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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
# General population cohort
generate_study_population:
run: cohortextractor:latest generate_cohort
--study-definition study_definition
--index-date-range "2018-03-01 to 2021-12-31 by month"
--output-dir=output/measures
--output-format=csv
outputs:
highly_sensitive:
cohort: output/measures/input_*.csv
generate_study_population_static_2019:
run: cohortextractor:latest generate_cohort --study-definition study_definition_static --index-date-range "2019-01-01" --output-dir=output/measures/tables --output-format=csv
outputs:
highly_sensitive:
cohort: output/input_static_2019-01-01.csv
generate_study_population_static_2020:
run: cohortextractor:latest generate_cohort --study-definition study_definition_static --index-date-range "2020-01-01" --output-dir=output/measures/tables --output-format=csv
outputs:
highly_sensitive:
cohort: output/input_static_2020-01-01.csv
generate_study_population_static_2021:
run: cohortextractor:latest generate_cohort --study-definition study_definition_static --index-date-range "2021-01-01" --output-dir=output/measures/tables --output-format=csv
outputs:
highly_sensitive:
cohort: output/input_static_2021-01-01.csv
# join_cohorts:
# run: >
# cohort-joiner:v0.0.56
# --lhs output/measures/input_*.csv
# --rhs output/input_static.csv
# --output-dir output/measures/joined
# needs: [generate_study_population, generate_study_population_static]
# outputs:
# highly_sensitive:
# cohort: output/measures/joined/input_*.csv
calculate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/measures
needs: [generate_study_population]
outputs:
moderately_sensitive:
measure: output/measures/measure_*_rate.csv
# Diabetes subpopulation
generate_study_population_dm:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_dm
--index-date-range "2018-03-01 to 2021-12-31 by month"
--output-dir=output/measures
--output-format=csv
outputs:
highly_sensitive:
cohort: output/measures/input_dm_*.csv
#join_cohorts_dm:
# run: >
# cohort-joiner:v0.0.56
# --lhs output/measures/input_dm_*.csv
# --rhs output/input_static.csv
# --output-dir output/measures/joined
# needs: [generate_study_population_dm, generate_study_population_static]
# outputs:
# highly_sensitive:
# cohort: output/measures/joined/input_dm_*.csv
calculate_measures_dm:
run: cohortextractor:latest generate_measures --study-definition study_definition_dm --output-dir=output/measures
needs: [generate_study_population_dm]
outputs:
moderately_sensitive:
measure: output/measures/measure_dm*_rate.csv
# Respiratory subpopulation
generate_study_population_resp:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_resp
--index-date-range "2018-03-01 to 2021-12-31 by month"
--output-dir=output/measures
--output-format=csv
outputs:
highly_sensitive:
cohort: output/measures/input_resp_*.csv
#join_cohorts_resp:
# run: >
# cohort-joiner:v0.0.56
# --lhs output/measures/input_resp_*.csv
# --rhs output/input_static.csv
# --output-dir output/measures/joined
# needs: [generate_study_population_resp, generate_study_population_static]
# outputs:
# highly_sensitive:
# cohort: output/measures/joined/input_resp_*.csv
calculate_measures_resp:
run: cohortextractor:latest generate_measures --study-definition study_definition_resp --output-dir=output/measures
needs: [generate_study_population_resp]
outputs:
moderately_sensitive:
measure: output/measures/measure_resp_*_rate.csv
create_baseline_tables:
run: stata-mp:latest analysis/101_baseline_tables.do
needs: [generate_study_population_static_2019, generate_study_population_static_2020, generate_study_population_static_2021]
outputs:
moderately_sensitive:
log: logs/table1_descriptives.log
output: output/tables/baseline_table_*.csv
graphs:
run: stata-mp:latest analysis/102_graphs.do
needs: [calculate_measures]
outputs:
moderately_sensitive:
log: logs/graphs.log
output: output/graphs/line_*.svg
data: output/graphs/line_*.csv
#check:
# run: stata-mp:latest analysis/data_check.do
# needs: [generate_study_population_dm, join_cohorts_dm]
#outputs:
# moderately_sensitive:
# log: logs/check.log