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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_cohorts_long:
run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2019-01-01 to 2020-12-01 by month" --output-dir=output/measures
outputs:
highly_sensitive:
cohort1: output/measures/input_measures_*.csv
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition_measures --output-dir=output/measures
needs: [generate_cohorts_long]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_*.csv
run_model_long:
run: r:latest analysis/03-createnattrends_codes.R
needs: [generate_cohorts_long]
outputs:
moderately_sensitive:
log: logs/log-03-createnattrends.txt
tb01: output/tables/sc03_tb01_nattrends.csv
fig01: output/plots/sc03_fig01_nattrends.svg
fig02: output/plots/sc03_fig02_nattrends.svg
fig03: output/plots/sc03_fig03_pracnatcoverage.svg
fig04: output/plots/sc03_fig04_pracbyregcoverage.svg
fig04b: output/plots/sc03_fig04b_pracbyregcoverage.svg
run_model_measures:
run: r:latest analysis/02-createtemporal.R
needs: [generate_cohorts_long,generate_measures]
outputs:
moderately_sensitive:
log: logs/log-02-createtemporal.txt
red_measures: output/tables/redacted_*.csv
#figall: output/plots/plot_each_*_practice.svg
figquant: output/plots/plot_quantiles_*_practice.svg
figlogquant: output/plots/plot_logquantiles_*_practice.svg
### Weekly tallies
generate_cohorts_weekly2021:
run: cohortextractor:latest generate_cohort --study-definition study_definition_measures_weekly --index-date-range "2020-01-06 to 2021-03-22 by week" --output-dir=output/measures-week
outputs:
highly_sensitive:
cohort: output/measures-week/input_measures_weekly_*.csv
generate_measures_weekly2021:
run: cohortextractor:latest generate_measures --study-definition study_definition_measures_weekly --output-dir=output/measures-week
needs: [generate_cohorts_weekly2021]
outputs:
moderately_sensitive:
measure_csv: output/measures-week/measure_*.csv
run_model_weekly2021:
run: r:latest analysis/04-weekly2021.R
needs: [generate_cohorts_weekly2021,generate_measures_weekly2021]
outputs:
moderately_sensitive:
log: logs/log-04-weekly2021.txt
tab1: output/tables/sc04-weeklynattrend.csv