generated from opensafely/research-template
/
project.yaml
49 lines (42 loc) · 1.62 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format=csv
outputs:
highly_sensitive:
cohort: output/input.csv
generate_enzyme_replace_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2015-01-01 to 2018-08-01 by month" --skip-existing --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/measures/inp*.feather
generate_enzyme_replace_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-09-01 to 2022-04-01 by month" --skip-existing --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/measures/in*.feather
generate_measures_enzymeRx:
run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
needs:
[
generate_enzyme_replace_1,
generate_enzyme_replace_2,
]
outputs:
moderately_sensitive:
measure_csv1: output/measures/measure_enzymeRx*_rate.csv
measure_csv2: output/measures/measure_ExByRegion*_rate.csv
describe_ERx_rates:
run: r:latest analysis/analysis_enzymeRx.R
needs:
[
generate_measures_enzymeRx,
]
outputs:
moderately_sensitive:
Fig1: output/ERx_number.png
Fig2: output/ERx_rates.png
Fig3: output/model_rates.png
Fig4: output/Region.png