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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 30000
actions:
generate_study_population_patient_characteristics_2019:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_patient_characteristics_2019
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_patient_characteristics_2019.csv.gz
generate_study_population_patient_characteristics_2020:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_patient_characteristics_2020
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_patient_characteristics_2020.csv.gz
generate_study_population_patient_characteristics_2021:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_patient_characteristics_2021
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_patient_characteristics_2021.csv.gz
table_1:
run: r:latest analysis/table_1.R
needs: [generate_study_population_patient_characteristics_2019]
outputs:
moderately_sensitive:
table1: output/table1_2019_overallcount.csv
table2: output/table1_2019.csv
table_1_2020:
run: r:latest analysis/table_1_2020.R
needs: [generate_study_population_patient_characteristics_2020]
outputs:
moderately_sensitive:
table1: output/table1_2020_overallcount.csv
table2: output/table1_2020.csv
table_1_2021:
run: r:latest analysis/table_1_2021.R
needs: [generate_study_population_patient_characteristics_2021]
outputs:
moderately_sensitive:
table1: output/table1_2021_overallcount.csv
table2: output/table1_2021.csv
generate_study_population:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition
--index-date-range "2019-01-01 to 2021-12-31 by month"
--skip-existing
--output-dir=output/measures
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_*.csv.gz
generate_measures:
run: cohortextractor:latest generate_measures
--study-definition study_definition
--skip-existing
--output-dir=output/measures
needs: [generate_study_population]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_*.csv
generate_study_population_covid:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_covid
--index-date-range "2019-01-01 to 2021-12-31 by month"
--skip-existing
--output-dir=output/measures
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_covid_*.csv.gz
generate_measures_covid:
run: cohortextractor:latest generate_measures
--study-definition study_definition_covid
--skip-existing
--output-dir=output/measures
needs: [generate_study_population_covid]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_allpopulation_*.csv
figure_1A:
run: r:latest analysis/figure_1A.R
needs: [generate_measures]
outputs:
moderately_sensitive:
plot1: output/figure_1A.jpeg
figure_1B:
run: r:latest analysis/figure_1B.R
needs: [generate_measures,generate_measures_covid]
outputs:
moderately_sensitive:
plot1: output/figure_1B.jpeg
table1: output/figure_1B_table.csv
figure_2:
run: r:latest analysis/figure_2.R
needs: [generate_measures]
outputs:
moderately_sensitive:
plot1: output/figure_2.1.jpeg
plot2: output/figure_2.2.jpeg
plot3: output/figure_2.3.jpeg
table1: output/figure_2.1_table.csv
generate_study_population_weekly:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_weekly
--index-date-range "2019-01-01 to 2021-12-31 by week"
--skip-existing
--output-dir=output/measures
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_weekly_*.csv.gz
generate_measures_weekly:
run: cohortextractor:latest generate_measures
--study-definition study_definition_weekly
--skip-existing
--output-dir=output/measures
needs: [generate_study_population_weekly]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_weekly_*.csv
figure_1A_weekly:
run: r:latest analysis/figure_1A_weekly.R
needs: [generate_measures_weekly]
outputs:
moderately_sensitive:
plot1: output/figure_1A_weekly.jpeg
### generate study cohort with the date of each prescriptions
generate_study_population_ab_type_2019:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_ab_type_2019
--index-date-range "2019-01-01 to 2019-12-31"
--skip-existing
--output-dir=output/measures
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_ab_type_2019_*.csv.gz
generate_study_population_ab_type_2020:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_ab_type_2020
--index-date-range "2020-01-01 to 2020-12-31"
--skip-existing
--output-dir=output/measures
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_ab_type_2020_*.csv.gz
generate_study_population_ab_type_2021:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_ab_type_2021
--index-date-range "2021-01-01 to 2021-12-31"
--skip-existing
--output-dir=output/measures
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_ab_type_2021_*.csv.gz
conversion_abtype_2019:
run: r:latest analysis/conversion_abtype_2019.R
needs: [generate_study_population_ab_type_2019]
outputs:
highly_sensitive:
rds1: output/measures/abtype_2019.rds
conversion_abtype_2020:
run: r:latest analysis/conversion_abtype_2020.R
needs: [generate_study_population_ab_type_2020]
outputs:
highly_sensitive:
rds1: output/measures/abtype_2020.rds
conversion_abtype_2021:
run: r:latest analysis/conversion_abtype_2021.R
needs: [generate_study_population_ab_type_2021]
outputs:
highly_sensitive:
rds1: output/measures/abtype_2021.rds
figure_2B:
run: r:latest analysis/figure_2B.R
needs: [conversion_abtype_2019,conversion_abtype_2020,conversion_abtype_2021]
outputs:
moderately_sensitive:
plot1: output/figure_2B.jpeg
table1: output/figure_2B_table.csv
ITS_var:
run: r:latest analysis/ITS_var.R
needs: [conversion_abtype_2019,conversion_abtype_2020,conversion_abtype_2021,generate_measures]
outputs:
moderately_sensitive:
table1: output/mon_uti.csv
table2: output/mon_cold.csv
table3: output/mon_cough.csv
table4: output/mon_copd.csv
table5: output/mon_throat.csv
table6: output/mon_lrti.csv
table7: output/mon_urti.csv
table8: output/mon_sinusitis.csv
table9: output/mon_ot_media.csv
table10: output/mon_ot_externa.csv
table11: output/mon_all.csv
table12: output/mon_all_coded.csv
table13: output/mon_all_uncoded.csv
describe_ITS_model_broad_mon_overall:
run: r:latest analysis/itsmodel/ITS_model_monthly.R
needs: [ITS_var]
outputs:
moderately_sensitive:
plot1: output/mon_overall_predicted_plot.jpeg
plot2: output/mon_overall_forest_C.jpeg
plot3: output/mon_overall_forest_B.jpeg
plot4: output/mon_overall_combined.jpeg
table1: output/mon_overall_predicted_table.csv
table2: output/mon_overall_forest_B_table.csv
table3: output/mon_overall_forest_C_table.csv
ITS_var_weekly:
run: r:latest analysis/ITS_var_weekly.R
needs: [conversion_abtype_2019,conversion_abtype_2020,conversion_abtype_2021,generate_measures_weekly]
outputs:
moderately_sensitive:
table1: output/week_uti.csv
table2: output/week_cold.csv
table3: output/week_cough.csv
table4: output/week_copd.csv
table5: output/week_throat.csv
table6: output/week_lrti.csv
table7: output/week_urti.csv
table8: output/week_sinusitis.csv
table9: output/week_ot_media.csv
table10: output/week_ot_externa.csv
table11: output/week_all.csv
describe_ITS_model_broad_week_overall:
run: r:latest analysis/itsmodel/ITS_model_weekly.R
needs: [ITS_var_weekly]
outputs:
moderately_sensitive:
plot1: output/week_overall_predicted_plot.jpeg
plot2: output/week_overall_forest_C.jpeg
plot3: output/week_overall_forest_B.jpeg
plot4: output/week_overall_combined.jpeg
table1: output/week_overall_predicted_table.csv
table2: output/week_overall_forest_B_table.csv
table3: output/week_overall_forest_C_table.csv
ITS_overall_uti_plot:
run: r:latest analysis/itsmodel/ITS_model_predict.R
needs: [describe_ITS_model_broad_mon_overall]
outputs:
moderately_sensitive:
plot1: output/overall_predicted.jpeg
plot2: output/UTI_predicted.jpeg
ITS_model_monthly_rest:
run: r:latest analysis/itsmodel/ITS_model_monthly_rest.R
needs: [ITS_var]
outputs:
moderately_sensitive:
plot1: output/mon_overall_predicted_rest.jpeg
Poisson_model_table:
run: r:latest analysis/itsmodel/Poisson_model_table.R
needs: [ITS_var]
outputs:
moderately_sensitive:
plot1: output/table2.csv
generate_study_population_2020_covid_window:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_2020_covid_window
--index-date-range "2020-01-01 to 2020-12-31 by month"
--skip-existing
--output-dir=output/measures
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_2020_covid_window_*.csv.gz
generate_measures_2020_covid_window:
run: cohortextractor:latest generate_measures
--study-definition study_definition_2020_covid_window
--skip-existing
--output-dir=output/measures
needs: [generate_study_population_2020_covid_window]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_covid_window_*.csv
generate_study_population_2021_covid_window:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_2021_covid_window
--index-date-range "2021-01-01 to 2021-12-31 by month"
--skip-existing
--output-dir=output/measures
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_2021_covid_window_*.csv.gz
generate_measures_2021_covid_window:
run: cohortextractor:latest generate_measures
--study-definition study_definition_2021_covid_window
--skip-existing
--output-dir=output/measures
needs: [generate_study_population_2021_covid_window]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_21_covid_window_*.csv
figure_3:
run: r:latest analysis/figure_3.R
needs: [generate_measures_2020_covid_window,generate_measures_2021_covid_window]
outputs:
moderately_sensitive:
plot1: output/figure_3.jpeg
table1: output/figure_3_table.csv
figure_3_2D:
run: r:latest analysis/figure_3_2D.R
needs: [generate_measures_2020_covid_window,generate_measures_2021_covid_window]
outputs:
moderately_sensitive:
plot1: output/figure_3_2D.jpeg
table1: output/figure_3_2D_table.csv
ab_type_table:
run: r:latest analysis/ab_type_table.R
needs: [generate_measures_2020_covid_window,generate_measures_2021_covid_window]
outputs:
moderately_sensitive:
table1: output/ab_type_table.csv
table2: output/ab_type_table_2D.csv
figure_Stype:
run: r:latest analysis/figure_Stype.R
needs: [generate_measures]
outputs:
moderately_sensitive:
plot1: output/figure_Stype.jpeg
table1: output/figure_Stype_table.csv
ITS_var_sen_2month:
run: r:latest analysis/ITS_var_sen_2month.R
needs: [conversion_abtype_2019,conversion_abtype_2020,conversion_abtype_2021,generate_measures]
outputs:
moderately_sensitive:
table1: output/sen_2mon_uti.csv
table2: output/sen_2mon_cold.csv
table3: output/sen_2mon_cough.csv
table4: output/sen_2mon_copd.csv
table5: output/sen_2mon_throat.csv
table6: output/sen_2mon_lrti.csv
table7: output/sen_2mon_urti.csv
table8: output/sen_2mon_sinusitis.csv
table9: output/sen_2mon_ot_media.csv
table10: output/sen_2mon_ot_externa.csv
table11: output/sen_2mon_all.csv
table12: output/sen_2mon_all_coded.csv
table13: output/sen_2mon_all_uncoded.csv
ITS_var_sen_3month:
run: r:latest analysis/ITS_var_sen_3month.R
needs: [conversion_abtype_2019,conversion_abtype_2020,conversion_abtype_2021,generate_measures]
outputs:
moderately_sensitive:
table1: output/sen_3mon_uti.csv
table2: output/sen_3mon_cold.csv
table3: output/sen_3mon_cough.csv
table4: output/sen_3mon_copd.csv
table5: output/sen_3mon_throat.csv
table6: output/sen_3mon_lrti.csv
table7: output/sen_3mon_urti.csv
table8: output/sen_3mon_sinusitis.csv
table9: output/sen_3mon_ot_media.csv
table10: output/sen_3mon_ot_externa.csv
table11: output/sen_3mon_all.csv
table12: output/sen_3mon_all_coded.csv
table13: output/sen_3mon_all_uncoded.csv
describe_ITS_model_broad_sen2mon:
run: r:latest analysis/itsmodel/ITS_model_monthly_sen2mon.R
needs: [ITS_var_sen_2month]
outputs:
moderately_sensitive:
plot1: output/sen_2mon_overall_predicted_plot.jpeg
plot2: output/sen_2mon_overall_forest_C.jpeg
plot3: output/sen_2mon_overall_forest_B.jpeg
plot4: output/sen_2mon_overall_combined.jpeg
table1: output/sen_2mon_overall_predicted_table.csv
table2: output/sen_2mon_overall_forest_B_table.csv
table3: output/sen_2mon_overall_forest_C_table.csv
describe_ITS_model_broad_sen3mon:
run: r:latest analysis/itsmodel/ITS_model_monthly_sen3mon.R
needs: [ITS_var_sen_3month]
outputs:
moderately_sensitive:
plot1: output/sen_3mon_overall_predicted_plot.jpeg
plot2: output/sen_3mon_overall_forest_C.jpeg
plot3: output/sen_3mon_overall_forest_B.jpeg
plot4: output/sen_3mon_overall_combined.jpeg
table1: output/sen_3mon_overall_predicted_table.csv
table2: output/sen_3mon_overall_forest_B_table.csv
table3: output/sen_3mon_overall_forest_C_table.csv
generate_study_population_2020_coinfection:
run: cohortextractor:latest generate_cohort
--with-end-date-fix
--study-definition study_definition_2020_coinfection
--index-date-range "2020-01-01 to 2020-12-31 by month"
--skip-existing
--output-dir=output/measures
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_2020_coinfection_*.csv.gz
generate_measures_2020_coinfection:
run: cohortextractor:latest generate_measures
--study-definition study_definition_2020_coinfection
--skip-existing
--output-dir=output/measures
needs: [generate_study_population_2020_coinfection]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_infection_coded_*.csv