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Job request: 20678

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
shielding_evaluation
ID:
psjzacqbduj7ud7c
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Johnny Filipe requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

  • Action:
    SEIR_fit
    Status:
    Status: Succeeded
    Job identifier:
    bpy2rhwza3lt7pwx

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 2000

actions:

  generate_dataset:
    run: >
      databuilder:v0 
        generate-dataset analysis/databuilder_definition.py --output output/dataset_all.csv.gz
    outputs:
      highly_sensitive:
        dataset_all: output/dataset_all.csv.gz
  
  clean_the_data: 
    run: > 
      r:latest
        analysis/010_import_data.R
    needs: [generate_dataset]
    outputs: 
      highly_sensitive:
        cleandata: output/data_edited.gz.parquet
      moderately_sensitive: 
        txt1: output/data_properties/clean_dataset_skim.txt
        txt2: output/data_properties/clean_dataset_tabulate.txt
      
  create_table1: 
    run: > 
      r:latest
        analysis/020_create_table1.R
    needs: [clean_the_data]
    outputs: 
      moderately_sensitive: 
        table1: output/tables/shielding_table1.html
        table1_r: output/tables/shielding_table1_redacted.html
        table1_data: output/table1_data.csv
        table2_shielding_v0: output/tables/shielding_table2.html
        table2_shielding_v1: output/tables/shielding_v1_table2.html
        table2_shielding_v2: output/tables/shielding_v2_table2.html
  
  plot_hospitalisations: 
    run: > 
      r:latest
        analysis/030_plot_hospitalisations.R
    needs: [clean_the_data]
    outputs: 
      moderately_sensitive: 
        shielding_comparison: output/data_properties/different_shielding.txt
        fig1_v1: output/figures/covid_hosp_over_time_v1.pdf
        fig2_v1: output/figures/covid_hosp_over_time_cumsum_v1.pdf
        fig1_v2: output/figures/covid_hosp_over_time_v2.pdf
        fig2_v2: output/figures/covid_hosp_over_time_cumsum_v2.pdf
  
  plot_shielding: 
    run: > 
      r:latest
        analysis/031_plot_shielding.R
    needs: [clean_the_data]
    outputs: 
      moderately_sensitive: 
        fig1_shielding: output/figures/shielding_over_time.pdf

  plot_hospitalisations2:
    run: > 
      r:latest
        analysis/040_plot_hospitalisations.R
    needs: [clean_the_data]
    outputs: 
      moderately_sensitive: 
        fig3: output/figures/covid_hosp_over_time2.pdf
        fig4: output/figures/covid_hosp_over_time_cumsum2.pdf
        
  plot_deaths2:
    run: > 
      r:latest
        analysis/050_plot_deaths.R
    needs: [clean_the_data]
    outputs: 
      moderately_sensitive:
        fig5a: output/figures/covid_deaths_lm.pdf
        fig5: output/figures/covid_deaths_over_time2.pdf
        fig6: output/figures/covid_deaths_over_time_cumsum2.pdf

  SEIR_fit:
    run: > 
      r:latest
        modelling/SEIRmodel_main.r
    needs: [clean_the_data]
    outputs:
      moderately_sensitive:
        txt10: output/modelling/SEIRmodel_run.txt
        dat10: output/modelling/R0_by_week.csv
        fig10: output/modelling/Infected_data_and_R0_by_week.pdf
        txt11: output/modelling/Contact_matrix_year-from-24Feb20_vector-lenght-9x9x52_norm=maxEV1_stats.txt
        fig11: output/modelling/MCMC_BT.pdf
        txt12: output/modelling/Bayesian_fit_report.txt
        fig12: output/figures/covid_hosp_over_time2again.pdf
  
  plot_hospitalisations2_East:
    run: > 
      r:latest
        analysis/060_plot_hospitalisations_East.R
    needs: [clean_the_data]
    outputs: 
      moderately_sensitive: 
        fig3E: output/figures/covid_hosp_over_time2_East.pdf
        fig4E: output/figures/covid_hosp_over_time_cumsum2_East.pdf

  plot_deaths2_East:
    run: > 
      r:latest
        analysis/070_plot_deaths_East.R
    needs: [clean_the_data]
    outputs: 
      moderately_sensitive: 
        fig5E: output/figures/covid_deaths_over_time2_East.pdf
        fig6E: output/figures/covid_deaths_over_time_cumsum2_East.pdf

  plot_hospitalisations2_EastMid:
    run: > 
      r:latest
        analysis/080_plot_hospitalisations_EastMid.R
    needs: [clean_the_data]
    outputs: 
      moderately_sensitive: 
        fig3EM: output/figures/covid_hosp_over_time2_EastMid.pdf
        fig4EM: output/figures/covid_hosp_over_time_cumsum2_EastMid.pdf

  plot_deaths2_EastMid:
    run: > 
      r:latest
        analysis/090_plot_deaths_EastMid.R
    needs: [clean_the_data]
    outputs: 
      moderately_sensitive: 
        fig5EM: output/figures/covid_deaths_over_time2_EastMid.pdf
        fig6EM: output/figures/covid_deaths_over_time_cumsum2_EastMid.pdf

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:07:47

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

Job information

Status
Succeeded
Backend
TPP
Workspace
shielding_evaluation
Requested by
Johnny Filipe
Branch
main
Force run dependencies
No
Git commit hash
3edc03b
Requested actions
  • SEIR_fit

Code comparison

Compare the code used in this Job Request