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project.yaml
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version: '3.0'
expectations:
population_size: 100000
actions:
## # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml DIRECTLY
## This file is created by create-project.R
## Edit and run create-project.R to update the project.yaml
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Pre-server scripts
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Inclusion/Exclusion Flow Chart Actions: Older Adults
## # # # # # # # # # # # # # # # # # # #
generate_flow_chart_data_older_adults_s1:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/older_adults_2016_2017_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_older_adults_2016_2017.arrow
-- older_adults season1_start_date season1_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/older_adults_2016_2017_flow_chart.arrow
process_flow_chart_data_older_adults_s1:
run: r:latest analysis/cohort_criteria.R older_adults season1_start_date season1_end_date
needs:
- generate_flow_chart_data_older_adults_s1
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_older_adults_2016_2017.csv
generate_flow_chart_data_older_adults_s2:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/older_adults_2017_2018_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_older_adults_2017_2018.arrow
-- older_adults season2_start_date season2_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/older_adults_2017_2018_flow_chart.arrow
process_flow_chart_data_older_adults_s2:
run: r:latest analysis/cohort_criteria.R older_adults season2_start_date season2_end_date
needs:
- generate_flow_chart_data_older_adults_s2
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_older_adults_2017_2018.csv
generate_flow_chart_data_older_adults_s3:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/older_adults_2018_2019_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_older_adults_2018_2019.arrow
-- older_adults season3_start_date season3_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/older_adults_2018_2019_flow_chart.arrow
process_flow_chart_data_older_adults_s3:
run: r:latest analysis/cohort_criteria.R older_adults season3_start_date season3_end_date
needs:
- generate_flow_chart_data_older_adults_s3
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_older_adults_2018_2019.csv
generate_flow_chart_data_older_adults_s4:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/older_adults_2019_2020_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_older_adults_2019_2020.arrow
-- older_adults season4_start_date season4_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/older_adults_2019_2020_flow_chart.arrow
process_flow_chart_data_older_adults_s4:
run: r:latest analysis/cohort_criteria.R older_adults season4_start_date season4_end_date
needs:
- generate_flow_chart_data_older_adults_s4
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_older_adults_2019_2020.csv
generate_flow_chart_data_older_adults_s5:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/older_adults_2020_2021_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_older_adults_2020_2021.arrow
-- older_adults season5_start_date season5_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/older_adults_2020_2021_flow_chart.arrow
process_flow_chart_data_older_adults_s5:
run: r:latest analysis/cohort_criteria.R older_adults season5_start_date season5_end_date
needs:
- generate_flow_chart_data_older_adults_s5
- process_household_information_s5
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_older_adults_2020_2021.csv
generate_flow_chart_data_older_adults_s6:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/older_adults_2021_2022_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_older_adults_2021_2022.arrow
-- older_adults season6_start_date season6_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/older_adults_2021_2022_flow_chart.arrow
process_flow_chart_data_older_adults_s6:
run: r:latest analysis/cohort_criteria.R older_adults season6_start_date season6_end_date
needs:
- generate_flow_chart_data_older_adults_s6
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_older_adults_2021_2022.csv
generate_flow_chart_data_older_adults_s7:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/older_adults_2022_2023_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_older_adults_2022_2023.arrow
-- older_adults season7_start_date season7_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/older_adults_2022_2023_flow_chart.arrow
process_flow_chart_data_older_adults_s7:
run: r:latest analysis/cohort_criteria.R older_adults season7_start_date season7_end_date
needs:
- generate_flow_chart_data_older_adults_s7
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_older_adults_2022_2023.csv
generate_flow_chart_data_older_adults_s8:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/older_adults_2023_2024_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_older_adults_2023_2024.arrow
-- older_adults season8_start_date season8_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/older_adults_2023_2024_flow_chart.arrow
process_flow_chart_data_older_adults_s8:
run: r:latest analysis/cohort_criteria.R older_adults season8_start_date season8_end_date
needs:
- generate_flow_chart_data_older_adults_s8
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_older_adults_2023_2024.csv
## # # # # # # # # # # # # # # # # # # #
## Inclusion/Exclusion Flow Chart Actions: Adults
## # # # # # # # # # # # # # # # # # # #
generate_flow_chart_data_adults_s1:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/adults_2016_2017_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_adults_2016_2017.arrow
-- adults season1_start_date season1_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/adults_2016_2017_flow_chart.arrow
process_flow_chart_data_adults_s1:
run: r:latest analysis/cohort_criteria.R adults season1_start_date season1_end_date
needs:
- generate_flow_chart_data_adults_s1
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_adults_2016_2017.csv
generate_flow_chart_data_adults_s2:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/adults_2017_2018_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_adults_2017_2018.arrow
-- adults season2_start_date season2_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/adults_2017_2018_flow_chart.arrow
process_flow_chart_data_adults_s2:
run: r:latest analysis/cohort_criteria.R adults season2_start_date season2_end_date
needs:
- generate_flow_chart_data_adults_s2
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_adults_2017_2018.csv
generate_flow_chart_data_adults_s3:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/adults_2018_2019_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_adults_2018_2019.arrow
-- adults season3_start_date season3_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/adults_2018_2019_flow_chart.arrow
process_flow_chart_data_adults_s3:
run: r:latest analysis/cohort_criteria.R adults season3_start_date season3_end_date
needs:
- generate_flow_chart_data_adults_s3
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_adults_2018_2019.csv
generate_flow_chart_data_adults_s4:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/adults_2019_2020_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_adults_2019_2020.arrow
-- adults season4_start_date season4_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/adults_2019_2020_flow_chart.arrow
process_flow_chart_data_adults_s4:
run: r:latest analysis/cohort_criteria.R adults season4_start_date season4_end_date
needs:
- generate_flow_chart_data_adults_s4
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_adults_2019_2020.csv
generate_flow_chart_data_adults_s5:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/adults_2020_2021_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_adults_2020_2021.arrow
-- adults season5_start_date season5_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/adults_2020_2021_flow_chart.arrow
process_flow_chart_data_adults_s5:
run: r:latest analysis/cohort_criteria.R adults season5_start_date season5_end_date
needs:
- generate_flow_chart_data_adults_s5
- process_household_information_s5
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_adults_2020_2021.csv
generate_flow_chart_data_adults_s6:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/adults_2021_2022_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_adults_2021_2022.arrow
-- adults season6_start_date season6_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/adults_2021_2022_flow_chart.arrow
process_flow_chart_data_adults_s6:
run: r:latest analysis/cohort_criteria.R adults season6_start_date season6_end_date
needs:
- generate_flow_chart_data_adults_s6
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_adults_2021_2022.csv
generate_flow_chart_data_adults_s7:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/adults_2022_2023_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_adults_2022_2023.arrow
-- adults season7_start_date season7_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/adults_2022_2023_flow_chart.arrow
process_flow_chart_data_adults_s7:
run: r:latest analysis/cohort_criteria.R adults season7_start_date season7_end_date
needs:
- generate_flow_chart_data_adults_s7
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_adults_2022_2023.csv
generate_flow_chart_data_adults_s8:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/adults_2023_2024_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_adults_2023_2024.arrow
-- adults season8_start_date season8_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/adults_2023_2024_flow_chart.arrow
process_flow_chart_data_adults_s8:
run: r:latest analysis/cohort_criteria.R adults season8_start_date season8_end_date
needs:
- generate_flow_chart_data_adults_s8
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_adults_2023_2024.csv
## # # # # # # # # # # # # # # # # # # #
## Inclusion/Exclusion Flow Chart Actions: Children and Adolescents
## # # # # # # # # # # # # # # # # # # #
generate_flow_chart_data_children_and_adolescents_s1:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/children_and_adolescents_2016_2017_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2016_2017.arrow
-- children_and_adolescents season1_start_date season1_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/children_and_adolescents_2016_2017_flow_chart.arrow
process_flow_chart_data_children_and_adolescents_s1:
run: r:latest analysis/cohort_criteria.R children_and_adolescents season1_start_date
season1_end_date
needs:
- generate_flow_chart_data_children_and_adolescents_s1
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_children_and_adolescents_2016_2017.csv
generate_flow_chart_data_children_and_adolescents_s2:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/children_and_adolescents_2017_2018_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2017_2018.arrow
-- children_and_adolescents season2_start_date season2_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/children_and_adolescents_2017_2018_flow_chart.arrow
process_flow_chart_data_children_and_adolescents_s2:
run: r:latest analysis/cohort_criteria.R children_and_adolescents season2_start_date
season2_end_date
needs:
- generate_flow_chart_data_children_and_adolescents_s2
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_children_and_adolescents_2017_2018.csv
generate_flow_chart_data_children_and_adolescents_s3:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/children_and_adolescents_2018_2019_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2018_2019.arrow
-- children_and_adolescents season3_start_date season3_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/children_and_adolescents_2018_2019_flow_chart.arrow
process_flow_chart_data_children_and_adolescents_s3:
run: r:latest analysis/cohort_criteria.R children_and_adolescents season3_start_date
season3_end_date
needs:
- generate_flow_chart_data_children_and_adolescents_s3
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_children_and_adolescents_2018_2019.csv
generate_flow_chart_data_children_and_adolescents_s4:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/children_and_adolescents_2019_2020_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2019_2020.arrow
-- children_and_adolescents season4_start_date season4_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/children_and_adolescents_2019_2020_flow_chart.arrow
process_flow_chart_data_children_and_adolescents_s4:
run: r:latest analysis/cohort_criteria.R children_and_adolescents season4_start_date
season4_end_date
needs:
- generate_flow_chart_data_children_and_adolescents_s4
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_children_and_adolescents_2019_2020.csv
generate_flow_chart_data_children_and_adolescents_s5:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/children_and_adolescents_2020_2021_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2020_2021.arrow
-- children_and_adolescents season5_start_date season5_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/children_and_adolescents_2020_2021_flow_chart.arrow
process_flow_chart_data_children_and_adolescents_s5:
run: r:latest analysis/cohort_criteria.R children_and_adolescents season5_start_date
season5_end_date
needs:
- generate_flow_chart_data_children_and_adolescents_s5
- process_household_information_s5
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_children_and_adolescents_2020_2021.csv
generate_flow_chart_data_children_and_adolescents_s6:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/children_and_adolescents_2021_2022_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2021_2022.arrow
-- children_and_adolescents season6_start_date season6_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/children_and_adolescents_2021_2022_flow_chart.arrow
process_flow_chart_data_children_and_adolescents_s6:
run: r:latest analysis/cohort_criteria.R children_and_adolescents season6_start_date
season6_end_date
needs:
- generate_flow_chart_data_children_and_adolescents_s6
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_children_and_adolescents_2021_2022.csv
generate_flow_chart_data_children_and_adolescents_s7:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/children_and_adolescents_2022_2023_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2022_2023.arrow
-- children_and_adolescents season7_start_date season7_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/children_and_adolescents_2022_2023_flow_chart.arrow
process_flow_chart_data_children_and_adolescents_s7:
run: r:latest analysis/cohort_criteria.R children_and_adolescents season7_start_date
season7_end_date
needs:
- generate_flow_chart_data_children_and_adolescents_s7
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_children_and_adolescents_2022_2023.csv
generate_flow_chart_data_children_and_adolescents_s8:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/children_and_adolescents_2023_2024_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2023_2024.arrow
-- children_and_adolescents season8_start_date season8_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/children_and_adolescents_2023_2024_flow_chart.arrow
process_flow_chart_data_children_and_adolescents_s8:
run: r:latest analysis/cohort_criteria.R children_and_adolescents season8_start_date
season8_end_date
needs:
- generate_flow_chart_data_children_and_adolescents_s8
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_children_and_adolescents_2023_2024.csv
## # # # # # # # # # # # # # # # # # # #
## Inclusion/Exclusion Flow Chart Actions: Infants
## # # # # # # # # # # # # # # # # # # #
generate_flow_chart_data_infants_s1:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/infants_2016_2017_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_2016_2017.arrow
-- infants season1_start_date season1_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/infants_2016_2017_flow_chart.arrow
process_flow_chart_data_infants_s1:
run: r:latest analysis/cohort_criteria.R infants season1_start_date season1_end_date
needs:
- generate_flow_chart_data_infants_s1
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_infants_2016_2017.csv
generate_flow_chart_data_infants_s2:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/infants_2017_2018_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_2017_2018.arrow
-- infants season2_start_date season2_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/infants_2017_2018_flow_chart.arrow
process_flow_chart_data_infants_s2:
run: r:latest analysis/cohort_criteria.R infants season2_start_date season2_end_date
needs:
- generate_flow_chart_data_infants_s2
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_infants_2017_2018.csv
generate_flow_chart_data_infants_s3:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/infants_2018_2019_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_2018_2019.arrow
-- infants season3_start_date season3_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/infants_2018_2019_flow_chart.arrow
process_flow_chart_data_infants_s3:
run: r:latest analysis/cohort_criteria.R infants season3_start_date season3_end_date
needs:
- generate_flow_chart_data_infants_s3
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_infants_2018_2019.csv
generate_flow_chart_data_infants_s4:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/infants_2019_2020_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_2019_2020.arrow
-- infants season4_start_date season4_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/infants_2019_2020_flow_chart.arrow
process_flow_chart_data_infants_s4:
run: r:latest analysis/cohort_criteria.R infants season4_start_date season4_end_date
needs:
- generate_flow_chart_data_infants_s4
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_infants_2019_2020.csv
generate_flow_chart_data_infants_s5:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/infants_2020_2021_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_2020_2021.arrow
-- infants season5_start_date season5_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/infants_2020_2021_flow_chart.arrow
process_flow_chart_data_infants_s5:
run: r:latest analysis/cohort_criteria.R infants season5_start_date season5_end_date
needs:
- generate_flow_chart_data_infants_s5
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_infants_2020_2021.csv
generate_flow_chart_data_infants_s6:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/infants_2021_2022_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_2021_2022.arrow
-- infants season6_start_date season6_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/infants_2021_2022_flow_chart.arrow
process_flow_chart_data_infants_s6:
run: r:latest analysis/cohort_criteria.R infants season6_start_date season6_end_date
needs:
- generate_flow_chart_data_infants_s6
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_infants_2021_2022.csv
generate_flow_chart_data_infants_s7:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/infants_2022_2023_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_2022_2023.arrow
-- infants season7_start_date season7_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/infants_2022_2023_flow_chart.arrow
process_flow_chart_data_infants_s7:
run: r:latest analysis/cohort_criteria.R infants season7_start_date season7_end_date
needs:
- generate_flow_chart_data_infants_s7
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_infants_2022_2023.csv
generate_flow_chart_data_infants_s8:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/infants_2023_2024_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_2023_2024.arrow
-- infants season8_start_date season8_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/infants_2023_2024_flow_chart.arrow
process_flow_chart_data_infants_s8:
run: r:latest analysis/cohort_criteria.R infants season8_start_date season8_end_date
needs:
- generate_flow_chart_data_infants_s8
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_infants_2023_2024.csv
## # # # # # # # # # # # # # # # # # # #
## Inclusion/Exclusion Flow Chart Actions: Infants Subgroup
## # # # # # # # # # # # # # # # # # # #
generate_flow_chart_data_mothers_s1:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart_mothers.py
--output output/flow_chart/mothers_2016_2017_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_2016_2017.arrow
-- season1_start_date season1_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/mothers_2016_2017_flow_chart.arrow
process_flow_chart_data_mothers_s1:
run: r:latest analysis/cohort_processing_mothers.R season1_start_date season1_end_date
needs:
- generate_flow_chart_data_mothers_s1
outputs:
highly_sensitive:
dataset: output/flow_chart/cohort_mothers_processed_2016_2017.arrow
generate_flow_chart_data_infants_subgroup_s1:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/infants_subgroup_2016_2017_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_2016_2017.arrow
-- infants_subgroup season1_start_date season1_end_date
needs:
- process_flow_chart_data_mothers_s1
outputs:
highly_sensitive:
dataset: output/flow_chart/infants_subgroup_2016_2017_flow_chart.arrow
process_flow_chart_data_infants_subgroup_s1:
run: r:latest analysis/cohort_criteria.R infants_subgroup season1_start_date season1_end_date
needs:
- generate_flow_chart_data_infants_subgroup_s1
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_infants_subgroup_2016_2017.csv
generate_flow_chart_data_mothers_s2:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart_mothers.py
--output output/flow_chart/mothers_2017_2018_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_2017_2018.arrow
-- season2_start_date season2_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/mothers_2017_2018_flow_chart.arrow
process_flow_chart_data_mothers_s2:
run: r:latest analysis/cohort_processing_mothers.R season2_start_date season2_end_date
needs:
- generate_flow_chart_data_mothers_s2
outputs:
highly_sensitive:
dataset: output/flow_chart/cohort_mothers_processed_2017_2018.arrow
generate_flow_chart_data_infants_subgroup_s2:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/infants_subgroup_2017_2018_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_2017_2018.arrow
-- infants_subgroup season2_start_date season2_end_date
needs:
- process_flow_chart_data_mothers_s2
outputs:
highly_sensitive:
dataset: output/flow_chart/infants_subgroup_2017_2018_flow_chart.arrow
process_flow_chart_data_infants_subgroup_s2:
run: r:latest analysis/cohort_criteria.R infants_subgroup season2_start_date season2_end_date
needs:
- generate_flow_chart_data_infants_subgroup_s2
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_infants_subgroup_2017_2018.csv
generate_flow_chart_data_mothers_s3:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart_mothers.py
--output output/flow_chart/mothers_2018_2019_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_2018_2019.arrow
-- season3_start_date season3_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/mothers_2018_2019_flow_chart.arrow
process_flow_chart_data_mothers_s3:
run: r:latest analysis/cohort_processing_mothers.R season3_start_date season3_end_date
needs:
- generate_flow_chart_data_mothers_s3
outputs:
highly_sensitive:
dataset: output/flow_chart/cohort_mothers_processed_2018_2019.arrow
generate_flow_chart_data_infants_subgroup_s3:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/infants_subgroup_2018_2019_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_2018_2019.arrow
-- infants_subgroup season3_start_date season3_end_date
needs:
- process_flow_chart_data_mothers_s3
outputs:
highly_sensitive:
dataset: output/flow_chart/infants_subgroup_2018_2019_flow_chart.arrow
process_flow_chart_data_infants_subgroup_s3:
run: r:latest analysis/cohort_criteria.R infants_subgroup season3_start_date season3_end_date
needs:
- generate_flow_chart_data_infants_subgroup_s3
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_infants_subgroup_2018_2019.csv
generate_flow_chart_data_mothers_s4:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart_mothers.py
--output output/flow_chart/mothers_2019_2020_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_2019_2020.arrow
-- season4_start_date season4_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/mothers_2019_2020_flow_chart.arrow
process_flow_chart_data_mothers_s4:
run: r:latest analysis/cohort_processing_mothers.R season4_start_date season4_end_date
needs:
- generate_flow_chart_data_mothers_s4
outputs:
highly_sensitive:
dataset: output/flow_chart/cohort_mothers_processed_2019_2020.arrow
generate_flow_chart_data_infants_subgroup_s4:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/infants_subgroup_2019_2020_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_2019_2020.arrow
-- infants_subgroup season4_start_date season4_end_date
needs:
- process_flow_chart_data_mothers_s4
outputs:
highly_sensitive:
dataset: output/flow_chart/infants_subgroup_2019_2020_flow_chart.arrow
process_flow_chart_data_infants_subgroup_s4:
run: r:latest analysis/cohort_criteria.R infants_subgroup season4_start_date season4_end_date
needs:
- generate_flow_chart_data_infants_subgroup_s4
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_infants_subgroup_2019_2020.csv
generate_flow_chart_data_mothers_s5:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart_mothers.py
--output output/flow_chart/mothers_2020_2021_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_2020_2021.arrow
-- season5_start_date season5_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/mothers_2020_2021_flow_chart.arrow
process_flow_chart_data_mothers_s5:
run: r:latest analysis/cohort_processing_mothers.R season5_start_date season5_end_date
needs:
- generate_flow_chart_data_mothers_s5
outputs:
highly_sensitive:
dataset: output/flow_chart/cohort_mothers_processed_2020_2021.arrow
generate_flow_chart_data_infants_subgroup_s5:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/infants_subgroup_2020_2021_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_2020_2021.arrow
-- infants_subgroup season5_start_date season5_end_date
needs:
- process_flow_chart_data_mothers_s5
outputs:
highly_sensitive:
dataset: output/flow_chart/infants_subgroup_2020_2021_flow_chart.arrow
process_flow_chart_data_infants_subgroup_s5:
run: r:latest analysis/cohort_criteria.R infants_subgroup season5_start_date season5_end_date
needs:
- generate_flow_chart_data_infants_subgroup_s5
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_infants_subgroup_2020_2021.csv
generate_flow_chart_data_mothers_s6:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart_mothers.py
--output output/flow_chart/mothers_2021_2022_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_2021_2022.arrow
-- season6_start_date season6_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/mothers_2021_2022_flow_chart.arrow
process_flow_chart_data_mothers_s6:
run: r:latest analysis/cohort_processing_mothers.R season6_start_date season6_end_date
needs:
- generate_flow_chart_data_mothers_s6
outputs:
highly_sensitive:
dataset: output/flow_chart/cohort_mothers_processed_2021_2022.arrow
generate_flow_chart_data_infants_subgroup_s6:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/infants_subgroup_2021_2022_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_2021_2022.arrow
-- infants_subgroup season6_start_date season6_end_date
needs:
- process_flow_chart_data_mothers_s6
outputs:
highly_sensitive:
dataset: output/flow_chart/infants_subgroup_2021_2022_flow_chart.arrow
process_flow_chart_data_infants_subgroup_s6:
run: r:latest analysis/cohort_criteria.R infants_subgroup season6_start_date season6_end_date
needs:
- generate_flow_chart_data_infants_subgroup_s6
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_infants_subgroup_2021_2022.csv
generate_flow_chart_data_mothers_s7:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart_mothers.py
--output output/flow_chart/mothers_2022_2023_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_2022_2023.arrow
-- season7_start_date season7_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/mothers_2022_2023_flow_chart.arrow
process_flow_chart_data_mothers_s7:
run: r:latest analysis/cohort_processing_mothers.R season7_start_date season7_end_date
needs:
- generate_flow_chart_data_mothers_s7
outputs:
highly_sensitive:
dataset: output/flow_chart/cohort_mothers_processed_2022_2023.arrow
generate_flow_chart_data_infants_subgroup_s7:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/infants_subgroup_2022_2023_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_2022_2023.arrow
-- infants_subgroup season7_start_date season7_end_date
needs:
- process_flow_chart_data_mothers_s7
outputs:
highly_sensitive:
dataset: output/flow_chart/infants_subgroup_2022_2023_flow_chart.arrow
process_flow_chart_data_infants_subgroup_s7:
run: r:latest analysis/cohort_criteria.R infants_subgroup season7_start_date season7_end_date
needs:
- generate_flow_chart_data_infants_subgroup_s7
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_infants_subgroup_2022_2023.csv
generate_flow_chart_data_mothers_s8:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart_mothers.py
--output output/flow_chart/mothers_2023_2024_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_2023_2024.arrow
-- season8_start_date season8_end_date
outputs:
highly_sensitive:
dataset: output/flow_chart/mothers_2023_2024_flow_chart.arrow
process_flow_chart_data_mothers_s8:
run: r:latest analysis/cohort_processing_mothers.R season8_start_date season8_end_date
needs:
- generate_flow_chart_data_mothers_s8
outputs:
highly_sensitive:
dataset: output/flow_chart/cohort_mothers_processed_2023_2024.arrow
generate_flow_chart_data_infants_subgroup_s8:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py
--output output/flow_chart/infants_subgroup_2023_2024_flow_chart.arrow
--dummy-data-file analysis/dummydata/dummyextract_infants_subgroup_2023_2024.arrow
-- infants_subgroup season8_start_date season8_end_date
needs:
- process_flow_chart_data_mothers_s8
outputs:
highly_sensitive:
dataset: output/flow_chart/infants_subgroup_2023_2024_flow_chart.arrow
process_flow_chart_data_infants_subgroup_s8:
run: r:latest analysis/cohort_criteria.R infants_subgroup season8_start_date season8_end_date
needs:
- generate_flow_chart_data_infants_subgroup_s8
outputs:
moderately_sensitive:
csv: output/flow_chart/flow_chart_processed_infants_subgroup_2023_2024.csv
## # # # # # # # # # # # # # # # # # # #
## Household Information Actions
## # # # # # # # # # # # # # # # # # # #
extract_household_information_s5:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition_household.py
--output output/data/input_household_2020_2021.arrow
--dummy-data-file analysis/dummydata/dummyextract_household_2020_2021.arrow
-- season5_start_date season5_end_date
outputs:
highly_sensitive:
dataset: output/data/input_household_2020_2021.arrow
process_household_information_s5:
run: r:latest analysis/data_processing_household.R season5_start_date season5_end_date
needs:
- extract_household_information_s5
outputs:
highly_sensitive:
arrow: output/data/input_household_processed_2020_2021.arrow
## # # # # # # # # # # # # # # # # # # #
## PRIMARY ANALYSES
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Cohort: Older Adults, Codelist Type: Specific,
## Investigation Type: Primary
## # # # # # # # # # # # # # # # # # # #
generate_dataset_older_adults_s1_specific_primary:
run: |-
ehrql:v1 generate-dataset analysis/dataset_definition.py
--output output/data/input_older_adults_2016_2017_specific_primary.arrow
--dummy-data-file analysis/dummydata/dummyextract_older_adults_2016_2017.arrow
-- older_adults season1_start_date season1_end_date specific primary
outputs:
highly_sensitive:
dataset: output/data/input_older_adults_2016_2017_specific_primary.arrow
process_dataset_older_adults_s1_specific_primary:
run: r:latest analysis/data_processing.R older_adults season1_start_date season1_end_date
specific primary
needs:
- generate_dataset_older_adults_s1_specific_primary
outputs:
highly_sensitive:
dataset: output/data/input_processed_older_adults_2016_2017_specific_primary.arrow
describe_dataset_older_adults_s1_specific_primary:
run: r:latest analysis/season_summary.R older_adults season1_start_date season1_end_date
specific primary
needs:
- process_dataset_older_adults_s1_specific_primary
outputs:
moderately_sensitive:
csv: output/results/rates/rates_older_adults_2016_2017_specific_primary.csv
calculate_rates_rolling_older_adults_s1_specific_primary:
run: r:latest analysis/rates_over_time.R older_adults season1_start_date season1_end_date
specific primary
needs:
- process_dataset_older_adults_s1_specific_primary
outputs:
moderately_sensitive:
dataset: output/results/rates/weekly/rates_over_time_*_older_adults_2016_2017_specific_primary.csv
analyse_dataset_older_adults_rsv_s1_specific_primary:
run: r:latest analysis/outcome_rsv/rsv_models_master.R older_adults season1_start_date
season1_end_date specific primary
needs:
- process_dataset_older_adults_s1_specific_primary
outputs: