generated from opensafely/research-template
/
project.yaml
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/
project.yaml
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version: '3.0'
expectations:
population_size: 50000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
create_cohorts:
run: stata-mp:latest analysis/000_define_covariates.do
needs: [generate_study_population]
outputs:
highly_sensitive:
log1: logs/start_create_analysis_dataset.smcl
data1: output/data/file_imid.dta
data2: output/data/file_joint.dta
data3: output/data/file_skin.dta
data4: output/data/file_bowel.dta
data5: output/data/file_imiddrugcategory.dta
data6: output/data/file_standtnf.dta
data7: output/data/file_standtnf3m.dta
data8: output/data/file_tnfmono.dta
data9: output/data/file_standil6.dta
data10: output/data/file_standil17.dta
data11: output/data/file_standil23.dta
data12: output/data/file_standjaki.dta
data13: output/data/file_standritux.dta
data14: output/data/file_standinflix.dta
data15: output/data/file_standvedolizumab.dta
data16: output/data/file_standabatacept.dta
create_cohorts_single_file:
run: stata-mp:latest analysis/001_define_covariates_single_file.do
needs: [generate_study_population]
outputs:
highly_sensitive:
log1: logs/start_create_analysis_dataset_single_file.smcl
data1: output/data/file_imid_all.dta
run_baseline_tables:
run: stata-mp:latest analysis/100_baseline_characteristics.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/descriptive_tables.smcl
run_cox_models_imid:
run: stata-mp:latest analysis/202_cox_models.do "imid"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_models_imid.smcl
data1: output/data/cox_model_summary_imid.dta
data2: output/data/cox_model_summary_haemonc_imid.dta
run_cox_models_joint:
run: stata-mp:latest analysis/202_cox_models.do "joint"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_models_joint.smcl
data1: output/data/cox_model_summary_joint.dta
data2: output/data/cox_model_summary_haemonc_joint.dta
run_cox_models_skin:
run: stata-mp:latest analysis/202_cox_models.do "skin"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_models_skin.smcl
data1: output/data/cox_model_summary_skin.dta
data2: output/data/cox_model_summary_haemonc_skin.dta
run_cox_models_bowel:
run: stata-mp:latest analysis/202_cox_models.do "bowel"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_models_bowel.smcl
data1: output/data/cox_model_summary_bowel.dta
data2: output/data/cox_model_summary_haemonc_bowel.dta
run_cox_models_imiddrugcategory:
run: stata-mp:latest analysis/202_cox_models.do "imiddrugcategory"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_models_imiddrugcategory.smcl
data1: output/data/cox_model_summary_imiddrugcategory.dta
data2: output/data/cox_model_summary_haemonc_imiddrugcategory.dta
run_cox_models_standtnf:
run: stata-mp:latest analysis/202_cox_models.do "standtnf"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_models_standtnf.smcl
data1: output/data/cox_model_summary_standtnf.dta
data2: output/data/cox_model_summary_haemonc_standtnf.dta
run_cox_models_standtnf3m:
run: stata-mp:latest analysis/202_cox_models.do "standtnf3m"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_models_standtnf3m.smcl
data1: output/data/cox_model_summary_standtnf3m.dta
data2: output/data/cox_model_summary_haemonc_standtnf3m.dta
run_cox_models_tnfmono:
run: stata-mp:latest analysis/202_cox_models.do "tnfmono"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_models_tnfmono.smcl
data1: output/data/cox_model_summary_tnfmono.dta
data2: output/data/cox_model_summary_haemonc_tnfmono.dta
run_cox_models_standil6:
run: stata-mp:latest analysis/202_cox_models.do "standil6"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_models_standil6.smcl
data1: output/data/cox_model_summary_standil6.dta
data2: output/data/cox_model_summary_haemonc_standil6.dta
run_cox_models_standil17:
run: stata-mp:latest analysis/202_cox_models.do "standil17"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_models_standil17.smcl
data1: output/data/cox_model_summary_standil17.dta
data2: output/data/cox_model_summary_haemonc_standil17.dta
run_cox_models_standil23:
run: stata-mp:latest analysis/202_cox_models.do "standil23"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_models_standil23.smcl
data1: output/data/cox_model_summary_standil23.dta
data2: output/data/cox_model_summary_haemonc_standil23.dta
run_cox_models_standjaki:
run: stata-mp:latest analysis/202_cox_models.do "standjaki"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_models_standjaki.smcl
data1: output/data/cox_model_summary_standjaki.dta
data2: output/data/cox_model_summary_haemonc_standjaki.dta
run_cox_models_standritux:
run: stata-mp:latest analysis/202_cox_models.do "standritux"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_models_standritux.smcl
data1: output/data/cox_model_summary_standritux.dta
data2: output/data/cox_model_summary_haemonc_standritux.dta
run_cox_models_standinflix:
run: stata-mp:latest analysis/202_cox_models.do "standinflix"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_models_standinflix.smcl
data1: output/data/cox_model_summary_standinflix.dta
data2: output/data/cox_model_summary_haemonc_standinflix.dta
run_cox_models_standvedolizumab:
run: stata-mp:latest analysis/202_cox_models.do "standvedolizumab"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_models_standvedolizumab.smcl
data1: output/data/cox_model_summary_standvedolizumab.dta
data2: output/data/cox_model_summary_haemonc_standvedolizumab.dta
run_cox_models_standabatacept:
run: stata-mp:latest analysis/202_cox_models.do "standabatacept"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_models_standabatacept.smcl
data1: output/data/cox_model_summary_standabatacept.dta
data2: output/data/cox_model_summary_haemonc_standabatacept.dta
run_cox_models_imid_ethnicity_1:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "imid" "1"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_imid_ethnicity_1.smcl
data1: output/data/cox_model_summary_imid_ethnicity_1.dta
data2: output/data/cox_model_summary_haemonc_imid_ethnicity_1.dta
run_cox_models_imid_ethnicity_2:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "imid" "2"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_imid_ethnicity_2.smcl
data1: output/data/cox_model_summary_imid_ethnicity_2.dta
data2: output/data/cox_model_summary_haemonc_imid_ethnicity_2.dta
run_cox_models_imid_ethnicity_3:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "imid" "3"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_imid_ethnicity_3.smcl
data1: output/data/cox_model_summary_imid_ethnicity_3.dta
data2: output/data/cox_model_summary_haemonc_imid_ethnicity_3.dta
run_cox_models_imid_ethnicity_4:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "imid" "4"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_imid_ethnicity_4.smcl
data1: output/data/cox_model_summary_imid_ethnicity_4.dta
data2: output/data/cox_model_summary_haemonc_imid_ethnicity_4.dta
run_cox_models_imid_ethnicity_5:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "imid" "5"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_imid_ethnicity_5.smcl
data1: output/data/cox_model_summary_imid_ethnicity_5.dta
data2: output/data/cox_model_summary_haemonc_imid_ethnicity_5.dta
run_cox_models_imid_ethnicity_u:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "imid" "u"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_imid_ethnicity_u.smcl
data1: output/data/cox_model_summary_imid_ethnicity_u.dta
data2: output/data/cox_model_summary_haemonc_imid_ethnicity_u.dta
run_cox_models_joint_ethnicity_1:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "joint" "1"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_joint_ethnicity_1.smcl
data1: output/data/cox_model_summary_joint_ethnicity_1.dta
data2: output/data/cox_model_summary_haemonc_joint_ethnicity_1.dta
run_cox_models_joint_ethnicity_2:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "joint" "2"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_joint_ethnicity_2.smcl
data1: output/data/cox_model_summary_joint_ethnicity_2.dta
data2: output/data/cox_model_summary_haemonc_joint_ethnicity_2.dta
run_cox_models_joint_ethnicity_3:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "joint" "3"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_joint_ethnicity_3.smcl
data1: output/data/cox_model_summary_joint_ethnicity_3.dta
data2: output/data/cox_model_summary_haemonc_joint_ethnicity_3.dta
run_cox_models_joint_ethnicity_4:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "joint" "4"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_joint_ethnicity_4.smcl
data1: output/data/cox_model_summary_joint_ethnicity_4.dta
data2: output/data/cox_model_summary_haemonc_joint_ethnicity_4.dta
run_cox_models_joint_ethnicity_5:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "joint" "5"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_joint_ethnicity_5.smcl
data1: output/data/cox_model_summary_joint_ethnicity_5.dta
data2: output/data/cox_model_summary_haemonc_joint_ethnicity_5.dta
run_cox_models_joint_ethnicity_u:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "joint" "u"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_joint_ethnicity_u.smcl
data1: output/data/cox_model_summary_joint_ethnicity_u.dta
data2: output/data/cox_model_summary_haemonc_joint_ethnicity_u.dta
run_cox_models_skin_ethnicity_1:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "skin" "1"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_skin_ethnicity_1.smcl
data1: output/data/cox_model_summary_skin_ethnicity_1.dta
data2: output/data/cox_model_summary_haemonc_skin_ethnicity_1.dta
run_cox_models_skin_ethnicity_2:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "skin" "2"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_skin_ethnicity_2.smcl
data1: output/data/cox_model_summary_skin_ethnicity_2.dta
data2: output/data/cox_model_summary_haemonc_skin_ethnicity_2.dta
run_cox_models_skin_ethnicity_3:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "skin" "3"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_skin_ethnicity_3.smcl
data1: output/data/cox_model_summary_skin_ethnicity_3.dta
data2: output/data/cox_model_summary_haemonc_skin_ethnicity_3.dta
run_cox_models_skin_ethnicity_4:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "skin" "4"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_skin_ethnicity_4.smcl
data1: output/data/cox_model_summary_skin_ethnicity_4.dta
data2: output/data/cox_model_summary_haemonc_skin_ethnicity_4.dta
run_cox_models_skin_ethnicity_5:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "skin" "5"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_skin_ethnicity_5.smcl
data1: output/data/cox_model_summary_skin_ethnicity_5.dta
data2: output/data/cox_model_summary_haemonc_skin_ethnicity_5.dta
run_cox_models_skin_ethnicity_u:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "skin" "u"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_skin_ethnicity_u.smcl
data1: output/data/cox_model_summary_skin_ethnicity_u.dta
data2: output/data/cox_model_summary_haemonc_skin_ethnicity_u.dta
run_cox_models_bowel_ethnicity_1:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "bowel" "1"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_bowel_ethnicity_1.smcl
data1: output/data/cox_model_summary_bowel_ethnicity_1.dta
data2: output/data/cox_model_summary_haemonc_bowel_ethnicity_1.dta
run_cox_models_bowel_ethnicity_2:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "bowel" "2"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_bowel_ethnicity_2.smcl
data1: output/data/cox_model_summary_bowel_ethnicity_2.dta
data2: output/data/cox_model_summary_haemonc_bowel_ethnicity_2.dta
run_cox_models_bowel_ethnicity_3:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "bowel" "3"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_bowel_ethnicity_3.smcl
data1: output/data/cox_model_summary_bowel_ethnicity_3.dta
data2: output/data/cox_model_summary_haemonc_bowel_ethnicity_3.dta
run_cox_models_bowel_ethnicity_4:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "bowel" "4"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_bowel_ethnicity_4.smcl
data1: output/data/cox_model_summary_bowel_ethnicity_4.dta
data2: output/data/cox_model_summary_haemonc_bowel_ethnicity_4.dta
run_cox_models_bowel_ethnicity_5:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "bowel" "5"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_bowel_ethnicity_5.smcl
data1: output/data/cox_model_summary_bowel_ethnicity_5.dta
data2: output/data/cox_model_summary_haemonc_bowel_ethnicity_5.dta
run_cox_models_bowel_ethnicity_u:
run: stata-mp:latest analysis/500_cox_models_ethnic.do "bowel" "u"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_bowel_ethnicity_u.smcl
data1: output/data/cox_model_summary_bowel_ethnicity_u.dta
data2: output/data/cox_model_summary_haemonc_bowel_ethnicity_u.dta
run_cox_models_genpop_ethnicity_vs_white:
run: stata-mp:latest analysis/501_cox_models_ethnicity_vs_white.do "genpop"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_genpop_ethnicity_vs_white.smcl
data1: output/data/cox_model_summary_genpop_ethnicity_vs_white.dta
run_cox_models_imid_ethnicity_vs_white:
run: stata-mp:latest analysis/501_cox_models_ethnicity_vs_white.do "imid"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_imid_ethnicity_vs_white.smcl
data1: output/data/cox_model_summary_imid_ethnicity_vs_white.dta
run_cox_models_joint_ethnicity_vs_white:
run: stata-mp:latest analysis/501_cox_models_ethnicity_vs_white.do "joint"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_joint_ethnicity_vs_white.smcl
data1: output/data/cox_model_summary_joint_ethnicity_vs_white.dta
run_cox_models_skin_ethnicity_vs_white:
run: stata-mp:latest analysis/501_cox_models_ethnicity_vs_white.do "skin"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_skin_ethnicity_vs_white.smcl
data1: output/data/cox_model_summary_skin_ethnicity_vs_white.dta
run_cox_models_bowel_ethnicity_vs_white:
run: stata-mp:latest analysis/501_cox_models_ethnicity_vs_white.do "bowel"
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
log1: logs/cox_models_bowel_ethnicity_vs_white.smcl
data1: output/data/cox_model_summary_bowel_ethnicity_vs_white.dta
run_survival_curves:
run: stata-mp:latest analysis/301_survival_curves.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/graphs.smcl
survcur_bowel_died: output/figures/survcur_bowel_died.svg
survcur_bowel_hospital: output/figures/survcur_bowel_hospital.svg
survcur_bowel_icuordeath: output/figures/survcur_bowel_icuordeath.svg
survcur_imid_died: output/figures/survcur_imid_died.svg
survcur_imid_hospital: output/figures/survcur_imid_hospital.svg
survcur_imid_icuordeath: output/figures/survcur_imid_icuordeath.svg
survcur_imiddrugcategory_died: output/figures/survcur_imiddrugcategory_died.svg
survcur_imiddrugcategory_hospital: output/figures/survcur_imiddrugcategory_hospital.svg
survcur_imiddrugcategory_icuordeath: output/figures/survcur_imiddrugcategory_icuordeath.svg
survcur_joint_died: output/figures/survcur_joint_died.svg
survcur_joint_hospital: output/figures/survcur_joint_hospital.svg
survcur_joint_icuordeath: output/figures/survcur_joint_icuordeath.svg
survcur_skin_died: output/figures/survcur_skin_died.svg
survcur_skin_hospital: output/figures/survcur_skin_hospital.svg
survcur_skin_icuordeath: output/figures/survcur_skin_icuordeath.svg
survhaz_bowel_died: output/figures/survhaz_bowel_died.svg
survhaz_bowel_hospital: output/figures/survhaz_bowel_hospital.svg
survhaz_bowel_icuordeath: output/figures/survhaz_bowel_icuordeath.svg
survhaz_imid_died: output/figures/survhaz_imid_died.svg
survhaz_imid_hospital: output/figures/survhaz_imid_hospital.svg
survhaz_imid_icuordeath: output/figures/survhaz_imid_icuordeath.svg
survhaz_imiddrugcategory_died: output/figures/survhaz_imiddrugcategory_died.svg
survhaz_imiddrugcategory_hospital: output/figures/survhaz_imiddrugcategory_hospital.svg
survhaz_imiddrugcategory_icuordeath: output/figures/survhaz_imiddrugcategory_icuordeath.svg
survhaz_joint_died: output/figures/survhaz_joint_died.svg
survhaz_joint_hospital: output/figures/survhaz_joint_hospital.svg
survhaz_joint_icuordeath: output/figures/survhaz_joint_icuordeath.svg
survhaz_skin_died: output/figures/survhaz_skin_died.svg
survhaz_skin_hospital: output/figures/survhaz_skin_hospital.svg
survhaz_skin_icuordeath: output/figures/survhaz_skin_icuordeath.svg
survrisk_bowel_died: output/figures/survrisk_bowel_died.svg
survrisk_bowel_hospital: output/figures/survrisk_bowel_hospital.svg
survrisk_bowel_icuordeath: output/figures/survrisk_bowel_icuordeath.svg
survrisk_imid_died: output/figures/survrisk_imid_died.svg
survrisk_imid_hospital: output/figures/survrisk_imid_hospital.svg
survrisk_imid_icuordeath: output/figures/survrisk_imid_icuordeath.svg
survrisk_imiddrugcategory_died: output/figures/survrisk_imiddrugcategory_died.svg
survrisk_imiddrugcategory_hospital: output/figures/survrisk_imiddrugcategory_hospital.svg
survrisk_imiddrugcategory_icuordeath: output/figures/survrisk_imiddrugcategory_icuordeath.svg
survrisk_joint_died: output/figures/survrisk_joint_died.svg
survrisk_joint_hospital: output/figures/survrisk_joint_hospital.svg
survrisk_joint_icuordeath: output/figures/survrisk_joint_icuordeath.svg
survrisk_skin_died: output/figures/survrisk_skin_died.svg
survrisk_skin_hospital: output/figures/survrisk_skin_hospital.svg
survrisk_skin_icuordeath: output/figures/survrisk_skin_icuordeath.svg
run_cox_spline_imid:
run: stata-mp:latest analysis/402_cox_models_agespline.do "imid"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_spline_imid.smcl
data1: output/data/cox_spline_summary_imid.dta
data2: output/data/cox_spline_summary_haemonc_imid.dta
run_cox_spline_joint:
run: stata-mp:latest analysis/402_cox_models_agespline.do "joint"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_spline_joint.smcl
data1: output/data/cox_spline_summary_joint.dta
data2: output/data/cox_spline_summary_haemonc_joint.dta
run_cox_spline_skin:
run: stata-mp:latest analysis/402_cox_models_agespline.do "skin"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_spline_skin.smcl
data1: output/data/cox_spline_summary_skin.dta
data2: output/data/cox_spline_summary_haemonc_skin.dta
run_cox_spline_bowel:
run: stata-mp:latest analysis/402_cox_models_agespline.do "bowel"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_spline_bowel.smcl
data1: output/data/cox_spline_summary_bowel.dta
data2: output/data/cox_spline_summary_haemonc_bowel.dta
run_cox_spline_imiddrugcategory:
run: stata-mp:latest analysis/402_cox_models_agespline.do "imiddrugcategory"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_spline_imiddrugcategory.smcl
data1: output/data/cox_spline_summary_imiddrugcategory.dta
data2: output/data/cox_spline_summary_haemonc_imiddrugcategory.dta
run_cox_spline_standtnf:
run: stata-mp:latest analysis/402_cox_models_agespline.do "standtnf"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_spline_standtnf.smcl
data1: output/data/cox_spline_summary_standtnf.dta
data2: output/data/cox_spline_summary_haemonc_standtnf.dta
run_cox_spline_standtnf3m:
run: stata-mp:latest analysis/402_cox_models_agespline.do "standtnf3m"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_spline_standtnf3m.smcl
data1: output/data/cox_spline_summary_standtnf3m.dta
data2: output/data/cox_spline_summary_haemonc_standtnf3m.dta
run_cox_spline_tnfmono:
run: stata-mp:latest analysis/402_cox_models_agespline.do "tnfmono"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_spline_tnfmono.smcl
data1: output/data/cox_spline_summary_tnfmono.dta
data2: output/data/cox_spline_summary_haemonc_tnfmono.dta
run_cox_spline_standil6:
run: stata-mp:latest analysis/402_cox_models_agespline.do "standil6"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_spline_standil6.smcl
data1: output/data/cox_spline_summary_standil6.dta
data2: output/data/cox_spline_summary_haemonc_standil6.dta
run_cox_spline_standil17:
run: stata-mp:latest analysis/402_cox_models_agespline.do "standil17"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_spline_standil17.smcl
data1: output/data/cox_spline_summary_standil17.dta
data2: output/data/cox_spline_summary_haemonc_standil17.dta
run_cox_spline_standil23:
run: stata-mp:latest analysis/402_cox_models_agespline.do "standil23"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_spline_standil23.smcl
data1: output/data/cox_spline_summary_standil23.dta
data2: output/data/cox_spline_summary_haemonc_standil23.dta
run_cox_spline_standjaki:
run: stata-mp:latest analysis/402_cox_models_agespline.do "standjaki"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_spline_standjaki.smcl
data1: output/data/cox_spline_summary_standjaki.dta
data2: output/data/cox_spline_summary_haemonc_standjaki.dta
run_cox_spline_standritux:
run: stata-mp:latest analysis/402_cox_models_agespline.do "standritux"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_spline_standritux.smcl
data1: output/data/cox_spline_summary_standritux.dta
data2: output/data/cox_spline_summary_haemonc_standritux.dta
run_cox_spline_standinflix:
run: stata-mp:latest analysis/402_cox_models_agespline.do "standinflix"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_spline_standinflix.smcl
data1: output/data/cox_spline_summary_standinflix.dta
data2: output/data/cox_spline_summary_haemonc_standinflix.dta
run_cox_spline_standvedolizumab:
run: stata-mp:latest analysis/402_cox_models_agespline.do "standvedolizumab"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_spline_standvedolizumab.smcl
data1: output/data/cox_spline_summary_standvedolizumab.dta
data2: output/data/cox_spline_summary_haemonc_standvedolizumab.dta
run_cox_spline_standabatacept:
run: stata-mp:latest analysis/402_cox_models_agespline.do "standabatacept"
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/cox_spline_standabatacept.smcl
data1: output/data/cox_spline_summary_standabatacept.dta
data2: output/data/cox_spline_summary_haemonc_standabatacept.dta
run_spline_export_csv:
run: stata-mp:latest analysis/403_spline_export_csv.do
needs: [run_cox_spline_imid,run_cox_spline_joint,run_cox_spline_bowel,run_cox_spline_skin,run_cox_spline_imiddrugcategory,run_cox_spline_standtnf,run_cox_spline_standtnf3m,run_cox_spline_standil6,run_cox_spline_standil17,run_cox_spline_standil23,run_cox_spline_standritux,run_cox_spline_standinflix,run_cox_spline_tnfmono,run_cox_spline_standjaki,run_cox_spline_standvedolizumab,run_cox_spline_standabatacept]
outputs:
moderately_sensitive:
log: logs/spline_export_csv.smcl
csv_spline_spline_imid: output/data/csv_spline_imid.csv
csvhaemonc_spline_imid: output/data/csvhaemonc_spline_imid.csv
csv_spline_joint: output/data/csv_spline_joint.csv
csvhaemonc_spline_joint: output/data/csvhaemonc_spline_joint.csv
csv_spline_skin: output/data/csv_spline_skin.csv
csvhaemonc_spline_skin: output/data/csvhaemonc_spline_skin.csv
csv_spline_bowel: output/data/csv_spline_bowel.csv
csvhaemonc_spline_bowel: output/data/csvhaemonc_spline_bowel.csv
csv_spline_imiddrugcategory: output/data/csv_spline_imiddrugcategory.csv
csvhaemonc_spline_imiddrugcategory: output/data/csvhaemonc_spline_imiddrugcategory.csv
csv_spline_standtnf: output/data/csv_spline_standtnf.csv
csvhaemonc_spline_standtnf: output/data/csvhaemonc_spline_standtnf.csv
csv_spline_standtnf3m: output/data/csv_spline_standtnf3m.csv
csvhaemonc_spline_standtnf3m: output/data/csvhaemonc_spline_standtnf3m.csv
csv_spline_tnfmono: output/data/csv_spline_tnfmono.csv
csvhaemonc_spline_tnfmono: output/data/csvhaemonc_spline_tnfmono.csv
csv_spline_standil6: output/data/csv_spline_standil6.csv
csvhaemonc_spline_standil6: output/data/csvhaemonc_spline_standil6.csv
csv_spline_standil17: output/data/csv_spline_standil17.csv
csvhaemonc_spline_standil17: output/data/csvhaemonc_spline_standil17.csv
csv_spline_standil23: output/data/csv_spline_standil23.csv
csvhaemonc_spline_standil23: output/data/csvhaemonc_spline_standil23.csv
csv_spline_standjaki: output/data/csv_spline_standjaki.csv
csvhaemonc_spline_standjaki: output/data/csvhaemonc_spline_standjaki.csv
csv_spline_standritux: output/data/csv_spline_standritux.csv
csvhaemonc_spline_standritux: output/data/csvhaemonc_spline_standritux.csv
csv_spline_standinflix: output/data/csv_spline_standinflix.csv
csvhaemonc_spline_standinflix: output/data/csvhaemonc_spline_standinflix.csv
csv_spline_standvedolizumab: output/data/csv_spline_standvedolizumab.csv
csvhaemonc_spline_standvedolizumab: output/data/csvhaemonc_spline_standvedolizumab.csv
csv_spline_standabatacept: output/data/csv_spline_standabatacept.csv
csvhaemonc_spline_standabatacept: output/data/csvhaemonc_spline_standabatacept.csv
run_schoenfeld:
run: stata-mp:latest analysis/401_schoenfeld.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
logschoenfeld: logs/cox_model_diagnostics.smcl
run_outcomes_check:
run: r:latest analysis/outcomes_check_withandwithoutpositivetest.R
needs: [create_cohorts]
outputs:
moderately_sensitive:
data1: output/data/outcomes_check.csv
run_export_csv:
run: stata-mp:latest analysis/400_export_csv.do
needs: [run_cox_models_imid,run_cox_models_joint,run_cox_models_skin,run_cox_models_bowel,run_cox_models_imiddrugcategory,run_cox_models_standtnf,run_cox_models_standtnf3m,run_cox_models_tnfmono,run_cox_models_standil6,run_cox_models_standil17,run_cox_models_standil23,run_cox_models_standjaki,run_cox_models_standritux,run_cox_models_standinflix,run_cox_models_standvedolizumab,run_cox_models_standabatacept]
outputs:
moderately_sensitive:
log: logs/export_csv.smcl
csv_imid: output/data/csv_imid.csv
csvhaemonc_imid: output/data/csvhaemonc_imid.csv
csv_joint: output/data/csv_joint.csv
csvhaemonc_joint: output/data/csvhaemonc_joint.csv
csv_skin: output/data/csv_skin.csv
csvhaemonc_skin: output/data/csvhaemonc_skin.csv
csv_bowel: output/data/csv_bowel.csv
csvhaemonc_bowel: output/data/csvhaemonc_bowel.csv
csv_imiddrugcategory: output/data/csv_imiddrugcategory.csv
csvhaemonc_imiddrugcategory: output/data/csvhaemonc_imiddrugcategory.csv
csv_standtnf: output/data/csv_standtnf.csv
csvhaemonc_standtnf: output/data/csvhaemonc_standtnf.csv
csv_standtnf3m: output/data/csv_standtnf3m.csv
csvhaemonc_standtnf3m: output/data/csvhaemonc_standtnf3m.csv
csv_tnfmono: output/data/csv_tnfmono.csv
csvhaemonc_tnfmono: output/data/csvhaemonc_tnfmono.csv
csv_standil6: output/data/csv_standil6.csv
csvhaemonc_standil6: output/data/csvhaemonc_standil6.csv
csv_standil17: output/data/csv_standil17.csv
csvhaemonc_standil17: output/data/csvhaemonc_standil17.csv
csv_standil23: output/data/csv_standil23.csv
csvhaemonc_standil23: output/data/csvhaemonc_standil23.csv
csv_standjaki: output/data/csv_standjaki.csv
csvhaemonc_standjaki: output/data/csvhaemonc_standjaki.csv
csv_standritux: output/data/csv_standritux.csv
csvhaemonc_standritux: output/data/csvhaemonc_standritux.csv
csv_standinflix: output/data/csv_standinflix.csv
csvhaemonc_standinflix: output/data/csvhaemonc_standinflix.csv
csv_standvedolizumab: output/data/csv_standvedolizumab.csv
csvhaemonc_standvedolizumab: output/data/csvhaemonc_standvedolizumab.csv
csv_standabatacept: output/data/csv_standabatacept.csv
csvhaemonc_standabatacept: output/data/csvhaemonc_standabatacept.csv
run_forest_plots:
run: r:latest analysis/r-immunosuppressant-meds-research/make_forest_plots_with_3_models.R
needs: [run_export_csv]
outputs:
moderately_sensitive:
merged_csv: output/data/merged_csv_normal.csv
merged_csv_haemoonc: output/data/merged_csv_haemonc.csv
forest_plot_vs_gen_pop: output/figures/forest_plot_vs_gen_pop.svg
forest_plot_vs_standard_systemic: output/figures/forest_plot_vs_standard_systemic.svg
run_export_csv_ethnicity:
run: stata-mp:latest analysis/600_export_csv_ethnicity.do
needs: [run_cox_models_imid_ethnicity_1,run_cox_models_imid_ethnicity_2,run_cox_models_imid_ethnicity_3,run_cox_models_imid_ethnicity_4,run_cox_models_imid_ethnicity_5,run_cox_models_imid_ethnicity_u,run_cox_models_joint_ethnicity_1,run_cox_models_joint_ethnicity_2,run_cox_models_joint_ethnicity_3,run_cox_models_joint_ethnicity_4,run_cox_models_joint_ethnicity_5,run_cox_models_joint_ethnicity_u,run_cox_models_skin_ethnicity_1,run_cox_models_skin_ethnicity_2,run_cox_models_skin_ethnicity_3,run_cox_models_skin_ethnicity_4,run_cox_models_skin_ethnicity_5,run_cox_models_skin_ethnicity_u,run_cox_models_bowel_ethnicity_1,run_cox_models_bowel_ethnicity_2,run_cox_models_bowel_ethnicity_3,run_cox_models_bowel_ethnicity_4,run_cox_models_bowel_ethnicity_5,run_cox_models_bowel_ethnicity_u]
outputs:
moderately_sensitive:
log: logs/export_csv_ethnicity.smcl
csv_imid_ethnicity_1_csv: output/data/csv_imid_ethnicity_1.csv
csv_imid_ethnicity_2_csv: output/data/csv_imid_ethnicity_2.csv
csv_imid_ethnicity_3_csv: output/data/csv_imid_ethnicity_3.csv
csv_imid_ethnicity_4_csv: output/data/csv_imid_ethnicity_4.csv
csv_imid_ethnicity_5_csv: output/data/csv_imid_ethnicity_5.csv
csv_imid_ethnicity_u_csv: output/data/csv_imid_ethnicity_u.csv
csv_joint_ethnicity_1_csv: output/data/csv_joint_ethnicity_1.csv
csv_joint_ethnicity_2_csv: output/data/csv_joint_ethnicity_2.csv
csv_joint_ethnicity_3_csv: output/data/csv_joint_ethnicity_3.csv
csv_joint_ethnicity_4_csv: output/data/csv_joint_ethnicity_4.csv
csv_joint_ethnicity_5_csv: output/data/csv_joint_ethnicity_5.csv
csv_joint_ethnicity_u_csv: output/data/csv_joint_ethnicity_u.csv
csv_skin_ethnicity_1_csv: output/data/csv_skin_ethnicity_1.csv
csv_skin_ethnicity_2_csv: output/data/csv_skin_ethnicity_2.csv
csv_skin_ethnicity_3_csv: output/data/csv_skin_ethnicity_3.csv
csv_skin_ethnicity_4_csv: output/data/csv_skin_ethnicity_4.csv
csv_skin_ethnicity_5_csv: output/data/csv_skin_ethnicity_5.csv
csv_skin_ethnicity_u_csv: output/data/csv_skin_ethnicity_u.csv
csv_bowel_ethnicity_1_csv: output/data/csv_bowel_ethnicity_1.csv
csv_bowel_ethnicity_2_csv: output/data/csv_bowel_ethnicity_2.csv
csv_bowel_ethnicity_3_csv: output/data/csv_bowel_ethnicity_3.csv
csv_bowel_ethnicity_4_csv: output/data/csv_bowel_ethnicity_4.csv
csv_bowel_ethnicity_5_csv: output/data/csv_bowel_ethnicity_5.csv
csv_bowel_ethnicity_u_csv: output/data/csv_bowel_ethnicity_u.csv
csvhaemonc_imid_ethnicity_1_csv: output/data/csvhaemonc_imid_ethnicity_1.csv
csvhaemonc_imid_ethnicity_2_csv: output/data/csvhaemonc_imid_ethnicity_2.csv
csvhaemonc_imid_ethnicity_3_csv: output/data/csvhaemonc_imid_ethnicity_3.csv
csvhaemonc_imid_ethnicity_4_csv: output/data/csvhaemonc_imid_ethnicity_4.csv
csvhaemonc_imid_ethnicity_5_csv: output/data/csvhaemonc_imid_ethnicity_5.csv
csvhaemonc_imid_ethnicity_u_csv: output/data/csvhaemonc_imid_ethnicity_u.csv
csvhaemonc_joint_ethnicity_1_csv: output/data/csvhaemonc_joint_ethnicity_1.csv
csvhaemonc_joint_ethnicity_2_csv: output/data/csvhaemonc_joint_ethnicity_2.csv
csvhaemonc_joint_ethnicity_3_csv: output/data/csvhaemonc_joint_ethnicity_3.csv
csvhaemonc_joint_ethnicity_4_csv: output/data/csvhaemonc_joint_ethnicity_4.csv
csvhaemonc_joint_ethnicity_5_csv: output/data/csvhaemonc_joint_ethnicity_5.csv
csvhaemonc_joint_ethnicity_u_csv: output/data/csvhaemonc_joint_ethnicity_u.csv
csvhaemonc_skin_ethnicity_1_csv: output/data/csvhaemonc_skin_ethnicity_1.csv
csvhaemonc_skin_ethnicity_2_csv: output/data/csvhaemonc_skin_ethnicity_2.csv
csvhaemonc_skin_ethnicity_3_csv: output/data/csvhaemonc_skin_ethnicity_3.csv
csvhaemonc_skin_ethnicity_4_csv: output/data/csvhaemonc_skin_ethnicity_4.csv
csvhaemonc_skin_ethnicity_5_csv: output/data/csvhaemonc_skin_ethnicity_5.csv
csvhaemonc_skin_ethnicity_u_csv: output/data/csvhaemonc_skin_ethnicity_u.csv
csvhaemonc_bowel_ethnicity_1_csv: output/data/csvhaemonc_bowel_ethnicity_1.csv
csvhaemonc_bowel_ethnicity_2_csv: output/data/csvhaemonc_bowel_ethnicity_2.csv
csvhaemonc_bowel_ethnicity_3_csv: output/data/csvhaemonc_bowel_ethnicity_3.csv
csvhaemonc_bowel_ethnicity_4_csv: output/data/csvhaemonc_bowel_ethnicity_4.csv
csvhaemonc_bowel_ethnicity_5_csv: output/data/csvhaemonc_bowel_ethnicity_5.csv
csvhaemonc_bowel_ethnicity_u_csv: output/data/csvhaemonc_bowel_ethnicity_u.csv
run_export_csv_ethnicity_vs_white:
run: stata-mp:latest analysis/601_export_csv_ethnicity_vs_white.do
needs: [run_cox_models_genpop_ethnicity_vs_white,run_cox_models_imid_ethnicity_vs_white,run_cox_models_joint_ethnicity_vs_white,run_cox_models_skin_ethnicity_vs_white,run_cox_models_bowel_ethnicity_vs_white]
outputs:
moderately_sensitive:
log: logs/export_csv_ethnicity_vs_white.smcl
csvrun_cox_models_genpop_ethnicity_vs_white: output/data/csv_genpop_ethnicity_vs_white.csv
csvrun_cox_models_imid_ethnicity_vs_white: output/data/csv_imid_ethnicity_vs_white.csv
csvrun_cox_models_joint_ethnicity_vs_white: output/data/csv_joint_ethnicity_vs_white.csv
csvrun_cox_models_skin_ethnicity_vs_white: output/data/csv_skin_ethnicity_vs_white.csv
csvrun_cox_models_bowel_ethnicity_vs_white: output/data/csv_bowel_ethnicity_vs_white.csv
run_forest_plots_ethnicity:
run: r:latest analysis/r-immunosuppressant-meds-research/make_forest_plots_with_3_models_ethnicity.R
needs: [run_export_csv_ethnicity]
outputs:
moderately_sensitive:
merged_csv_ethnicity: output/data/merged_csv_normal_ethnicity.csv
merged_csv_haemoonc_ethnicity: output/data/merged_csv_haemonc_ethnicity.csv
model_data_ethnicity: output/data/model_data_ethnicity.csv
forest_plot_vs_gen_pop_ethnicity_1: output/figures/forest_plot_vs_gen_pop_ethnicity_1.svg
forest_plot_vs_gen_pop_ethnicity_2: output/figures/forest_plot_vs_gen_pop_ethnicity_2.svg
forest_plot_vs_gen_pop_ethnicity_3: output/figures/forest_plot_vs_gen_pop_ethnicity_3.svg
forest_plot_vs_gen_pop_ethnicity_4: output/figures/forest_plot_vs_gen_pop_ethnicity_4.svg
forest_plot_vs_gen_pop_ethnicity_5: output/figures/forest_plot_vs_gen_pop_ethnicity_5.svg
forest_plot_vs_gen_pop_ethnicity_u: output/figures/forest_plot_vs_gen_pop_ethnicity_u.svg
forest_plot_vs_gen_pop_ethnicity_died: output/figures/forest_plot_vs_gen_pop_ethnicity_died.svg
forest_plot_vs_gen_pop_ethnicity_hospital: output/figures/forest_plot_vs_gen_pop_ethnicity_hospital.svg
forest_plot_vs_gen_pop_ethnicity_icuordeath: output/figures/forest_plot_vs_gen_pop_ethnicity_icuordeath.svg
run_forest_plots_ethnicity_vs_white:
run: r:latest analysis/r-immunosuppressant-meds-research/make_forest_plots_with_3_models_ethnicity_vs_white.R
needs: [run_export_csv_ethnicity_vs_white]
outputs:
moderately_sensitive:
merged_csv_ethnicity_vs_white: output/data/merged_csv_normal_ethnicity_vs_white.csv
forest_plot_ethnicity_vs_white_died: output/figures/forest_plot_ethnicity_vs_white_died.svg
forest_plot_ethnicity_vs_white_icuordeath: output/figures/forest_plot_ethnicity_vs_white_icuordeath.svg
forest_plot_ethnicity_vs_white_hospital: output/figures/forest_plot_ethnicity_vs_white_hospital.svg
run_merge_csvs_spline:
run: r:latest analysis/r-immunosuppressant-meds-research/merge_csvs_spline.R
needs: [run_spline_export_csv]
outputs:
moderately_sensitive:
merged_csv_splline: output/data/merged_csv_normal_spline.csv
merged_csv_spline_haemonc: output/data/merged_csv_haemonc_spline.csv
run_extract_n_subjects:
run: r:latest analysis/r-immunosuppressant-meds-research/extract_n_subjects.R
needs: [run_cox_models_imid,run_cox_models_joint,run_cox_models_bowel,run_cox_models_skin,run_cox_models_imiddrugcategory,run_cox_models_standtnf,run_cox_models_standtnf3m,run_cox_models_tnfmono,run_cox_models_standil6,run_cox_models_standil17,run_cox_models_standil23,run_cox_models_standjaki,run_cox_models_standritux,run_cox_models_standinflix,run_cox_models_standvedolizumab,run_cox_models_standabatacept]
outputs:
moderately_sensitive:
merged_csv: output/data/subject_numbers.csv
run_pyramid_plots:
run: stata-mp:latest analysis/602_pyramid_plots.do
needs: [create_cohorts_single_file]
outputs:
moderately_sensitive:
pyramid_plot_genpop_1: output/figures/pyramidplot_genpop_1.svg
pyramid_plot_genpop_2: output/figures/pyramidplot_genpop_2.svg
pyramid_plot_genpop_3: output/figures/pyramidplot_genpop_3.svg
pyramid_plot_genpop_4: output/figures/pyramidplot_genpop_4.svg
pyramid_plot_genpop_5: output/figures/pyramidplot_genpop_5.svg
pyramid_plot_imid_1: output/figures/pyramidplot_imid_1.svg
pyramid_plot_imid_2: output/figures/pyramidplot_imid_2.svg
pyramid_plot_imid_3: output/figures/pyramidplot_imid_3.svg
pyramid_plot_imid_4: output/figures/pyramidplot_imid_4.svg
pyramid_plot_imid_5: output/figures/pyramidplot_imid_5.svg
pyramid_plot_joint_1: output/figures/pyramidplot_joint_1.svg
pyramid_plot_joint_2: output/figures/pyramidplot_joint_2.svg
pyramid_plot_joint_3: output/figures/pyramidplot_joint_3.svg
pyramid_plot_joint_4: output/figures/pyramidplot_joint_4.svg
pyramid_plot_joint_5: output/figures/pyramidplot_joint_5.svg
pyramid_plot_skin_1: output/figures/pyramidplot_skin_1.svg
pyramid_plot_skin_2: output/figures/pyramidplot_skin_2.svg
pyramid_plot_skin_3: output/figures/pyramidplot_skin_3.svg
pyramid_plot_skin_4: output/figures/pyramidplot_skin_4.svg
pyramid_plot_skin_5: output/figures/pyramidplot_skin_5.svg
pyramid_plot_bowel_1: output/figures/pyramidplot_bowel_1.svg
pyramid_plot_bowel_2: output/figures/pyramidplot_bowel_2.svg
pyramid_plot_bowel_3: output/figures/pyramidplot_bowel_3.svg
pyramid_plot_bowel_4: output/figures/pyramidplot_bowel_4.svg
pyramid_plot_bowel_5: output/figures/pyramidplot_bowel_5.svg
pyramid_plot_log: logs/pyramid_plots.smcl
age_sex_summary_genpop: output/data/age_sex_summary_genpop.csv
age_sex_summary_imid: output/data/age_sex_summary_imid.csv
age_sex_summary_joint: output/data/age_sex_summary_joint.csv
age_sex_summary_skin: output/data/age_sex_summary_skin.csv
age_sex_summary_bowel: output/data/age_sex_summary_bowel.csv