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
These timestamps are generated and stored using the UTC timezone on the backend.