplant - needs: [perform_ccw_analysis_plr_transplant, perform_ccw_analysis_mol_plr_transplant, perform_ccw_analysis_sot_plr_transplant] - outputs: - moderately_sensitive: - html: output/plr/tables/transplant/table_ccw_plr_transplant.csv - - create_table_ccw_plr_transplant_ba2: - run: r:latest analysis/table_ccw.R - --period ba2 - --model plr - --subgrp transplant - needs: [perform_ccw_analysis_plr_transplant_ba2, perform_ccw_analysis_mol_plr_transplant_ba2, perform_ccw_analysis_sot_plr_transplant_ba2] - outputs: - moderately_sensitive: - html: output/plr/tables/transplant/ba2_table_ccw_plr_transplant.csv \ No newline at end of file + html: output/plr/tables/grace3/ba2_table_ccw_plr_grace3.csv \ No newline at end of file