generated from opensafely/research-template
/
project.yaml
5172 lines (4748 loc) · 382 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 200000
actions:
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml DIRECTLY
## This file is created by create_project_actions.R
## Edit and run create_project_actions.R to update the project.yaml
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
vax_eligibility_inputs:
run: r:latest analysis/metadates.R
outputs:
highly_sensitive:
study_dates_json: output/study_dates.json
vax_jcvi_groups: output/vax_jcvi_groups.csv
vax_eligible_dates: output/vax_eligible_dates.csv
generate_study_population_prelim:
run: cohortextractor:latest generate_cohort --study-definition study_definition_prelim
--output-format feather
needs:
- vax_eligibility_inputs
outputs:
highly_sensitive:
cohort: output/input_prelim.feather
generate_index_dates:
run: r:latest analysis/prelim.R
needs:
- vax_eligibility_inputs
- generate_study_population_prelim
outputs:
highly_sensitive:
index_dates: output/index_dates.csv
generate_study_population_prevax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax
--output-format feather
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_prevax.feather
generate_study_population_vax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vax
--output-format feather
needs:
- generate_index_dates
- vax_eligibility_inputs
outputs:
highly_sensitive:
cohort: output/input_vax.feather
generate_study_population_unvax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax
--output-format feather
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_unvax.feather
## Generate deregistered_date variable
generate_deregistered_date:
run: cohortextractor:latest generate_cohort --study-definition study_definition_dereg
--output-format csv.gz
outputs:
highly_sensitive:
cohort: output/input_dereg.csv.gz
generate_index_dates_v2:
run: r:latest analysis/prelim_v2.R
needs:
- vax_eligibility_inputs
- generate_study_population_prelim
- generate_deregistered_date
outputs:
highly_sensitive:
index_dates: output/index_dates_v2.csv.gz
preprocess_data_prevax:
run: r:latest analysis/preprocess/preprocess_data.R prevax
needs:
- generate_index_dates
- generate_study_population_prelim
- generate_study_population_prevax
- generate_study_population_vax
- generate_study_population_unvax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_prevax_*.txt
highly_sensitive:
cohort: output/input_prevax.rds
venn: output/venn_prevax.rds
preprocess_data_vax:
run: r:latest analysis/preprocess/preprocess_data.R vax
needs:
- generate_index_dates
- generate_study_population_prelim
- generate_study_population_prevax
- generate_study_population_vax
- generate_study_population_unvax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_vax_*.txt
highly_sensitive:
cohort: output/input_vax.rds
venn: output/venn_vax.rds
preprocess_data_unvax:
run: r:latest analysis/preprocess/preprocess_data.R unvax
needs:
- generate_index_dates
- generate_study_population_prelim
- generate_study_population_prevax
- generate_study_population_vax
- generate_study_population_unvax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_unvax_*.txt
highly_sensitive:
cohort: output/input_unvax.rds
venn: output/venn_unvax.rds
stage1_data_cleaning_prevax:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R prevax
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- vax_eligibility_inputs
- generate_deregistered_date
outputs:
moderately_sensitive:
refactoring: output/not-for-review/meta_data_factors_prevax.csv
QA_rules: output/review/descriptives/QA_summary_prevax_*.csv
IE_criteria: output/review/descriptives/Cohort_flow_prevax_*.csv
histograms: output/not-for-review/numeric_histograms_prevax_*.svg
highly_sensitive:
cohort: output/input_prevax_*.rds
cohort_csv: output/input_prevax_*.csv.gz
stage1_data_cleaning_vax:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R vax
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- vax_eligibility_inputs
- generate_deregistered_date
outputs:
moderately_sensitive:
refactoring: output/not-for-review/meta_data_factors_vax.csv
QA_rules: output/review/descriptives/QA_summary_vax_*.csv
IE_criteria: output/review/descriptives/Cohort_flow_vax_*.csv
histograms: output/not-for-review/numeric_histograms_vax_*.svg
highly_sensitive:
cohort: output/input_vax_*.rds
cohort_csv: output/input_vax_*.csv.gz
stage1_data_cleaning_vax_v2:
run: r:latest analysis/preprocess/Stage1_data_cleaning_v2.R vax
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- vax_eligibility_inputs
- generate_deregistered_date
outputs:
moderately_sensitive:
refactoring: output/not-for-review/meta_data_factors_vax_v2.csv
QA_rules: output/review/descriptives/QA_summary_vax_*_v2.csv
IE_criteria: output/review/descriptives/Cohort_flow_vax_*_v2.csv
histograms: output/not-for-review/numeric_histograms_vax_*_v2.svg
highly_sensitive:
cohort: output/input_vax_*_v2.rds
cohort_csv: output/input_vax_*_v2.csv.gz
stage1_data_cleaning_unvax:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R unvax
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- vax_eligibility_inputs
- generate_deregistered_date
outputs:
moderately_sensitive:
refactoring: output/not-for-review/meta_data_factors_unvax.csv
QA_rules: output/review/descriptives/QA_summary_unvax_*.csv
IE_criteria: output/review/descriptives/Cohort_flow_unvax_*.csv
histograms: output/not-for-review/numeric_histograms_unvax_*.svg
highly_sensitive:
cohort: output/input_unvax_*.rds
cohort_csv: output/input_unvax_*.csv.gz
stage1_end_date_table_prevax:
run: r:latest analysis/preprocess/create_follow_up_end_date.R prevax
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- stage1_data_cleaning_prevax
- vax_eligibility_inputs
- generate_deregistered_date
outputs:
highly_sensitive:
end_date_table: output/follow_up_end_dates_prevax_*.rds
end_date_table_csv: output/follow_up_end_dates_prevax_*.csv.gz
stage1_end_date_table_vax:
run: r:latest analysis/preprocess/create_follow_up_end_date.R vax
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- stage1_data_cleaning_vax
- vax_eligibility_inputs
- generate_deregistered_date
outputs:
highly_sensitive:
end_date_table: output/follow_up_end_dates_vax_*.rds
end_date_table_csv: output/follow_up_end_dates_vax_*.csv.gz
stage1_end_date_table_unvax:
run: r:latest analysis/preprocess/create_follow_up_end_date.R unvax
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- stage1_data_cleaning_unvax
- vax_eligibility_inputs
- generate_deregistered_date
outputs:
highly_sensitive:
end_date_table: output/follow_up_end_dates_unvax_*.rds
end_date_table_csv: output/follow_up_end_dates_unvax_*.csv.gz
generate_study_population_prevax_diabetes_analyis:
run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax_diabetes_analysis
--output-format feather
needs:
- vax_eligibility_inputs
- stage1_data_cleaning_prevax
- stage1_end_date_table_prevax
outputs:
highly_sensitive:
cohort: output/input_prevax_diabetes_analysis.feather
generate_study_population_vax_diabetes_analyis:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vax_diabetes_analysis
--output-format feather
needs:
- vax_eligibility_inputs
- stage1_data_cleaning_vax
- stage1_end_date_table_vax
outputs:
highly_sensitive:
cohort: output/input_vax_diabetes_analysis.feather
generate_study_population_unvax_diabetes_analyis:
run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax_diabetes_analysis
--output-format feather
needs:
- vax_eligibility_inputs
- stage1_data_cleaning_unvax
- stage1_end_date_table_unvax
outputs:
highly_sensitive:
cohort: output/input_unvax_diabetes_analysis.feather
add_persistent_diabetes_outcomes:
run: r:latest analysis/descriptives/add_persistent_diabetes_outcomes.R prevax
needs:
- generate_study_population_prevax_diabetes_analyis
- stage1_data_cleaning_prevax
outputs:
highly_sensitive:
cohort_new: output/input_prevax_stage1_diabetes.rds
stage2_missing_table1_all:
run: r:latest analysis/descriptives/Stage2_missing_table1.R all
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- add_persistent_diabetes_outcomes
outputs:
moderately_sensitive:
Missing_RangeChecks: output/not-for-review/Check_missing_range_*.csv
DateChecks: output/not-for-review/Check_dates_range_*.csv
Descriptive_Table: output/review/descriptives/Table1_*.csv
stage3_diabetes_flow_prevax:
run: r:latest analysis/descriptives/diabetes_flowchart.R prevax
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
moderately_sensitive:
flow_df: output/review/figure-data/diabetes_flow_values_prevax_*.csv
stage3_diabetes_flow_vax:
run: r:latest analysis/descriptives/diabetes_flowchart.R vax
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
moderately_sensitive:
flow_df: output/review/figure-data/diabetes_flow_values_vax_*.csv
stage3_diabetes_flow_unvax:
run: r:latest analysis/descriptives/diabetes_flowchart.R unvax
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
moderately_sensitive:
flow_df: output/review/figure-data/diabetes_flow_values_unvax_*.csv
## Table 2 - vax
table2_vax:
run: r:latest analysis/table2.R vax
needs:
- make_model_input-cohort_vax-main-t1dm
- make_model_input-cohort_vax-sub_covid_hospitalised-t1dm
- make_model_input-cohort_vax-sub_covid_nonhospitalised-t1dm
- make_model_input-cohort_vax-main-t2dm
- make_model_input-cohort_vax-sub_covid_hospitalised-t2dm
- make_model_input-cohort_vax-sub_covid_nonhospitalised-t2dm
- make_model_input-cohort_vax-main-otherdm
- make_model_input-cohort_vax-sub_covid_hospitalised-otherdm
- make_model_input-cohort_vax-sub_covid_nonhospitalised-otherdm
- make_model_input-cohort_vax-main-gestationaldm
- make_model_input-cohort_vax-sub_covid_hospitalised-gestationaldm
- make_model_input-cohort_vax-sub_covid_nonhospitalised-gestationaldm
outputs:
moderately_sensitive:
table2: output/table2_vax.csv
table2_rounded: output/table2_vax_rounded.csv
## Table 2 - unvax
table2_unvax:
run: r:latest analysis/table2.R unvax
needs:
- make_model_input-cohort_unvax-main-t1dm
- make_model_input-cohort_unvax-sub_covid_hospitalised-t1dm
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-t1dm
- make_model_input-cohort_unvax-main-t2dm
- make_model_input-cohort_unvax-sub_covid_hospitalised-t2dm
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-t2dm
- make_model_input-cohort_unvax-main-otherdm
- make_model_input-cohort_unvax-sub_covid_hospitalised-otherdm
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-otherdm
- make_model_input-cohort_unvax-main-gestationaldm
- make_model_input-cohort_unvax-sub_covid_hospitalised-gestationaldm
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-gestationaldm
outputs:
moderately_sensitive:
table2: output/table2_unvax.csv
table2_rounded: output/table2_unvax_rounded.csv
## Table 2 - prevax
table2_prevax:
run: r:latest analysis/table2.R prevax
needs:
- make_model_input-cohort_prevax-main-t1dm_extended_follow_up
- make_model_input-cohort_prevax-sub_covid_hospitalised-t1dm_extended_follow_up
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-t1dm_extended_follow_up
- make_model_input-cohort_prevax-main-t2dm_extended_follow_up
- make_model_input-cohort_prevax-sub_covid_hospitalised-t2dm_extended_follow_up
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-t2dm_extended_follow_up
- make_model_input-cohort_prevax-main-otherdm_extended_follow_up
- make_model_input-cohort_prevax-sub_covid_hospitalised-otherdm_extended_follow_up
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-otherdm_extended_follow_up
- make_model_input-cohort_prevax-main-gestationaldm_extended_follow_up
- make_model_input-cohort_prevax-sub_covid_hospitalised-gestationaldm_extended_follow_up
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-gestationaldm_extended_follow_up
- make_model_input-cohort_prevax-main-t2dm_follow_extended_follow_up
- make_model_input-cohort_prevax-sub_covid_hospitalised-t2dm_follow_extended_follow_up
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-t2dm_follow_extended_follow_up
- make_model_input-cohort_prevax-main_fup4m-t2dm_extended_follow_up
- make_model_input-cohort_prevax-sub_covid_hospitalised_fup4m-t2dm_extended_follow_up
- make_model_input-cohort_prevax-sub_covid_nonhospitalised_fup4m-t2dm_extended_follow_up
- make_model_input-cohort_prevax-main_fup4m-t2dm_follow_extended_follow_up
- make_model_input-cohort_prevax-sub_covid_hospitalised_fup4m-t2dm_follow_extended_follow_up
- make_model_input-cohort_prevax-sub_covid_nonhospitalised_fup4m-t2dm_follow_extended_follow_up
outputs:
moderately_sensitive:
table2: output/table2_prevax.csv
table2_rounded: output/table2_prevax_rounded.csv
## Stage 5 - Apply models
make_model_input-cohort_vax-main-t1dm:
run: r:latest analysis/make_model_input.R cohort_vax-main-t1dm
needs:
- stage1_data_cleaning_vax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-t1dm.rds
cox_ipw-cohort_vax-main-t1dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-main-t1dm.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_vax-main-t1dm.csv
needs:
- make_model_input-cohort_vax-main-t1dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-t1dm.csv
make_model_input-cohort_unvax-main-t1dm:
run: r:latest analysis/make_model_input.R cohort_unvax-main-t1dm
needs:
- stage1_data_cleaning_unvax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-t1dm.rds
cox_ipw-cohort_unvax-main-t1dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-main-t1dm.rds --ipw=FALSE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_unvax-main-t1dm.csv
needs:
- make_model_input-cohort_unvax-main-t1dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-t1dm.csv
make_model_input-cohort_vax-sub_covid_hospitalised-t1dm:
run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_hospitalised-t1dm
needs:
- stage1_data_cleaning_vax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_hospitalised-t1dm.rds
cox_ipw-cohort_vax-sub_covid_hospitalised-t1dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_covid_hospitalised-t1dm.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-t1dm.csv
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-t1dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_hospitalised-t1dm.csv
make_model_input-cohort_unvax-sub_covid_hospitalised-t1dm:
run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_hospitalised-t1dm
needs:
- stage1_data_cleaning_unvax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-t1dm.rds
cox_ipw-cohort_unvax-sub_covid_hospitalised-t1dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-t1dm.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-t1dm.csv
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-t1dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-t1dm.csv
make_model_input-cohort_vax-sub_covid_nonhospitalised-t1dm:
run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_nonhospitalised-t1dm
needs:
- stage1_data_cleaning_vax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_nonhospitalised-t1dm.rds
cox_ipw-cohort_vax-sub_covid_nonhospitalised-t1dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-t1dm.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_vax-sub_covid_nonhospitalised-t1dm.csv
needs:
- make_model_input-cohort_vax-sub_covid_nonhospitalised-t1dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-t1dm.csv
make_model_input-cohort_unvax-sub_covid_nonhospitalised-t1dm:
run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-t1dm
needs:
- stage1_data_cleaning_unvax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_covid_nonhospitalised-t1dm.rds
cox_ipw-cohort_unvax-sub_covid_nonhospitalised-t1dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-t1dm.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-t1dm.csv
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-t1dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-t1dm.csv
make_model_input-cohort_vax-main-t2dm:
run: r:latest analysis/make_model_input.R cohort_vax-main-t2dm
needs:
- stage1_data_cleaning_vax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-t2dm.rds
cox_ipw-cohort_vax-main-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-main-t2dm.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_vax-main-t2dm.csv
needs:
- make_model_input-cohort_vax-main-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-t2dm.csv
make_model_input-cohort_unvax-main-t2dm:
run: r:latest analysis/make_model_input.R cohort_unvax-main-t2dm
needs:
- stage1_data_cleaning_unvax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-t2dm.rds
cox_ipw-cohort_unvax-main-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-main-t2dm.rds --ipw=FALSE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_unvax-main-t2dm.csv
needs:
- make_model_input-cohort_unvax-main-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-t2dm.csv
make_model_input-cohort_vax-sub_covid_hospitalised-t2dm:
run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_hospitalised-t2dm
needs:
- stage1_data_cleaning_vax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_hospitalised-t2dm.rds
cox_ipw-cohort_vax-sub_covid_hospitalised-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_covid_hospitalised-t2dm.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-t2dm.csv
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_hospitalised-t2dm.csv
make_model_input-cohort_unvax-sub_covid_hospitalised-t2dm:
run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_hospitalised-t2dm
needs:
- stage1_data_cleaning_unvax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-t2dm.rds
cox_ipw-cohort_unvax-sub_covid_hospitalised-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-t2dm.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-t2dm.csv
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-t2dm.csv
make_model_input-cohort_vax-sub_covid_nonhospitalised-t2dm:
run: r:latest analysis/make_model_input.R cohort_vax-sub_covid_nonhospitalised-t2dm
needs:
- stage1_data_cleaning_vax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_nonhospitalised-t2dm.rds
cox_ipw-cohort_vax-sub_covid_nonhospitalised-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_covid_nonhospitalised-t2dm.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_vax-sub_covid_nonhospitalised-t2dm.csv
needs:
- make_model_input-cohort_vax-sub_covid_nonhospitalised-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-t2dm.csv
make_model_input-cohort_unvax-sub_covid_nonhospitalised-t2dm:
run: r:latest analysis/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-t2dm
needs:
- stage1_data_cleaning_unvax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_covid_nonhospitalised-t2dm.rds
cox_ipw-cohort_unvax-sub_covid_nonhospitalised-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-t2dm.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_unvax-sub_covid_nonhospitalised-t2dm.csv
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-t2dm.csv
make_model_input-cohort_vax-sub_age_18_39-t2dm:
run: r:latest analysis/make_model_input.R cohort_vax-sub_age_18_39-t2dm
needs:
- stage1_data_cleaning_vax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-t2dm.rds
cox_ipw-cohort_vax-sub_age_18_39-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_18_39-t2dm.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_vax-sub_age_18_39-t2dm.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-t2dm.csv
make_model_input-cohort_unvax-sub_age_18_39-t2dm:
run: r:latest analysis/make_model_input.R cohort_unvax-sub_age_18_39-t2dm
needs:
- stage1_data_cleaning_unvax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-t2dm.rds
cox_ipw-cohort_unvax-sub_age_18_39-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_18_39-t2dm.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_unvax-sub_age_18_39-t2dm.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-t2dm.csv
make_model_input-cohort_vax-sub_age_40_59-t2dm:
run: r:latest analysis/make_model_input.R cohort_vax-sub_age_40_59-t2dm
needs:
- stage1_data_cleaning_vax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_40_59-t2dm.rds
cox_ipw-cohort_vax-sub_age_40_59-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_40_59-t2dm.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_vax-sub_age_40_59-t2dm.csv
needs:
- make_model_input-cohort_vax-sub_age_40_59-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_40_59-t2dm.csv
make_model_input-cohort_unvax-sub_age_40_59-t2dm:
run: r:latest analysis/make_model_input.R cohort_unvax-sub_age_40_59-t2dm
needs:
- stage1_data_cleaning_unvax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_40_59-t2dm.rds
cox_ipw-cohort_unvax-sub_age_40_59-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_40_59-t2dm.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_unvax-sub_age_40_59-t2dm.csv
needs:
- make_model_input-cohort_unvax-sub_age_40_59-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_40_59-t2dm.csv
make_model_input-cohort_vax-sub_age_60_79-t2dm:
run: r:latest analysis/make_model_input.R cohort_vax-sub_age_60_79-t2dm
needs:
- stage1_data_cleaning_vax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_60_79-t2dm.rds
cox_ipw-cohort_vax-sub_age_60_79-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_60_79-t2dm.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_vax-sub_age_60_79-t2dm.csv
needs:
- make_model_input-cohort_vax-sub_age_60_79-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_60_79-t2dm.csv
make_model_input-cohort_unvax-sub_age_60_79-t2dm:
run: r:latest analysis/make_model_input.R cohort_unvax-sub_age_60_79-t2dm
needs:
- stage1_data_cleaning_unvax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_60_79-t2dm.rds
cox_ipw-cohort_unvax-sub_age_60_79-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_60_79-t2dm.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_unvax-sub_age_60_79-t2dm.csv
needs:
- make_model_input-cohort_unvax-sub_age_60_79-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_60_79-t2dm.csv
make_model_input-cohort_vax-sub_age_80_110-t2dm:
run: r:latest analysis/make_model_input.R cohort_vax-sub_age_80_110-t2dm
needs:
- stage1_data_cleaning_vax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_80_110-t2dm.rds
cox_ipw-cohort_vax-sub_age_80_110-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_age_80_110-t2dm.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_vax-sub_age_80_110-t2dm.csv
needs:
- make_model_input-cohort_vax-sub_age_80_110-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_80_110-t2dm.csv
make_model_input-cohort_unvax-sub_age_80_110-t2dm:
run: r:latest analysis/make_model_input.R cohort_unvax-sub_age_80_110-t2dm
needs:
- stage1_data_cleaning_unvax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_80_110-t2dm.rds
cox_ipw-cohort_unvax-sub_age_80_110-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_age_80_110-t2dm.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_unvax-sub_age_80_110-t2dm.csv
needs:
- make_model_input-cohort_unvax-sub_age_80_110-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_80_110-t2dm.csv
make_model_input-cohort_vax-sub_sex_male-t2dm:
run: r:latest analysis/make_model_input.R cohort_vax-sub_sex_male-t2dm
needs:
- stage1_data_cleaning_vax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_sex_male-t2dm.rds
cox_ipw-cohort_vax-sub_sex_male-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_sex_male-t2dm.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_vax-sub_sex_male-t2dm.csv
needs:
- make_model_input-cohort_vax-sub_sex_male-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_sex_male-t2dm.csv
make_model_input-cohort_unvax-sub_sex_male-t2dm:
run: r:latest analysis/make_model_input.R cohort_unvax-sub_sex_male-t2dm
needs:
- stage1_data_cleaning_unvax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_sex_male-t2dm.rds
cox_ipw-cohort_unvax-sub_sex_male-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_sex_male-t2dm.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_unvax-sub_sex_male-t2dm.csv
needs:
- make_model_input-cohort_unvax-sub_sex_male-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_sex_male-t2dm.csv
make_model_input-cohort_vax-sub_sex_female-t2dm:
run: r:latest analysis/make_model_input.R cohort_vax-sub_sex_female-t2dm
needs:
- stage1_data_cleaning_vax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_sex_female-t2dm.rds
cox_ipw-cohort_vax-sub_sex_female-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_sex_female-t2dm.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_vax-sub_sex_female-t2dm.csv
needs:
- make_model_input-cohort_vax-sub_sex_female-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_sex_female-t2dm.csv
make_model_input-cohort_unvax-sub_sex_female-t2dm:
run: r:latest analysis/make_model_input.R cohort_unvax-sub_sex_female-t2dm
needs:
- stage1_data_cleaning_unvax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_sex_female-t2dm.rds
cox_ipw-cohort_unvax-sub_sex_female-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_sex_female-t2dm.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=NULL
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_unvax-sub_sex_female-t2dm.csv
needs:
- make_model_input-cohort_unvax-sub_sex_female-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_sex_female-t2dm.csv
make_model_input-cohort_vax-sub_ethnicity_white-t2dm:
run: r:latest analysis/make_model_input.R cohort_vax-sub_ethnicity_white-t2dm
needs:
- stage1_data_cleaning_vax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_ethnicity_white-t2dm.rds
cox_ipw-cohort_vax-sub_ethnicity_white-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-sub_ethnicity_white-t2dm.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --save_analysis_ready=FALSE
--run_analysis=TRUE --df_output=model_output-cohort_vax-sub_ethnicity_white-t2dm.csv
needs:
- make_model_input-cohort_vax-sub_ethnicity_white-t2dm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_ethnicity_white-t2dm.csv
make_model_input-cohort_unvax-sub_ethnicity_white-t2dm:
run: r:latest analysis/make_model_input.R cohort_unvax-sub_ethnicity_white-t2dm
needs:
- stage1_data_cleaning_unvax
- generate_index_dates_v2
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_ethnicity_white-t2dm.rds
cox_ipw-cohort_unvax-sub_ethnicity_white-t2dm:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-sub_ethnicity_white-t2dm.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_deprivation;cov_num_consulation_rate;cov_cat_smoking_status;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_cat_bmi_groups;cov_bin_prediabetes;cov_bin_diabetes_gestational
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50