generated from opensafely/research-template
/
project.yaml
663 lines (582 loc) · 27.5 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 10000
actions:
generate_study_population_covid_2020:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_covid_2020
--output-dir=output/cohorts
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/cohorts/input_covid_2020.csv.gz
generate_study_population_covid_2021:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_covid_2021
--output-dir=output/cohorts
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/cohorts/input_covid_2021.csv.gz
generate_study_population_general_match_vars_2019:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_general_match_vars
--output-dir=output/cohorts
--output-format=csv.gz
--index-date-range="2019-02-01"
outputs:
highly_sensitive:
cohort: output/cohorts/input_general_match_vars_2019-02-01.csv.gz
generate_study_population_general_match_vars_2020:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_general_match_vars
--output-dir=output/cohorts
--output-format=csv.gz
--index-date-range="2020-02-01"
outputs:
highly_sensitive:
cohort: output/cohorts/input_general_match_vars_2020-02-01.csv.gz
generate_study_population_general_match_vars_2021:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_general_match_vars
--output-dir=output/cohorts
--output-format=csv.gz
--index-date-range="2021-02-01"
outputs:
highly_sensitive:
cohort: output/cohorts/input_general_match_vars_2021-02-01.csv.gz
generate_study_population_pneumonia_2019:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_pneumonia_2019
--output-dir=output/cohorts
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/cohorts/input_pneumonia_2019.csv.gz
matching_2019:
run: python:latest python analysis/match_running.py "2019" --output-dir=output/cohorts
needs: [generate_study_population_covid_2020, generate_study_population_general_match_vars_2019]
outputs:
moderately_sensitive:
matching_report: output/cohorts/matching_report_general_2019.txt
highly_sensitive:
matched_cohort: output/cohorts/matched_matches_general_2019.csv
matching_2020:
run: python:latest python analysis/match_running.py "2020" --output-dir=output/cohorts
needs: [generate_study_population_covid_2020, generate_study_population_general_match_vars_2020]
outputs:
moderately_sensitive:
matching_report: output/cohorts/matching_report_general_2020.txt
highly_sensitive:
matched_cohort: output/cohorts/matched_matches_general_2020.csv
matching_2021:
run: python:latest python analysis/match_running.py "2021" --output-dir=output/cohorts
needs: [generate_study_population_covid_2021, generate_study_population_general_match_vars_2021]
outputs:
moderately_sensitive:
matching_report: output/cohorts/matching_report_general_2021.txt
highly_sensitive:
matched_cohort: output/cohorts/matched_matches_general_2021.csv
generate_study_population_matched_2019:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_matched_2019
--output-dir=output/cohorts
--output-format=csv.gz
needs: [matching_2019]
outputs:
highly_sensitive:
cohort: output/cohorts/input_matched_2019.csv.gz
generate_study_population_matched_2020:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_matched_2020
--output-dir=output/cohorts
--output-format=csv.gz
needs: [matching_2020]
outputs:
highly_sensitive:
cohort: output/cohorts/input_matched_2020.csv.gz
generate_study_population_matched_2021:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_matched_2021
--output-dir=output/cohorts
--output-format=csv.gz
needs: [matching_2021]
outputs:
highly_sensitive:
cohort: output/cohorts/input_matched_2021.csv.gz
reconcile_sick_note_spells_covid_2020:
run: python:latest python analysis/reconcile_sick_note_spells.py "_covid_2020"
needs: [generate_study_population_covid_2020]
outputs:
highly_sensitive:
cohort_with_duration: output/cohorts/input_covid_2020_with_duration.csv
reconcile_sick_note_spells_covid_2021:
run: python:latest python analysis/reconcile_sick_note_spells.py "_covid_2021"
needs: [generate_study_population_covid_2021]
outputs:
highly_sensitive:
cohort_with_duration: output/cohorts/input_covid_2021_with_duration.csv
reconcile_sick_note_spells_general_2019:
run: python:latest python analysis/reconcile_sick_note_spells.py "_matched_2019"
needs: [generate_study_population_matched_2019]
outputs:
highly_sensitive:
cohort_with_duration: output/cohorts/input_matched_2019_with_duration.csv
reconcile_sick_note_spells_general_2020:
run: python:latest python analysis/reconcile_sick_note_spells.py "_matched_2020"
needs: [generate_study_population_matched_2020]
outputs:
highly_sensitive:
cohort_with_duration: output/cohorts/input_matched_2020_with_duration.csv
reconcile_sick_note_spells_general_2021:
run: python:latest python analysis/reconcile_sick_note_spells.py "_matched_2021"
needs: [generate_study_population_matched_2021]
outputs:
highly_sensitive:
cohort_with_duration: output/cohorts/input_matched_2021_with_duration.csv
reconcile_sick_note_spells_pneumonia_2019:
run: python:latest python analysis/reconcile_sick_note_spells.py "_pneumonia_2019"
needs: [generate_study_population_pneumonia_2019]
outputs:
highly_sensitive:
cohort_with_duration: output/cohorts/input_pneumonia_2019_with_duration.csv
covid_2020_rates_cohort:
run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "covid_2020" --output-dir=output/cohorts
needs: [reconcile_sick_note_spells_covid_2020]
outputs:
highly_sensitive:
analysis_dataset: output/cohorts/cohort_rates_*.dta
covid_2021_rates_cohort:
run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "covid_2021" --output-dir=output/cohorts
needs: [reconcile_sick_note_spells_covid_2021]
outputs:
highly_sensitive:
analysis_dataset: output/cohorts/cohort_rates*.dta
general_2019_rates_cohort:
run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "matched_2019" --output-dir=output/cohorts
needs: [reconcile_sick_note_spells_general_2019]
outputs:
highly_sensitive:
analysis_dataset: output/cohorts/cohort_rates_matched_2019.dta
general_2020_rates_cohort:
run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "matched_2020" --output-dir=output/cohorts
needs: [reconcile_sick_note_spells_general_2020]
outputs:
highly_sensitive:
analysis_dataset: output/cohorts/cohort_rates_matched_2020.dta
general_2021_rates_cohort:
run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "matched_2021" --output-dir=output/cohorts
needs: [reconcile_sick_note_spells_general_2021]
outputs:
highly_sensitive:
analysis_dataset: output/cohorts/cohort_rates_matched_2021.dta
pneumonia_2019_rates_cohort:
run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "pneumonia_2019" --output-dir=output/cohorts
needs: [reconcile_sick_note_spells_pneumonia_2019]
outputs:
highly_sensitive:
analysis_dataset: output/cohorts/cohort_rates_pneumonia_2019.dta
covid_2020_rates:
run: stata-mp:latest analysis/rates/100_cr_simple_rates.do "covid_2020" --output-dir=output/tabfig
needs: [covid_2020_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_covid_2020.csv
covid_2021_rates:
run: stata-mp:latest analysis/rates/100_cr_simple_rates.do "covid_2021" --output-dir=output/tabfig
needs: [covid_2021_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_covid_2021.csv
general_2019_rates:
run: stata-mp:latest analysis/rates/100_cr_simple_rates.do "matched_2019" --output-dir=output/tabfig
needs: [general_2019_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_matched_2019.csv
general_2020_rates:
run: stata-mp:latest analysis/rates/100_cr_simple_rates.do "matched_2020" --output-dir=output/tabfig
needs: [general_2020_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_matched_2020.csv
general_2021_rates:
run: stata-mp:latest analysis/rates/100_cr_simple_rates.do "matched_2021" --output-dir=output/tabfig
needs: [general_2021_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_matched_2021.csv
pneumonia_2019_rates:
run: stata-mp:latest analysis/rates/100_cr_simple_rates_hosp.do "pneumonia_2019" --output-dir=output/tabfig
needs: [pneumonia_2019_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_hosp_pneumonia_2019.csv
covid_hosp_2020_rates:
run: stata-mp:latest analysis/rates/100_cr_simple_rates_hosp.do "covid_2020" --output-dir=output/tabfig
needs: [covid_2020_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_hosp_covid_2020.csv
covid_hosp_2021_rates:
run: stata-mp:latest analysis/rates/100_cr_simple_rates_hosp.do "covid_2021" --output-dir=output/tabfig
needs: [covid_2021_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_hosp_covid_2021.csv
append_cohorts:
run: stata-mp:latest analysis/cox_models/200_cr_data_management_matching.do --output-dir=output/cohorts
needs: [covid_2021_rates_cohort, covid_2020_rates_cohort, pneumonia_2019_rates_cohort, general_2021_rates_cohort, general_2020_rates_cohort, general_2019_rates_cohort]
outputs:
moderately_sensitive:
log: output/cohorts/append_cohorts.txt
highly_sensitive:
dataset: output/cohorts/combined_covid_2020_pneumonia.dta
dataset2: output/cohorts/combined_covid_2021_pneumonia.dta
dataset3: output/cohorts/combined_covid_2020_general_2019.dta
dataset4: output/cohorts/combined_covid_2021_general_2019.dta
dataset5: output/cohorts/combined_covid_general_2020.dta
dataset6: output/cohorts/combined_covid_general_2021.dta
cox_models:
run: stata-mp:latest analysis/cox_models/201_cox_models.do
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models.txt
dataset: output/tabfig/cox_model_summary.csv
# Cox model overall stratified by age
cox_models_age:
run: stata-mp:latest analysis/cox_models/203_cox_models_stratified.do "age_group"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_summary_age_group.txt
dataset: output/tabfig/cox_model_summary_age_group*.csv
# Cox model overall stratified by ethnicity
cox_models_ethnicity:
run: stata-mp:latest analysis/cox_models/203_cox_models_stratified.do "ethnicity"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_summary_ethnicity.txt
dataset: output/tabfig/cox_model_summary_ethnicity.csv
# Cox model overall stratified by IMD
cox_models_imd:
run: stata-mp:latest analysis/cox_models/203_cox_models_stratified.do "imd"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_summary_imd.txt
dataset: output/tabfig/cox_model_summary_imd.csv
# Cox model overall stratified by region
cox_models_region:
run: stata-mp:latest analysis/cox_models/203_cox_models_stratified.do "region_9"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_summary_region_9.txt
dataset: output/tabfig/cox_model_summary_region_9.csv
# Cox model overall stratified by sex
cox_models_sex:
run: stata-mp:latest analysis/cox_models/203_cox_models_stratified.do "male"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_summary_male.txt
dataset: output/tabfig/cox_model_summary_male.csv
# Cox modes split by follow-up time
cox_models_split_2020_pneumo:
run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "2020_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_pneumonia.txt
dataset: output/tabfig/cox_model_split_summary_2020_pneumonia.csv
cox_models_split_2021_pneumo:
run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "2021_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_pneumonia.txt
dataset: output/tabfig/cox_model_split_summary_2021_pneumonia.csv
cox_models_split_2020_gen_2019:
run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "2020_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_general_2019.txt
dataset: output/tabfig/cox_model_split_summary_2020_general_2019.csv
cox_models_split_2021_gen_2019:
run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "2021_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_general_2019.txt
dataset: output/tabfig/cox_model_split_summary_2021_general_2019.csv
cox_models_split_gen_2020:
run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "general_2020"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2020.txt
dataset: output/tabfig/cox_model_split_summary_general_2020.csv
cox_models_split_gen_2021:
run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "general_2021"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2021.txt
dataset: output/tabfig/cox_model_split_summary_general_2021.csv
# Cox modes split by follow-up time - stratified by age
cox_models_split_2020_pneumo_age:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "2020_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_pneumonia_age_group.txt
dataset: output/tabfig/cox_model_split_summary_2020_pneumonia_age_group.csv
cox_models_split_2021_pneumo_age:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "2021_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_pneumonia_age_group.txt
dataset: output/tabfig/cox_model_split_summary_2021_pneumonia_age_group.csv
cox_models_split_2020_gen_2019_age:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "2020_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_general_2019_age_group.txt
dataset: output/tabfig/cox_model_split_summary_2020_general_2019_age_group.csv
cox_models_split_2021_gen_2019_age:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "2021_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_general_2019_age_group.txt
dataset: output/tabfig/cox_model_split_summary_2021_general_2019_age_group.csv
cox_models_split_gen_2020_age:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "general_2020"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2020_age_group.txt
dataset: output/tabfig/cox_model_split_summary_general_2020_age_group.csv
cox_models_split_gen_2021_age:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "general_2021"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2021_age_group.txt
dataset: output/tabfig/cox_model_split_summary_general_2021_age_group.csv
# Cox models split by follow-up time - stratified by ethnicity
cox_models_split_2020_pneumo_ethnicity:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "2020_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_pneumonia_ethnicity.txt
dataset: output/tabfig/cox_model_split_summary_2020_pneumonia_ethnicity.csv
cox_models_split_2021_pneumo_ethnicity:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "2021_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_pneumonia_ethnicity.txt
dataset: output/tabfig/cox_model_split_summary_2021_pneumonia_ethnicity.csv
cox_models_split_2020_gen_2019_ethnicity:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "2020_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_general_2019_ethnicity.txt
dataset: output/tabfig/cox_model_split_summary_2020_general_2019_ethnicity.csv
cox_models_split_2021_gen_2019_ethnicity:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "2021_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_general_2019_ethnicity.txt
dataset: output/tabfig/cox_model_split_summary_2021_general_2019_ethnicity.csv
cox_models_split_gen_2020_ethnicity:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "general_2020"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2020_ethnicity.txt
dataset: output/tabfig/cox_model_split_summary_general_2020_ethnicity.csv
cox_models_split_gen_2021_ethnicity:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "general_2021"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2021_ethnicity.txt
dataset: output/tabfig/cox_model_split_summary_general_2021_ethnicity.csv
# Cox models split by follow-up time - stratified by IMD
cox_models_split_2020_pneumo_imd:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "2020_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_pneumonia_imd.txt
dataset: output/tabfig/cox_model_split_summary_2020_pneumonia_imd.csv
cox_models_split_2021_pneumo_imd:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "2021_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_pneumonia_imd.txt
dataset: output/tabfig/cox_model_split_summary_2021_pneumonia_imd.csv
cox_models_split_2020_gen_2019_imd:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "2020_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_general_2019_imd.txt
dataset: output/tabfig/cox_model_split_summary_2020_general_2019_imd.csv
cox_models_split_2021_gen_2019_imd:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "2021_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_general_2019_imd.txt
dataset: output/tabfig/cox_model_split_summary_2021_general_2019_imd.csv
cox_models_split_gen_2020_imd:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "general_2020"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2020_imd.txt
dataset: output/tabfig/cox_model_split_summary_general_2020_imd.csv
cox_models_split_gen_2021_imd:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "general_2021"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2021_imd.txt
dataset: output/tabfig/cox_model_split_summary_general_2021_imd.csv
# Cox models split by follow-up time - stratified by region
cox_models_split_2020_pneumo_region:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "2020_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_pneumonia_region.txt
dataset: output/tabfig/cox_model_split_summary_2020_pneumonia_region.csv
cox_models_split_2021_pneumo_region:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "2021_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_pneumonia_region.txt
dataset: output/tabfig/cox_model_split_summary_2021_pneumonia_region.csv
cox_models_split_2020_gen_2019_region:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "2020_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_general_2019_region.txt
dataset: output/tabfig/cox_model_split_summary_2020_general_2019_region.csv
cox_models_split_2021_gen_2019_region:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "2021_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_general_2019_region.txt
dataset: output/tabfig/cox_model_split_summary_2021_general_2019_region.csv
cox_models_split_gen_2020_region:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "general_2020"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2020_region.txt
dataset: output/tabfig/cox_model_split_summary_general_2020_region.csv
cox_models_split_gen_2021_region:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "general_2021"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2021_region.txt
dataset: output/tabfig/cox_model_split_summary_general_2021_region.csv
# Cox models split by follow-up time - stratified by sex
cox_models_split_2020_pneumo_sex:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "2020_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_pneumonia_sex.txt
dataset: output/tabfig/cox_model_split_summary_2020_pneumonia_sex.csv
cox_models_split_2021_pneumo_sex:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "2021_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_pneumonia_sex.txt
dataset: output/tabfig/cox_model_split_summary_2021_pneumonia_sex.csv
cox_models_split_2020_gen_2019_sex:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "2020_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_general_2019_sex.txt
dataset: output/tabfig/cox_model_split_summary_2020_general_2019_sex.csv
cox_models_split_2021_gen_2019_sex:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "2021_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_general_2019_sex.txt
dataset: output/tabfig/cox_model_split_summary_2021_general_2019_sex.csv
cox_models_split_gen_2020_sex:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "general_2020"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2020_sex.txt
dataset: output/tabfig/cox_model_split_summary_general_2020_sex.csv
cox_models_split_gen_2021_sex:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "general_2021"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2021_sex.txt
dataset: output/tabfig/cox_model_split_summary_general_2021_sex.csv
# describe_duration_diagnoses:
# run: jupyter:latest jupyter nbconvert /workspace/notebooks/describe_duration_diagnoses.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# needs: [covid_2021_rates_cohort, covid_2020_rates_cohort, general_2019_rates_cohort, general_2020_rates_cohort, general_2021_rates_cohort, pneumonia_2019_rates_cohort]
# outputs:
# moderately_sensitive:
# notebook: output/describe_duration_diagnoses.html
# table: output/tabfig/med_mean_overall.csv
# table2: output/tabfig/med_mean_age_group.csv
# table3: output/tabfig/med_mean_sex.csv
# table4: output/tabfig/med_mean_ethnicity.csv
# table5: output/tabfig/med_mean_imd.csv
# table6: output/tabfig/med_mean_region.csv
# subplots: output/tabfig/diag_*.png
table1:
run: r:latest analysis/descriptive/1_table1_demo_clinical.R
needs: [append_cohorts]
outputs:
moderately_sensitive:
table: output/tabfig/table1_*.csv
visualise_diagnoses:
run: r:latest analysis/descriptive/2_visualise_diagnoses.R
needs: [append_cohorts]
outputs:
moderately_sensitive:
table: output/tabfig/diag_by_cohort.csv
plot: output/tabfig/diag_all.png
check_died:
run: r:latest analysis/descriptive/3_check_died.R
needs: [covid_2020_rates_cohort, covid_2021_rates_cohort, general_2019_rates_cohort,
general_2020_rates_cohort, general_2021_rates_cohort, pneumonia_2019_rates_cohort,
reconcile_sick_note_spells_general_2020, reconcile_sick_note_spells_general_2019,
reconcile_sick_note_spells_general_2021]
outputs:
moderately_sensitive:
table1: output/tabfig/check_died_*.csv
# table3: output/tabfig/check_ons*.csv
table4: output/tabfig/check_index*.csv
table5: output/tabfig/check_deregister*.csv