generated from opensafely/research-template
/
project.yaml
183 lines (167 loc) · 7.75 KB
/
project.yaml
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version: "3.0"
expectations:
population_size: 1000
actions:
generate_cohort_2019:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2019
outputs:
highly_sensitive:
cohort: output/input_2019.csv
generate_cohort_2020:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2020
outputs:
highly_sensitive:
cohort: output/input_2020.csv
generate_measures_cohorts:
run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2019-02-01 to 2020-11-30 by month"
outputs:
highly_sensitive:
cohort1: output/input_measures_*.csv
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition_measures
needs: [generate_measures_cohorts]
outputs:
moderately_sensitive:
measure1: output/measure_covid_death_all.csv
measure2: output/measure_covid_death_sex.csv
measure3: output/measure_covid_death_age.csv
measure4: output/measure_covid_death_sex_age.csv
measure5: output/measure_allcause_death_all.csv
measure6: output/measure_allcause_death_sex.csv
measure7: output/measure_allcause_death_age.csv
measure8: output/measure_allcause_death_sex_age.csv
measure9: output/measure_noncovid_death_all.csv
measure10: output/measure_noncovid_death_sex.csv
measure11: output/measure_noncovid_death_age.csv
measure12: output/measure_noncovid_death_sex_age.csv
measure13: output/measure_covid_death_sex_age_five.csv
measure14: output/measure_allcause_death_sex_age_five.csv
measure15: output/measure_noncovid_death_sex_age_five.csv
measure16: output/measure_covid_death_all_chdetail.csv
measure17: output/measure_covid_death_sex_chdetail.csv
measure18: output/measure_covid_death_age_chdetail.csv
measure19: output/measure_covid_death_sex_age_chdetail.csv
measure20: output/measure_allcause_death_all_chdetail.csv
measure21: output/measure_allcause_death_sex_chdetail.csv
measure22: output/measure_allcause_death_age_chdetail.csv
measure23: output/measure_allcause_death_sex_age_chdetail.csv
measure24: output/measure_noncovid_death_all_chdetail.csv
measure25: output/measure_noncovid_death_sex_chdetail.csv
measure26: output/measure_noncovid_death_age_chdetail.csv
measure27: output/measure_noncovid_death_sex_age_chdetail.csv
010_data_management_2019:
run: r:latest analysis/010_data_management.R ./output/input_2019.csv ./data/study_population_2019.csv
needs: [generate_cohort_2019]
outputs:
highly_sensitive:
data1: data/study_population_2019.csv
010_data_management_2020:
run: r:latest analysis/010_data_management.R ./output/input_2020.csv ./data/study_population_2020.csv
needs: [generate_cohort_2020]
outputs:
highly_sensitive:
data2: data/study_population_2020.csv
020_baseline_characteristics_2019:
run: r:latest analysis/020_baseline_characteristics.R ./data/study_population_2019.csv ./analysis/outfiles/table_1a.txt
needs: [generate_cohort_2019, 010_data_management_2019]
outputs:
moderately_sensitive:
table1a: analysis/outfiles/table_1a.txt
020_baseline_characteristics_2020:
run: r:latest analysis/020_baseline_characteristics.R ./data/study_population_2020.csv ./analysis/outfiles/table_1b.txt
needs: [generate_cohort_2020, 010_data_management_2020]
outputs:
moderately_sensitive:
table1b: analysis/outfiles/table_1b.txt
025_carehome_characteristics:
run: r:latest analysis/025_carehome_characteristics.R ./data/study_population_2020.csv
needs: [010_data_management_2020]
outputs:
moderately_sensitive:
log: analysis/outfiles/carehome_characteristics.txt
030_descriptive_mortality_rates.R:
run: r:latest analysis/030_descriptive_mortality_rates.R
needs: [generate_measures_cohorts, generate_measures]
outputs:
moderately_sensitive:
table_2a: analysis/outfiles/table_2a.txt
table_2b: analysis/outfiles/table_2b.txt
table_2c: analysis/outfiles/table_2c.txt
table_2d: analysis/outfiles/table_2d.txt
table_3a: analysis/outfiles/table_3a.txt
table_3b: analysis/outfiles/table_3b.txt
table_3c: analysis/outfiles/table_3c.txt
table_3d: analysis/outfiles/table_3d.txt
table_4a: analysis/outfiles/table_4a.txt
table_4b: analysis/outfiles/table_4b.txt
table_4c: analysis/outfiles/table_4c.txt
table_4d: analysis/outfiles/table_4d.txt
plot_1a: analysis/outfiles/plot_1a.png
plot_1b: analysis/outfiles/plot_1b.png
plot_1c: analysis/outfiles/plot_1c.png
plot_2a: analysis/outfiles/plot_2a.png
plot_2b: analysis/outfiles/plot_2b.png
plot_2c: analysis/outfiles/plot_2c.png
plot_3a: analysis/outfiles/plot_3a.png
plot_3b: analysis/outfiles/plot_3b.png
plot_3c: analysis/outfiles/plot_3c.png
035_comparative_mortality_rates.R:
run: r:latest analysis/035_comparative_mortality_rates.R
needs: [generate_measures_cohorts, generate_measures]
outputs:
moderately_sensitive:
table_5a: analysis/outfiles/table_5a.txt
table_5b: analysis/outfiles/table_5b.txt
table_5c: analysis/outfiles/table_5c.txt
table_5d: analysis/outfiles/table_5d.txt
table_6a: analysis/outfiles/table_6a.txt
table_6b: analysis/outfiles/table_6b.txt
table_6c: analysis/outfiles/table_6c.txt
table_6d: analysis/outfiles/table_6d.txt
table_7a: analysis/outfiles/table_7a.txt
table_7b: analysis/outfiles/table_7b.txt
table_7c: analysis/outfiles/table_7c.txt
table_7d: analysis/outfiles/table_7d.txt
plot_8a: analysis/outfiles/plot_4a.png
plot_8b: analysis/outfiles/plot_4b.png
plot_8c: analysis/outfiles/plot_4c.png
plot_5a: analysis/outfiles/plot_5a.png
plot_5b: analysis/outfiles/plot_5b.png
plot_5c: analysis/outfiles/plot_5c.png
plot_6a: analysis/outfiles/plot_6a.png
plot_6b: analysis/outfiles/plot_6b.png
plot_6c: analysis/outfiles/plot_6c.png
040_cause_of_death.R:
run: r:latest analysis/040_cause_of_death.R
needs: [generate_measures_cohorts]
outputs:
moderately_sensitive:
table_8a: analysis/outfiles/table_8a.txt
table_8b: analysis/outfiles/table_8b.txt
plot_7a: analysis/outfiles/plot_7a.png
plot_7b: analysis/outfiles/plot_7b.png
050_standardisation.R:
run: r:latest analysis/050_standardisation.R
needs: [generate_measures_cohorts, generate_measures]
outputs:
moderately_sensitive:
table_9a: analysis/outfiles/table_9a.txt
table_9b: analysis/outfiles/table_9b.txt
table_9c: analysis/outfiles/table_9c.txt
plot_8a: analysis/outfiles/plot_8a.png
plot_8b: analysis/outfiles/plot_8b.png
plot_8c: analysis/outfiles/plot_8c.png
plot_9a: analysis/outfiles/plot_9a.png
plot_9b: analysis/outfiles/plot_9b.png
plot_9c: analysis/outfiles/plot_9c.png
generate_measures_sensitivity_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_measures_tppdeath --index-date-range "2016-02-01 to 2020-11-30 by month"
outputs:
highly_sensitive:
cohort_sensitivity: output/input_measures_tppdeath_*.csv
generate_measures_sensitivity:
run: cohortextractor:latest generate_measures --study-definition study_definition_measures_tppdeath
needs: [generate_measures_sensitivity_cohort]
outputs:
moderately_sensitive:
measure_sensitivity: output/measure_allcause_tppdeath_all.csv