Job request: 6387
This page shows the technical details of what happened when authorised researcher Linda Nab requested one or more actions to be run against real patient data in the project, within a secure environment.
By cross-referencing the indicated Requested Actions with the
Pipeline section below, you can infer what
various outputs were written to. Outputs marked as
can never be viewed directly by a researcher; they can only
request that code runs against them. Outputs marked as
can be viewed by an approved researcher by logging into a highly
secure environment. Only outputs marked as
can be requested for release to the public, via a controlled
output review service.
version: '3.0' expectations: population_size: 1000 actions: # Extract data # When argument --index-date-range is changed, change has to be made in ./analysis/config.json too generate_study_population: run: > cohortextractor:latest generate_cohort --study-definition study_definition --skip-existing --output-format=csv.gz --index-date-range "2020-03-01 to 2021-12-01 by month" outputs: highly_sensitive: cohort: output/input_*.csv.gz # Extract ethnicity generate_study_population_ethnicity: run: > cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-format=csv.gz outputs: highly_sensitive: cohort: output/input_ethnicity.csv.gz # Join data join_cohorts: run: > cohort-joiner:v0.0.7 --lhs output/input_202*.csv.gz --rhs output/input_ethnicity.csv.gz --output-dir=output/joined needs: [generate_study_population, generate_study_population_ethnicity] outputs: highly_sensitive: cohort: output/joined/input_202*.csv.gz # Calculate mortality rates (crude + subgroup specific) calculate_measures: run: > cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/joined needs: [join_cohorts] outputs: moderately_sensitive: measure: output/joined/measure_*_mortality_rate.csv # Standardise crude mortality rate standardise_crude_rates: run: r:latest analysis/crude_rates_standardise.R needs: [calculate_measures] outputs: moderately_sensitive: csvs: output/rates/crude_*monthly_std.csv # Standardise subgroup specific mortality rates standardise_subgroup_rates: run: r:latest analysis/subgroups_rates_standardise.R needs: [calculate_measures] outputs: moderately_sensitive: csvs: output/rates/*_monthly_std.csv # Plot and save graphs depicting the crude rates visualise_crude_rates: run: r:latest analysis/crude_rates_visualise.R needs: [standardise_crude_rates] outputs: moderately_sensitive: pngs: output/figures/rates_crude/*.png # Plot and save graphs depicting the subgroup specific mortality rates visualise_subgroup_rates: run: r:latest analysis/subgroups_rates_visualise.R needs: [standardise_subgroup_rates] outputs: moderately_sensitive: pngs: output/figures/rates_subgroups/*.png
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