Job request: 10688

View Repo View project.yaml

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

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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

ID Status Action
yypen7lelsbzhry3 succeeded Analysis_cox_stroke_isch
f2xyqxqrd6aftjkw succeeded Analysis_cox_tia
upjdwwyrvogjc5qd succeeded Analysis_cox_stroke_sah_hs
fshcxk7wx2ou4sy5 succeeded Analysis_cox_hf
qppspmycr5ydbyty succeeded Analysis_cox_angina
h34nvs72py4vmpnp succeeded Analysis_cox_ate
kwapiqlb2vvkg4gh succeeded Analysis_cox_vte
oz5fdw4wlsrp6v2r succeeded Analysis_cox_ami_primary_position
uwdrgemnpl322ns6 succeeded Analysis_cox_stroke_isch_primary_position
wgvdjynbvhlxkyu5 succeeded Analysis_cox_dvt_primary_position
kd7sixydzlvgyvno succeeded Analysis_cox_pe_primary_position
dqyfmgm6cayypipk succeeded Analysis_cox_tia_primary_position
mrjwz6kwlhigco3n succeeded Analysis_cox_stroke_sah_hs_primary_position
4nm24rmsxi4l22ks succeeded Analysis_cox_hf_primary_position
y5og6vhm2csvrpiq succeeded Analysis_cox_angina_primary_position
w23x4hntvz7yxbza succeeded Analysis_cox_ate_primary_position
ere4gazlvoqz3jht succeeded Analysis_cox_vte_primary_position

Pipeline

Show Hide project.yaml 
version: '3.0'

expectations:

  population_size: 100000

actions:

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create_project_actions.R 
  ## Edit and run create_project_actions.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  vax_eligibility_inputs:
    run: r:latest analysis/vax_eligibility_inputs.R
    outputs:
      highly_sensitive:
        vax_study_dates_json: output/vax_study_dates.json
        vax_jcvi_groups: output/vax_jcvi_groups.csv
        vax_eligible_dates: output/vax_eligible_dates.csv

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
      --output-format feather
    needs:
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  preprocess_data:
    run: r:latest analysis/preprocess/preprocess_data.R
    needs:
    - generate_study_population
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_stage0.txt
      highly_sensitive:
        cohort: output/input.rds
        venn: output/venn.rds

  stage1_data_cleaning:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R
    needs:
    - preprocess_data
    outputs:
      moderately_sensitive:
        QA_rules: output/review/descriptives/QA_summary.csv
        refactoring: output/not-for-review/meta_data_factors.csv
        IE_criteria: output/review/descriptives/cohort_flow.csv
        histograms: output/not-for-review/numeric_histograms.svg
      highly_sensitive:
        cohort: output/input_stage1.rds

  stage1_end_date_table:
    run: r:latest analysis/preprocess/create_follow_up_end_date.R
    needs:
    - preprocess_data
    - stage1_data_cleaning
    outputs:
      highly_sensitive:
        end_date_table: output/follow_up_end_dates.rds

  stage2_missing_table1:
    run: r:latest analysis/descriptives/Stage2_Missing_Table1.R
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        Missing_RangeChecks: output/not-for-review/Check_missing_range.csv
        DateChecks: output/not-for-review/Check_dates_range.csv
        Descriptive_Table: output/review/descriptives/Table1_pre_vaccination_cvd.csv

  stage_2_events_split_by_covariate_level:
    run: r:latest analysis/preprocess/covariates_split_by_time_period.R
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        counts_by_covariate_level: output/not-for-review/event_counts_by_covariate_level_*.csv
        selected_covariates: output/not-for-review/non_zero_selected_covariates_*.csv

  table_2:
    run: r:latest analysis/descriptives/table_2.R
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        table_2: output/review/descriptives/table2_pre_vaccination_cvd.csv

  venn_diagram:
    run: r:latest analysis/descriptives/venn_diagram.R
    needs:
    - preprocess_data
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        venn_diagram: output/review/venn-diagrams/venn_diagram_*

  ## Apply cox model for ami 

  Analysis_cox_ami:
    run: r:latest analysis/model/01_cox_pipeline.R ami
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ami_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ami_*_time_periods.txt

  ## Apply cox model for stroke_isch 

  Analysis_cox_stroke_isch:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_isch_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_*_time_periods.txt

  ## Apply cox model for dvt 

  Analysis_cox_dvt:
    run: r:latest analysis/model/01_cox_pipeline.R dvt
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_dvt_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_dvt_*_time_periods.txt

  ## Apply cox model for pe 

  Analysis_cox_pe:
    run: r:latest analysis/model/01_cox_pipeline.R pe
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_pe_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_pe_*_time_periods.txt

  ## Apply cox model for tia 

  Analysis_cox_tia:
    run: r:latest analysis/model/01_cox_pipeline.R tia
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_tia_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_tia_*_time_periods.txt

  ## Apply cox model for stroke_sah_hs 

  Analysis_cox_stroke_sah_hs:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_*_time_periods.txt

  ## Apply cox model for hf 

  Analysis_cox_hf:
    run: r:latest analysis/model/01_cox_pipeline.R hf
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_hf_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_hf_*_time_periods.txt

  ## Apply cox model for angina 

  Analysis_cox_angina:
    run: r:latest analysis/model/01_cox_pipeline.R angina
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_angina_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_angina_*_time_periods.txt

  ## Apply cox model for ate 

  Analysis_cox_ate:
    run: r:latest analysis/model/01_cox_pipeline.R ate
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ate_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ate_*_time_periods.txt

  ## Apply cox model for vte 

  Analysis_cox_vte:
    run: r:latest analysis/model/01_cox_pipeline.R vte
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_vte_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_vte_*_time_periods.txt

  ## Apply cox model for ami_primary_position 

  Analysis_cox_ami_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R ami_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ami_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ami_primary_position_*_time_periods.txt

  ## Apply cox model for stroke_isch_primary_position 

  Analysis_cox_stroke_isch_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_isch_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_primary_position_*_time_periods.txt

  ## Apply cox model for dvt_primary_position 

  Analysis_cox_dvt_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R dvt_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_dvt_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_dvt_primary_position_*_time_periods.txt

  ## Apply cox model for pe_primary_position 

  Analysis_cox_pe_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R pe_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_pe_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_pe_primary_position_*_time_periods.txt

  ## Apply cox model for tia_primary_position 

  Analysis_cox_tia_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R tia_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_tia_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_tia_primary_position_*_time_periods.txt

  ## Apply cox model for stroke_sah_hs_primary_position 

  Analysis_cox_stroke_sah_hs_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_primary_position_*_time_periods.txt

  ## Apply cox model for hf_primary_position 

  Analysis_cox_hf_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R hf_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_hf_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_hf_primary_position_*_time_periods.txt

  ## Apply cox model for angina_primary_position 

  Analysis_cox_angina_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R angina_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_angina_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_angina_primary_position_*_time_periods.txt

  ## Apply cox model for ate_primary_position 

  Analysis_cox_ate_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R ate_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ate_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ate_primary_position_*_time_periods.txt

  ## Apply cox model for vte_primary_position 

  Analysis_cox_vte_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R vte_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    - stage_2_events_split_by_covariate_level
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_vte_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_vte_primary_position_*_time_periods.txt

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 181:35:16

Config