generated from opensafely/research-template
/
project.yaml
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/
project.yaml
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version: '3.0'
expectations:
population_size: 10000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-07-14 to 2021-03-15 by week" --skip-existing --output-format=csv.gz --output-dir=output/measures
outputs:
highly_sensitive:
cohort: output/measures/input_*.csv.gz
generate_practice_variables:
run: cohortextractor:latest generate_cohort --study-definition study_definition_practice --skip-existing --output-format=dta --output-dir=output
outputs:
highly_sensitive:
cohort: output/input_practice.dta
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
needs: [generate_study_population]
outputs:
highly_sensitive:
measure_csv: output/measures/measure_*.csv
run_practice_variables:
run: stata-mp:latest analysis/practice_variables.do
needs: [generate_practice_variables]
outputs:
moderately_sensitive:
model: output/practice_variables.dta
model2: output/practice_variables.xlsx
run_model:
run: stata-mp:latest analysis/model.do
needs: [generate_measures, run_practice_variables]
outputs:
moderately_sensitive:
model1: output/PerProtocol.xlsx
model2: output/DiD_weekly.xlsx
check: output/weekly_check.xlsx
check2: output/practice_weekly_glmm.xlsx
model3: output/CITS_weekly.xlsx
model4: output/CITS_RandInt.xlsx
plot1: output/rti_plot.pdf
plot2: output/arti_plot.pdf
plot3: output/gastro_plot.pdf
plot4: output/coviddiag_plot.pdf
plot5: output/covidsympsens_plot.pdf
plot6: output/covidsympspec_plot.pdf
plot7: output/antibio_plot.pdf
plot8: output/adm_plot.pdf
# run_process_evaluation:
# run: stata-mp:latest analysis/process_eval.do
# outputs:
# moderately_sensitive:
# model1: output/process_eval_main.xlsx
# model2: output/process_eval_alternative.xlsx