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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 50000
actions:
## 1. EXTRACT DATA FOR EXPOSED - **NOTE THIS IS FOR WAVE 2 ONLY**
generate_community_cases_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_communitycases
outputs:
highly_sensitive:
cohort: output/input_covid_communitycases.csv
# 1a. CHECK EXTRACTED CASE RAW DATA
# check_case_extract:
# run: stata-mp:latest analysis/1a_longCovidSymp_checkCaseExtract.do
# needs: [create_analysis_file]
# outputs:
# moderately_sensitive:
# log: logs/1a_longCovidSymp_checkCaseExtract.log
# 2. EXTRACT DATA FOR POTENTIAL COMPARATORS
# new extract potential comparators code... I guess I'll have to this twice for each control group
# or potentially 3 times: 2018 matches, 2019 matches, contemporary matches?
# *** contemporary potential comparators
generate_potential_controls_contemporary:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controls_contemporary
outputs:
highly_sensitive:
cohort: output/input_controls_contemporary.csv
# *** contemporary potential comparators - flowcheck
generate_potential_controls_contemporaryFlowCheck:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controls_contemporaryFlowCheck
outputs:
highly_sensitive:
cohort: output/input_controls_contemporaryFlowCheck.csv
# *** historical potential comparators (2018)
generate_potential_controls_historical:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controls_historical
outputs:
highly_sensitive:
cohort: output/input_controls_historical.csv
# *** correct death dates due to error in documentation
correct_case_death_dates:
run: stata-mp:latest analysis/000_correct_death_dates_cr.do cases
needs: [generate_community_cases_cohort]
outputs:
highly_sensitive:
casecohort: output/input_covidcommunitycasesCorrectedDeathDate.csv
moderately_sensitive:
log: logs/000_set_correct_death_dates_cases_cr.log
correct_contemporary_control_death_dates:
run: stata-mp:latest analysis/000_correct_death_dates_cr.do contemporary
needs: [generate_potential_controls_contemporary]
outputs:
highly_sensitive:
controlcohort: output/input_controls_contemporaryCorrectedDeathDate.csv
moderately_sensitive:
log: logs/000_set_correct_death_dates_contemporary_cr.log
correct_historical_control_death_dates:
run: stata-mp:latest analysis/000_correct_death_dates_cr.do historical
needs: [generate_potential_controls_historical]
outputs:
highly_sensitive:
historicalcontrolcohort: output/input_controls_historicalCorrectedDeathDate.csv
moderately_sensitive:
log: logs/000_set_correct_death_dates_historical_cr.log
## 2a CORRECT CASE INDEX DATE IN CASES ONLY (ADD 28 DAYS TO ORIGNAL INDEX DATE)
set_case_index_date:
run: stata-mp:latest analysis/00_set_case_index_date_cr.do
needs: [correct_case_death_dates]
outputs:
highly_sensitive:
cohort: output/input_covid_communitycases_correctedCaseIndex.csv
moderately_sensitive:
log: logs/00_set_case_index_date_cr.log
# ****NOTE: FOR DUMMY DATA STATA FILE 00B NEEDS RUN HERE (NOT USING THE COHORT EXTRACTOR) IN ORDER TO CREATE SENSIBLE STPS****
# 2b. CHECK NUMBERS IN EACH STP PRIOR TO SPLITTING AND APPENDING STEPS BELOW
# *** contemporary potential comparators
checkSTPs_in_original_extract:
run: stata-mp:latest analysis/00a_checkSTPs_in_original_extract_an.do
needs: [set_case_index_date, generate_potential_controls_contemporary, generate_potential_controls_historical]
outputs:
moderately_sensitive:
log: logs/00a_checkSTPs_in_original_extract_an.log
# 3. SPLIT CONTEMPORARY CASES AND COMPARATORS UP BY STP
01_longCovidSymp_split_by_stp:
run: stata-mp:latest analysis/01_longCovidSymp_cr_split_by_stp.do
needs: [set_case_index_date, correct_contemporary_control_death_dates]
outputs:
highly_sensitive:
case_stp5: output/input_controls_contemporary_stp5.csv
case_stp6: output/input_controls_contemporary_stp6.csv
case_stp7: output/input_controls_contemporary_stp7.csv
case_stp8: output/input_controls_contemporary_stp8.csv
case_stp9: output/input_controls_contemporary_stp9.csv
case_stp10: output/input_controls_contemporary_stp10.csv
case_stp12: output/input_controls_contemporary_stp12.csv
case_stp13: output/input_controls_contemporary_stp13.csv
case_stp14: output/input_controls_contemporary_stp14.csv
case_stp15: output/input_controls_contemporary_stp15.csv
case_stp16: output/input_controls_contemporary_stp16.csv
case_stp17: output/input_controls_contemporary_stp17.csv
case_stp20: output/input_controls_contemporary_stp20.csv
case_stp21: output/input_controls_contemporary_stp21.csv
case_stp22: output/input_controls_contemporary_stp22.csv
case_stp23: output/input_controls_contemporary_stp23.csv
case_stp24: output/input_controls_contemporary_stp24.csv
case_stp25: output/input_controls_contemporary_stp25.csv
case_stp26: output/input_controls_contemporary_stp26.csv
case_stp27: output/input_controls_contemporary_stp27.csv
case_stp29: output/input_controls_contemporary_stp29.csv
case_stp33: output/input_controls_contemporary_stp33.csv
case_stp35: output/input_controls_contemporary_stp35.csv
case_stp36: output/input_controls_contemporary_stp36.csv
case_stp37: output/input_controls_contemporary_stp37.csv
case_stp40: output/input_controls_contemporary_stp40.csv
case_stp41: output/input_controls_contemporary_stp41.csv
case_stp42: output/input_controls_contemporary_stp42.csv
case_stp43: output/input_controls_contemporary_stp43.csv
case_stp44: output/input_controls_contemporary_stp44.csv
case_stp49: output/input_controls_contemporary_stp49.csv
control_stp5: output/input_covid_communitycases_stp5.csv
control_stp6: output/input_covid_communitycases_stp6.csv
control_stp7: output/input_covid_communitycases_stp7.csv
control_stp8: output/input_covid_communitycases_stp8.csv
control_stp9: output/input_covid_communitycases_stp9.csv
control_stp10: output/input_covid_communitycases_stp10.csv
control_stp12: output/input_covid_communitycases_stp12.csv
control_stp13: output/input_covid_communitycases_stp13.csv
control_stp14: output/input_covid_communitycases_stp14.csv
control_stp15: output/input_covid_communitycases_stp15.csv
control_stp16: output/input_covid_communitycases_stp16.csv
control_stp17: output/input_covid_communitycases_stp17.csv
control_stp20: output/input_covid_communitycases_stp20.csv
control_stp21: output/input_covid_communitycases_stp21.csv
control_stp22: output/input_covid_communitycases_stp22.csv
control_stp23: output/input_covid_communitycases_stp23.csv
control_stp24: output/input_covid_communitycases_stp24.csv
control_stp25: output/input_covid_communitycases_stp25.csv
control_stp26: output/input_covid_communitycases_stp26.csv
control_stp27: output/input_covid_communitycases_stp27.csv
control_stp29: output/input_covid_communitycases_stp29.csv
control_stp33: output/input_covid_communitycases_stp33.csv
control_stp35: output/input_covid_communitycases_stp35.csv
control_stp36: output/input_covid_communitycases_stp36.csv
control_stp37: output/input_covid_communitycases_stp37.csv
control_stp40: output/input_covid_communitycases_stp40.csv
control_stp41: output/input_covid_communitycases_stp41.csv
control_stp42: output/input_covid_communitycases_stp42.csv
control_stp43: output/input_covid_communitycases_stp43.csv
control_stp44: output/input_covid_communitycases_stp44.csv
control_stp49: output/input_covid_communitycases_stp49.csv
moderately_sensitive:
log: logs/01_longCovidSymp_split_by_stp.log
# 3. SPLIT HISTORICAL COMPARATORS UP BY STP
01b_longCovidSymp_splitHistorical_by_stp:
run: stata-mp:latest analysis/01b_longCovidSymp_cr_splitComparator_by_stp.do historical
needs: [correct_historical_control_death_dates]
outputs:
highly_sensitive:
case_stp5: output/input_controls_historical_stp5.csv
case_stp6: output/input_controls_historical_stp6.csv
case_stp7: output/input_controls_historical_stp7.csv
case_stp8: output/input_controls_historical_stp8.csv
case_stp9: output/input_controls_historical_stp9.csv
case_stp10: output/input_controls_historical_stp10.csv
case_stp12: output/input_controls_historical_stp12.csv
case_stp13: output/input_controls_historical_stp13.csv
case_stp14: output/input_controls_historical_stp14.csv
case_stp15: output/input_controls_historical_stp15.csv
case_stp16: output/input_controls_historical_stp16.csv
case_stp17: output/input_controls_historical_stp17.csv
case_stp20: output/input_controls_historical_stp20.csv
case_stp21: output/input_controls_historical_stp21.csv
case_stp22: output/input_controls_historical_stp22.csv
case_stp23: output/input_controls_historical_stp23.csv
case_stp24: output/input_controls_historical_stp24.csv
case_stp25: output/input_controls_historical_stp25.csv
case_stp26: output/input_controls_historical_stp26.csv
case_stp27: output/input_controls_historical_stp27.csv
case_stp29: output/input_controls_historical_stp29.csv
case_stp33: output/input_controls_historical_stp33.csv
case_stp35: output/input_controls_historical_stp35.csv
case_stp36: output/input_controls_historical_stp36.csv
case_stp37: output/input_controls_historical_stp37.csv
case_stp40: output/input_controls_historical_stp40.csv
case_stp41: output/input_controls_historical_stp41.csv
case_stp42: output/input_controls_historical_stp42.csv
case_stp43: output/input_controls_historical_stp43.csv
case_stp44: output/input_controls_historical_stp44.csv
case_stp49: output/input_controls_historical_stp49.csv
moderately_sensitive:
log: logs/01b_longCovidSymp_splithistorical_by_stp.log
# 4. MATCH CASES TO CONTEMPORARY COMPARATORS
# *** contemporary potential comparators for each stp
match_contemporary_stp5:
run: python:latest python analysis/match_contemporary_stp5.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp5: output/matched_cases_stp5.csv
matched_matches_stp5: output/matched_matches_stp5.csv
matched_all_stp5: output/matched_combined_stp5.csv
moderately_sensitive:
matching_report_stp5: output/matching_report_stp5.txt
match_contemporary_stp6:
run: python:latest python analysis/match_contemporary_stp6.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp6: output/matched_cases_stp6.csv
matched_matches_stp6: output/matched_matches_stp6.csv
matched_all_stp6: output/matched_combined_stp6.csv
moderately_sensitive:
matching_report_stp6: output/matching_report_stp6.txt
match_contemporary_stp7:
run: python:latest python analysis/match_contemporary_stp7.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp7: output/matched_cases_stp7.csv
matched_matches_stp7: output/matched_matches_stp7.csv
matched_all_stp7: output/matched_combined_stp7.csv
moderately_sensitive:
matching_report_stp7: output/matching_report_stp7.txt
match_contemporary_stp8:
run: python:latest python analysis/match_contemporary_stp8.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp8: output/matched_cases_stp8.csv
matched_matches_stp8: output/matched_matches_stp8.csv
matched_all_stp8: output/matched_combined_stp8.csv
moderately_sensitive:
matching_report_stp8: output/matching_report_stp8.txt
match_contemporary_stp9:
run: python:latest python analysis/match_contemporary_stp9.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp9: output/matched_cases_stp9.csv
matched_matches_stp9: output/matched_matches_stp9.csv
matched_all_stp9: output/matched_combined_stp9.csv
moderately_sensitive:
matching_report_stp9: output/matching_report_stp9.txt
match_contemporary_stp10:
run: python:latest python analysis/match_contemporary_stp10.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp10: output/matched_cases_stp10.csv
matched_matches_stp10: output/matched_matches_stp10.csv
matched_all_stp10: output/matched_combined_stp10.csv
moderately_sensitive:
matching_report_stp10: output/matching_report_stp10.txt
match_contemporary_stp12:
run: python:latest python analysis/match_contemporary_stp12.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp12: output/matched_cases_stp12.csv
matched_matches_stp12: output/matched_matches_stp12.csv
matched_all_stp12: output/matched_combined_stp12.csv
moderately_sensitive:
matching_report_stp12: output/matching_report_stp12.txt
match_contemporary_stp13:
run: python:latest python analysis/match_contemporary_stp13.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp13: output/matched_cases_stp13.csv
matched_matches_stp13: output/matched_matches_stp13.csv
matched_all_stp13: output/matched_combined_stp13.csv
moderately_sensitive:
matching_report_stp13: output/matching_report_stp13.txt
match_contemporary_stp14:
run: python:latest python analysis/match_contemporary_stp14.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp14: output/matched_cases_stp14.csv
matched_matches_stp14: output/matched_matches_stp14.csv
matched_all_stp14: output/matched_combined_stp14.csv
moderately_sensitive:
matching_report_stp14: output/matching_report_stp14.txt
match_contemporary_stp15:
run: python:latest python analysis/match_contemporary_stp15.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp15: output/matched_cases_stp15.csv
matched_matches_stp15: output/matched_matches_stp15.csv
matched_all_stp15: output/matched_combined_stp15.csv
moderately_sensitive:
matching_report_stp15: output/matching_report_stp15.txt
match_contemporary_stp16:
run: python:latest python analysis/match_contemporary_stp16.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp16: output/matched_cases_stp16.csv
matched_matches_stp16: output/matched_matches_stp16.csv
matched_all_stp16: output/matched_combined_stp16.csv
moderately_sensitive:
matching_report_stp16: output/matching_report_stp16.txt
match_contemporary_stp17:
run: python:latest python analysis/match_contemporary_stp17.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp17: output/matched_cases_stp17.csv
matched_matches_stp17: output/matched_matches_stp17.csv
matched_all_stp17: output/matched_combined_stp17.csv
moderately_sensitive:
matching_report_stp17: output/matching_report_stp17.txt
match_contemporary_stp20:
run: python:latest python analysis/match_contemporary_stp20.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp20: output/matched_cases_stp20.csv
matched_matches_stp20: output/matched_matches_stp20.csv
matched_all_stp20: output/matched_combined_stp20.csv
moderately_sensitive:
matching_report_stp20: output/matching_report_stp20.txt
match_contemporary_stp21:
run: python:latest python analysis/match_contemporary_stp21.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp21: output/matched_cases_stp21.csv
matched_matches_stp21: output/matched_matches_stp21.csv
matched_all_stp21: output/matched_combined_stp21.csv
moderately_sensitive:
matching_report_stp21: output/matching_report_stp21.txt
match_contemporary_stp22:
run: python:latest python analysis/match_contemporary_stp22.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp22: output/matched_cases_stp22.csv
matched_matches_stp22: output/matched_matches_stp22.csv
matched_all_stp22: output/matched_combined_stp22.csv
moderately_sensitive:
matching_report_stp22: output/matching_report_stp22.txt
match_contemporary_stp23:
run: python:latest python analysis/match_contemporary_stp23.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp23: output/matched_cases_stp23.csv
matched_matches_stp23: output/matched_matches_stp23.csv
matched_all_stp23: output/matched_combined_stp23.csv
moderately_sensitive:
matching_report_stp23: output/matching_report_stp23.txt
match_contemporary_stp24:
run: python:latest python analysis/match_contemporary_stp24.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp24: output/matched_cases_stp24.csv
matched_matches_stp24: output/matched_matches_stp24.csv
matched_all_stp24: output/matched_combined_stp24.csv
moderately_sensitive:
matching_report_stp24: output/matching_report_stp24.txt
match_contemporary_stp25:
run: python:latest python analysis/match_contemporary_stp25.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp25: output/matched_cases_stp25.csv
matched_matches_stp25: output/matched_matches_stp25.csv
matched_all_stp25: output/matched_combined_stp25.csv
moderately_sensitive:
matching_report_stp25: output/matching_report_stp25.txt
match_contemporary_stp26:
run: python:latest python analysis/match_contemporary_stp26.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp26: output/matched_cases_stp26.csv
matched_matches_stp26: output/matched_matches_stp26.csv
matched_all_stp26: output/matched_combined_stp26.csv
moderately_sensitive:
matching_report_stp26: output/matching_report_stp26.txt
match_contemporary_stp27:
run: python:latest python analysis/match_contemporary_stp27.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp27: output/matched_cases_stp27.csv
matched_matches_stp27: output/matched_matches_stp27.csv
matched_all_stp27: output/matched_combined_stp27.csv
moderately_sensitive:
matching_report_stp27: output/matching_report_stp27.txt
match_contemporary_stp29:
run: python:latest python analysis/match_contemporary_stp29.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp29: output/matched_cases_stp29.csv
matched_matches_stp29: output/matched_matches_stp29.csv
matched_all_stp29: output/matched_combined_stp29.csv
moderately_sensitive:
matching_report_stp29: output/matching_report_stp29.txt
match_contemporary_stp33:
run: python:latest python analysis/match_contemporary_stp33.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp33: output/matched_cases_stp33.csv
matched_matches_stp33: output/matched_matches_stp33.csv
matched_all_stp33: output/matched_combined_stp33.csv
moderately_sensitive:
matching_report_stp33: output/matching_report_stp33.txt
match_contemporary_stp35:
run: python:latest python analysis/match_contemporary_stp35.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp35: output/matched_cases_stp35.csv
matched_matches_stp35: output/matched_matches_stp35.csv
matched_all_stp35: output/matched_combined_stp35.csv
moderately_sensitive:
matching_report_stp35: output/matching_report_stp35.txt
match_contemporary_stp36:
run: python:latest python analysis/match_contemporary_stp36.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp36: output/matched_cases_stp36.csv
matched_matches_stp36: output/matched_matches_stp36.csv
matched_all_stp36: output/matched_combined_stp36.csv
moderately_sensitive:
matching_report_stp36: output/matching_report_stp36.txt
match_contemporary_stp37:
run: python:latest python analysis/match_contemporary_stp37.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp37: output/matched_cases_stp37.csv
matched_matches_stp37: output/matched_matches_stp37.csv
matched_all_stp37: output/matched_combined_stp37.csv
moderately_sensitive:
matching_report_stp37: output/matching_report_stp37.txt
match_contemporary_stp40:
run: python:latest python analysis/match_contemporary_stp40.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp40: output/matched_cases_stp40.csv
matched_matches_stp40: output/matched_matches_stp40.csv
matched_all_stp40: output/matched_combined_stp40.csv
moderately_sensitive:
matching_report_stp40: output/matching_report_stp40.txt
match_contemporary_stp41:
run: python:latest python analysis/match_contemporary_stp41.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp41: output/matched_cases_stp41.csv
matched_matches_stp41: output/matched_matches_stp41.csv
matched_all_stp41: output/matched_combined_stp41.csv
moderately_sensitive:
matching_report_stp41: output/matching_report_stp41.txt
match_contemporary_stp42:
run: python:latest python analysis/match_contemporary_stp42.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp42: output/matched_cases_stp42.csv
matched_matches_stp42: output/matched_matches_stp42.csv
matched_all_stp42: output/matched_combined_stp42.csv
moderately_sensitive:
matching_report_stp41: output/matching_report_stp42.txt
match_contemporary_stp43:
run: python:latest python analysis/match_contemporary_stp43.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp43: output/matched_cases_stp43.csv
matched_matches_stp43: output/matched_matches_stp43.csv
matched_all_stp43: output/matched_combined_stp43.csv
moderately_sensitive:
matching_report_stp43: output/matching_report_stp43.txt
match_contemporary_stp44:
run: python:latest python analysis/match_contemporary_stp44.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp44: output/matched_cases_stp44.csv
matched_matches_stp44: output/matched_matches_stp44.csv
matched_all_stp44: output/matched_combined_stp44.csv
moderately_sensitive:
matching_report_stp44: output/matching_report_stp44.txt
match_contemporary_stp49:
run: python:latest python analysis/match_contemporary_stp49.py
needs: [01_longCovidSymp_split_by_stp]
outputs:
highly_sensitive:
matched_cases_stp49: output/matched_cases_stp49.csv
matched_matches_stp49: output/matched_matches_stp49.csv
matched_all_stp49: output/matched_combined_stp49.csv
moderately_sensitive:
matching_report_stp49: output/matching_report_stp49.txt
# 4b. MATCH CASES TO HISTORICAL COMPARATORS
#*** historical potential comparators for each stp
match_historical_stp5:
run: python:latest python analysis/match_historical_stp5.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp5: output/matched_cases_historical_stp5.csv
matched_matches_historical_stp5: output/matched_matches_historical_stp5.csv
matched_historical_all_stp5: output/matched_combined_historical_stp5.csv
moderately_sensitive:
matching_report_historical_stp5: output/matching_report_historical_stp5.txt
match_historical_stp6:
run: python:latest python analysis/match_historical_stp6.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp6: output/matched_cases_historical_stp6.csv
matched_matches_historical_stp6: output/matched_matches_historical_stp6.csv
matched_historical_all_stp6: output/matched_combined_historical_stp6.csv
moderately_sensitive:
matching_report_historical_stp6: output/matching_report_historical_stp6.txt
match_historical_stp7:
run: python:latest python analysis/match_historical_stp7.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp7: output/matched_cases_historical_stp7.csv
matched_matches_historical_stp7: output/matched_matches_historical_stp7.csv
matched_historical_all_stp7: output/matched_combined_historical_stp7.csv
moderately_sensitive:
matching_report_historical_stp7: output/matching_report_historical_stp7.txt
match_historical_stp8:
run: python:latest python analysis/match_historical_stp8.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp8: output/matched_cases_historical_stp8.csv
matched_matches_historical_stp8: output/matched_matches_historical_stp8.csv
matched_historical_all_stp8: output/matched_combined_historical_stp8.csv
moderately_sensitive:
matching_report_historical_stp8: output/matching_report_historical_stp8.txt
match_historical_stp9:
run: python:latest python analysis/match_historical_stp9.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp9: output/matched_cases_historical_stp9.csv
matched_matches_historical_stp9: output/matched_matches_historical_stp9.csv
matched_historical_all_stp9: output/matched_combined_historical_stp9.csv
moderately_sensitive:
matching_report_historical_stp9: output/matching_report_historical_stp9.txt
match_historical_stp10:
run: python:latest python analysis/match_historical_stp10.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp10: output/matched_cases_historical_stp10.csv
matched_matches_historical_stp10: output/matched_matches_historical_stp10.csv
matched_historical_all_stp10: output/matched_combined_historical_stp10.csv
moderately_sensitive:
matching_report_historical_stp10: output/matching_report_historical_stp10.txt
match_historical_stp12:
run: python:latest python analysis/match_historical_stp12.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp12: output/matched_cases_historical_stp12.csv
matched_matches_historical_stp12: output/matched_matches_historical_stp12.csv
matched_historical_all_stp12: output/matched_combined_historical_stp12.csv
moderately_sensitive:
matching_report_historical_stp12: output/matching_report_historical_stp12.txt
match_historical_stp13:
run: python:latest python analysis/match_historical_stp13.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp13: output/matched_cases_historical_stp13.csv
matched_matches_historical_stp13: output/matched_matches_historical_stp13.csv
matched_historical_all_stp13: output/matched_combined_historical_stp13.csv
moderately_sensitive:
matching_report_historical_stp13: output/matching_report_historical_stp13.txt
match_historical_stp14:
run: python:latest python analysis/match_historical_stp14.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp14: output/matched_cases_historical_stp14.csv
matched_matches_historical_stp14: output/matched_matches_historical_stp14.csv
matched_historical_all_stp14: output/matched_combined_historical_stp14.csv
moderately_sensitive:
matching_report_historical_stp14: output/matching_report_historical_stp14.txt
match_historical_stp15:
run: python:latest python analysis/match_historical_stp15.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp15: output/matched_cases_historical_stp15.csv
matched_matches_historical_stp15: output/matched_matches_historical_stp15.csv
matched_historical_all_stp15: output/matched_combined_historical_stp15.csv
moderately_sensitive:
matching_report_historical_stp15: output/matching_report_historical_stp15.txt
match_historical_stp16:
run: python:latest python analysis/match_historical_stp16.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp16: output/matched_cases_historical_stp16.csv
matched_matches_historical_stp16: output/matched_matches_historical_stp16.csv
matched_historical_all_stp16: output/matched_combined_historical_stp16.csv
moderately_sensitive:
matching_report_historical_stp16: output/matching_report_historical_stp16.txt
match_historical_stp17:
run: python:latest python analysis/match_historical_stp17.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp17: output/matched_cases_historical_stp17.csv
matched_matches_historical_stp17: output/matched_matches_historical_stp17.csv
matched_historical_all_stp17: output/matched_combined_historical_stp17.csv
moderately_sensitive:
matching_report_historical_stp17: output/matching_report_historical_stp17.txt
match_historical_stp20:
run: python:latest python analysis/match_historical_stp20.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp20: output/matched_cases_historical_stp20.csv
matched_matches_historical_stp20: output/matched_matches_historical_stp20.csv
matched_historical_all_stp20: output/matched_combined_historical_stp20.csv
moderately_sensitive:
matching_report_historical_stp20: output/matching_report_historical_stp20.txt
match_historical_stp21:
run: python:latest python analysis/match_historical_stp21.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp21: output/matched_cases_historical_stp21.csv
matched_matches_historical_stp21: output/matched_matches_historical_stp21.csv
matched_historical_all_stp21: output/matched_combined_historical_stp21.csv
moderately_sensitive:
matching_report_historical_stp21: output/matching_report_historical_stp21.txt
match_historical_stp22:
run: python:latest python analysis/match_historical_stp22.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp22: output/matched_cases_historical_stp22.csv
matched_matches_historical_stp22: output/matched_matches_historical_stp22.csv
matched_historical_all_stp22: output/matched_combined_historical_stp22.csv
moderately_sensitive:
matching_report_historical_stp22: output/matching_report_historical_stp22.txt
match_historical_stp23:
run: python:latest python analysis/match_historical_stp23.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp23: output/matched_cases_historical_stp23.csv
matched_matches_historical_stp23: output/matched_matches_historical_stp23.csv
matched_historical_all_stp23: output/matched_combined_historical_stp23.csv
moderately_sensitive:
matching_report_historical_stp23: output/matching_report_historical_stp23.txt
match_historical_stp24:
run: python:latest python analysis/match_historical_stp24.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp24: output/matched_cases_historical_stp24.csv
matched_matches_historical_stp24: output/matched_matches_historical_stp24.csv
matched_historical_all_stp24: output/matched_combined_historical_stp24.csv
moderately_sensitive:
matching_report_historical_stp24: output/matching_report_historical_stp24.txt
match_historical_stp25:
run: python:latest python analysis/match_historical_stp25.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp25: output/matched_cases_historical_stp25.csv
matched_matches_historical_stp25: output/matched_matches_historical_stp25.csv
matched_historical_all_stp25: output/matched_combined_historical_stp25.csv
moderately_sensitive:
matching_report_historical_stp25: output/matching_report_historical_stp25.txt
match_historical_stp26:
run: python:latest python analysis/match_historical_stp26.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp26: output/matched_cases_historical_stp26.csv
matched_matches_historical_stp26: output/matched_matches_historical_stp26.csv
matched_historical_all_stp26: output/matched_combined_historical_stp26.csv
moderately_sensitive:
matching_report_historical_stp26: output/matching_report_historical_stp26.txt
match_historical_stp27:
run: python:latest python analysis/match_historical_stp27.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp27: output/matched_cases_historical_stp27.csv
matched_matches_historical_stp27: output/matched_matches_historical_stp27.csv
matched_historical_all_stp27: output/matched_combined_historical_stp27.csv
moderately_sensitive:
matching_report_historical_stp27: output/matching_report_historical_stp27.txt
match_historical_stp29:
run: python:latest python analysis/match_historical_stp29.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp29: output/matched_cases_historical_stp29.csv
matched_matches_historical_stp29: output/matched_matches_historical_stp29.csv
matched_historical_all_stp29: output/matched_combined_historical_stp29.csv
moderately_sensitive:
matching_report_historical_stp29: output/matching_report_historical_stp29.txt
match_historical_stp33:
run: python:latest python analysis/match_historical_stp33.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp33: output/matched_cases_historical_stp33.csv
matched_matches_historical_stp33: output/matched_matches_historical_stp33.csv
matched_historical_all_stp33: output/matched_combined_historical_stp33.csv
moderately_sensitive:
matching_report_historical_stp33: output/matching_report_historical_stp33.txt
match_historical_stp35:
run: python:latest python analysis/match_historical_stp35.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp35: output/matched_cases_historical_stp35.csv
matched_matches_historical_stp35: output/matched_matches_historical_stp35.csv
matched_historical_all_stp35: output/matched_combined_historical_stp35.csv
moderately_sensitive:
matching_report_historical_stp35: output/matching_report_historical_stp35.txt
match_historical_stp36:
run: python:latest python analysis/match_historical_stp36.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp36: output/matched_cases_historical_stp36.csv
matched_matches_historical_stp36: output/matched_matches_historical_stp36.csv
matched_historical_all_stp36: output/matched_combined_historical_stp36.csv
moderately_sensitive:
matching_report_historical_stp36: output/matching_report_historical_stp36.txt
match_historical_stp37:
run: python:latest python analysis/match_historical_stp37.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp37: output/matched_cases_historical_stp37.csv
matched_matches_historical_stp37: output/matched_matches_historical_stp37.csv
matched_historical_all_stp37: output/matched_combined_historical_stp37.csv
moderately_sensitive:
matching_report_historical_stp37: output/matching_report_historical_stp37.txt
match_historical_stp40:
run: python:latest python analysis/match_historical_stp40.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp40: output/matched_cases_historical_stp40.csv
matched_matches_historical_stp40: output/matched_matches_historical_stp40.csv
matched_historical_all_stp40: output/matched_combined_historical_stp40.csv
moderately_sensitive:
matching_report_historical_stp40: output/matching_report_historical_stp40.txt
match_historical_stp41:
run: python:latest python analysis/match_historical_stp41.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp41: output/matched_cases_historical_stp41.csv
matched_matches_historical_stp41: output/matched_matches_historical_stp41.csv
matched_historical_all_stp41: output/matched_combined_historical_stp41.csv
moderately_sensitive:
matching_report_historical_stp41: output/matching_report_historical_stp41.txt
match_historical_stp42:
run: python:latest python analysis/match_historical_stp42.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp42: output/matched_cases_historical_stp42.csv
matched_matches_historical_stp42: output/matched_matches_historical_stp42.csv
matched_historical_all_stp42: output/matched_combined_historical_stp42.csv
moderately_sensitive:
matching_report_historical_stp41: output/matching_report_historical_stp42.txt
match_historical_stp43:
run: python:latest python analysis/match_historical_stp43.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp43: output/matched_cases_historical_stp43.csv
matched_matches_historical_stp43: output/matched_matches_historical_stp43.csv
matched_historical_all_stp43: output/matched_combined_historical_stp43.csv
moderately_sensitive:
matching_report_historical_stp43: output/matching_report_historical_stp43.txt
match_historical_stp44:
run: python:latest python analysis/match_historical_stp44.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp44: output/matched_cases_historical_stp44.csv
matched_matches_historical_stp44: output/matched_matches_historical_stp44.csv
matched_historical_all_stp44: output/matched_combined_historical_stp44.csv
moderately_sensitive:
matching_report_historical_stp44: output/matching_report_historical_stp44.txt
match_historical_stp49:
run: python:latest python analysis/match_historical_stp49.py
needs: [01_longCovidSymp_split_by_stp, 01b_longCovidSymp_splitHistorical_by_stp]
outputs:
highly_sensitive:
matched_cases_historical_stp49: output/matched_cases_historical_stp49.csv
matched_matches_historical_stp49: output/matched_matches_historical_stp49.csv
matched_historical_all_stp49: output/matched_combined_historical_stp49.csv
moderately_sensitive:
matching_report_historical_stp49: output/matching_report_historical_stp49.txt
# 5. CHECK VARIABLES IN MATCHED FILES
# *** contemporary potential comparators for each stp
checkVars_inMatchedFiles:
run: stata-mp:latest analysis/05_check_vars_after_matching.do contemporary
needs: [match_contemporary_stp29]
outputs:
moderately_sensitive:
log: logs/05_check_varscontemporary_after_matching.log
checkVars_inHistoricalMatchedFiles:
run: stata-mp:latest analysis/05_check_vars_after_matching.do historical
needs: [match_historical_stp29]
outputs:
moderately_sensitive:
log: logs/05_check_varshistorical_after_matching.log
# 6. COMBINE MATCHED CASES AND MATCHED COMPARATORS BY STP
combine_matched_CASESstps:
run: stata-mp:latest analysis/06a_longCovidSymp_cr_combine_CASEstps_after_matching.do contemporary
needs: [match_contemporary_stp5, match_contemporary_stp6, match_contemporary_stp7, match_contemporary_stp8, match_contemporary_stp9,
match_contemporary_stp10, match_contemporary_stp12, match_contemporary_stp13, match_contemporary_stp14, match_contemporary_stp15,
match_contemporary_stp16, match_contemporary_stp17, match_contemporary_stp20, match_contemporary_stp21, match_contemporary_stp22,
match_contemporary_stp23, match_contemporary_stp24, match_contemporary_stp25, match_contemporary_stp26, match_contemporary_stp27,
match_contemporary_stp29, match_contemporary_stp33, match_contemporary_stp35, match_contemporary_stp36, match_contemporary_stp37,
match_contemporary_stp40, match_contemporary_stp41, match_contemporary_stp42, match_contemporary_stp43, match_contemporary_stp44,
match_contemporary_stp49]
outputs:
highly_sensitive:
matched_cases_allstps: output/input_covid_matched_cases_contemporary_allSTPs.csv
moderately_sensitive:
log: logs/06a_longCovidSymp_cr_combine_contemporary_CASEstps_after_matching.log
combine_matched_COMPARATORstps:
run: stata-mp:latest analysis/06b_longCovidSymp_cr_combine_COMPARATORstps_after_matching.do contemporary
needs: [match_contemporary_stp5, match_contemporary_stp6, match_contemporary_stp7, match_contemporary_stp8, match_contemporary_stp9,
match_contemporary_stp10, match_contemporary_stp12, match_contemporary_stp13, match_contemporary_stp14, match_contemporary_stp15,
match_contemporary_stp16, match_contemporary_stp17, match_contemporary_stp20, match_contemporary_stp21, match_contemporary_stp22,
match_contemporary_stp23, match_contemporary_stp24, match_contemporary_stp25, match_contemporary_stp26, match_contemporary_stp27,
match_contemporary_stp29, match_contemporary_stp33, match_contemporary_stp35, match_contemporary_stp36, match_contemporary_stp37,
match_contemporary_stp40, match_contemporary_stp41, match_contemporary_stp42, match_contemporary_stp43, match_contemporary_stp44,
match_contemporary_stp49]
outputs:
highly_sensitive:
matched_matches_allstps: output/input_covid_matched_matches_contemporary_allSTPs.csv
moderately_sensitive:
log: logs/06b_longCovidSymp_cr_combine_contemporary_COMPARATORstps_after_matching.log
# 6. COMBINE MATCHED CASES AND MATCHED HISTORICAL COMPARATORS BY STP
combine_matched_historical_CASESstps:
run: stata-mp:latest analysis/06a_longCovidSymp_cr_combine_CASEstps_after_matching.do historical
needs: [match_historical_stp5, match_historical_stp6, match_historical_stp7, match_historical_stp8, match_historical_stp9,
match_historical_stp10, match_historical_stp12, match_historical_stp13, match_historical_stp14, match_historical_stp15,
match_historical_stp16, match_historical_stp17, match_historical_stp20, match_historical_stp21, match_historical_stp22,
match_historical_stp23, match_historical_stp24, match_historical_stp25, match_historical_stp26, match_historical_stp27,
match_historical_stp29, match_historical_stp33, match_historical_stp35, match_historical_stp36, match_historical_stp37,
match_historical_stp40, match_historical_stp41, match_historical_stp42, match_historical_stp43, match_historical_stp44,
match_historical_stp49]
outputs:
highly_sensitive:
matched_cases_allstps: output/input_covid_matched_cases_historical_allSTPs.csv
moderately_sensitive:
log: logs/06a_longCovidSymp_cr_combine_historical_CASEstps_after_matching.log
combine_matched_historical_COMPARATORstps:
run: stata-mp:latest analysis/06b_longCovidSymp_cr_combine_COMPARATORstps_after_matching.do historical
needs: [match_historical_stp5, match_historical_stp6, match_historical_stp7, match_historical_stp8, match_historical_stp9,
match_historical_stp10, match_historical_stp12, match_historical_stp13, match_historical_stp14, match_historical_stp15,
match_historical_stp16, match_historical_stp17, match_historical_stp20, match_historical_stp21, match_historical_stp22,
match_historical_stp23, match_historical_stp24, match_historical_stp25, match_historical_stp26, match_historical_stp27,
match_historical_stp29, match_historical_stp33, match_historical_stp35, match_historical_stp36, match_historical_stp37,
match_historical_stp40, match_historical_stp41, match_historical_stp42, match_historical_stp43, match_historical_stp44,
match_historical_stp49]
outputs:
highly_sensitive:
matched_matches_allstps: output/input_covid_matched_matches_historical_allSTPs.csv
moderately_sensitive:
log: logs/06b_longCovidSymp_cr_combine_historical_COMPARATORstps_after_matching.log
#6a. CHECK VARIABLES FOR COMBINED CASES AND COMBINED CONTROLS PRIOR TO ADDING MORE VARIABLES
check_contemporary_combinedFiles:
run: stata-mp:latest analysis/6f_longCovidSymp_checkCombinedFiles.do contemporary
needs: [combine_matched_CASESstps, combine_matched_COMPARATORstps]