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project.yaml
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project.yaml
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######################################
# This script defines the project pipeline - it specifies the execution orders for all the code in this
# repo using a series of actions.
######################################
version: '3.0'
expectations:
population_size: 100000
actions:
# Generate study population and extract baseline characteristics at Sep 3, 2022
generate_study_pop_baseline:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_baseline
--output-dir=feather
--output-format=feather
outputs:
highly_sensitive:
cohort: output/input_baseline.feather
# Data cleaning, defining exclusions, saving final study pop
data_process_baseline:
run: r:latest analysis/processing/data_process_baseline.R
needs: [generate_study_pop_baseline]
outputs:
highly_sensitive:
cohort: output/cohort/cohort_*.csv
moderately_sensitive:
descriptive: output/descriptive/total_*.csv
# Extract outcomes pre-campaign (index date = Sep 3)
outcomes_sep:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_outcomes_1
--index-date-range "2022-09-03"
--output-dir=feather
--output-format=feather
needs: [data_process_baseline]
outputs:
highly_sensitive:
cohort: output/index/input_*.feather
# Extract outcomes mid-campaign (index date = Oct 15)
outcomes_oct:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_outcomes_1
--index-date-range "2022-10-15"
--output-dir=feather
--output-format=feather
needs: [data_process_baseline]
outputs:
highly_sensitive:
cohort: output/index/input*.feather
# Extract outcomes during-campaign (index date = Nov 26) - checks
outcomes_nov_check:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_outcomes_1
--index-date-range "2022-11-26"
--output-dir=feather
--output-format=feather
needs: [data_process_baseline]
outputs:
highly_sensitive:
cohort: output/index/inp*.feather
# Extract outcomes during-campaign (index date = Nov 26)
outcomes_nov:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_outcomes_2
--index-date-range "2022-11-26 to 2022-12-05 by week"
--output-dir=feather
--output-format=feather
needs: [data_process_baseline]
outputs:
highly_sensitive:
cohort: output/index/inpu*.feather
# Data cleaning of outcome data (control periods)
data_process_outcomes_1:
run: r:latest analysis/processing/data_process_outcomes_1.R
needs: [outcomes_sep, outcomes_oct, outcomes_nov_check]
outputs:
highly_sensitive:
outcomes: output/cohort/outcomes*.csv
# Data cleaning of outcome data (Nov onward)
data_process_outcomes_2:
run: r:latest analysis/processing/data_process_outcomes_2.R
needs: [outcomes_nov]
outputs:
highly_sensitive:
outcomes: output/cohort/outcome*.csv
# Plots of COVID booster uptake by age
booster_uptake:
run: r:latest analysis/descriptive/cumulative_vax_byage.R
needs: [data_process_baseline]
outputs:
moderately_sensitive:
rates_csv: output/cumulative_rates/final_*.csv
plot: output/cumulative_rates/plot_*.png
# Aggregate data by age
aggregate_outcomes_byage:
run: r:latest analysis/processing/aggregate_outcomes.R
needs: [data_process_outcomes_1, data_process_outcomes_2]
outputs:
moderately_sensitive:
outcomes: output/covid_outcomes/by_start_date/outcomes_*.csv
# no_patients: output/descriptive/total_n_by_date.csv
# Outcome plots #
# plot_outcomes:
# run: r:latest analysis/descriptive/plot_outcomes_byage.R
# needs: [aggregate_outcomes_byage]
# outputs:
# moderately_sensitive:
# plot: output/covid_outcomes/figures/plot_*.png
# ITT analysis #
itt_analysis:
run: r:latest analysis/statistical_analysis/itt_analysis.R
needs: [data_process_outcomes_1, data_process_outcomes_2]
outputs:
moderately_sensitive:
predicted_csv: output/modelling/predicted_*.csv
coefficients_csv: output/modelling/coef_*.csv
plot: output/modelling/figures/plot*.png
# ITT analysis #
itt_analysis_check:
run: r:latest analysis/statistical_analysis/itt_analysis_check.R
needs: [data_process_outcomes_1]
outputs:
moderately_sensitive:
plot: output/modelling/figures/plo*.png
# IV analysis #
iv_analysis:
run: r:latest analysis/statistical_analysis/iv_analysis.R
needs: [data_process_outcomes_1, data_process_outcomes_2]
outputs:
moderately_sensitive:
predicted_csv: output/modelling/iv/predicted_*.csv
coefficients_csv: output/modelling/iv/coef_*.csv
# Latest date of outcome
latest_date_outcomes:
run: r:latest analysis/descriptive/latest_date_outcomes.R
needs: [data_process_outcomes_2]
outputs:
moderately_sensitive:
plot: output/descriptive/over*.png
# Discontinuity of demographics
demographics:
run: r:latest analysis/descriptive/demographics_byage.R
needs: [generate_study_pop_baseline, data_process_baseline]
outputs:
moderately_sensitive:
measures_csv: output/descriptive/demographics_*.csv
# Flu vaccine uptake #
# flu_vax:
# run: r:latest analysis/descriptive/flu_vax_byage.R
# needs: [generate_study_pop]
# outputs:
# moderately_sensitive:
# measure_csv: output/cumulative_rates/flu_*.csv
# plot: output/cumulative_rates/plot_flu_vax_byage.png
# IV analysis #