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Job request: 2003

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
learning-disabilities-full
ID:
juq3lx45dhgt4pzm
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Elizabeth (Fizz) Williamson 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 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

  • Action:
    cox_MI_child
    Status:
    Status: Failed
    Job identifier:
    mjlb37xelu3unbsh

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 50000

actions:


#########################
#  LD study flow chart  #
#########################

  flow_chart1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart --index-date-range "2020-03-01"
    outputs:
      highly_sensitive:
        cohort: output/input_flow_chart_2020-03-01.csv

  flow_chart2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart --index-date-range "2020-09-01"
    outputs:
      highly_sensitive:
        cohort: output/input_flow_chart_2020-09-01.csv

  generate_flowchart:
    run: stata-mp:latest analysis/000_flow_chart.do
    needs: [flow_chart1, flow_chart2]
    outputs:
      moderately_sensitive:
        cohort: logs/000_flow_chart.log


##############################
#  Create analysis datasets  #
##############################

  generate_cohort1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-03-01"
    outputs:
      highly_sensitive:
        cohort: output/input_2020-03-01.csv

  generate_cohort2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-09-01"
    outputs:
      highly_sensitive:
        cohort: output/input_2020-09-01.csv

  clean:
    run: stata-mp:latest analysis/001_clean_input_data.do
    needs: [generate_cohort1, generate_cohort2]
    outputs:
     highly_sensitive:
        clean1: analysis/data_base_cohort1.dta
        clean2: analysis/data_base_cohort2.dta
     moderately_sensitive:
        log: logs/001_clean_input_data.log

  create_analysis:
    run: stata-mp:latest analysis/002_create_ld_analysis_dataset.do
    needs: [clean]
    outputs:
     highly_sensitive:
        an_data1: analysis/data_ldanalysis_cohort1.dta
        an_data2: analysis/data_ldanalysis_cohort2.dta
     moderately_sensitive:
        log: logs/002_create_ld_analysis_dataset.log

  create_analysis_ar:
    run: stata-mp:latest analysis/003_create_ar_analysis_dataset.do
    needs: [clean]
    outputs:
     highly_sensitive:
        an_data1: analysis/data_aranalysis_cohort1.dta
        an_data2: analysis/data_aranalysis_cohort2.dta
     moderately_sensitive:
        log: logs/003_create_ar_analysis_dataset.log

########################
#  Basic descriptives  #
########################

  describe_cohort:
    run: stata-mp:latest analysis/AL001_describe_cohort.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL001_describe_cohort.log

  tabulate_cohort:
    run: stata-mp:latest analysis/AL002_tabulate_cohort_descriptives.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL002_tabulate_cohort_descriptives.log
        model: output/basetable1.txt

  tabulate_cohort_all:
    run: stata-mp:latest analysis/AL002_tabulate_cohort_descriptives_nonCC.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL002_tabulate_cohort_descriptives_nonCC.log
        model: output/basetable1_all.txt

  numbers:
    run: stata-mp:latest analysis/AL012_numbers.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL012_numbers.log

  describe_cohort_ar:
    run: stata-mp:latest analysis/AAR001_describe_cohort.do
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR001_describe_cohort.log

  tabulate_cohort_ar:
    run: stata-mp:latest analysis/AR001b_tabulate_cohort_descriptives.do
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AR001b_tabulate_cohort_descriptives.log
        model: output/basetable1_ar.txt

  cumulative_incidence:
    run: stata-mp:latest analysis/AL003_cumulative_incidence.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL003_cumulative_incidence.log
        graph1: output/cumincidence_coviddeath.svg
        graph2: output/cumincidence_composite.svg


###############################################
#  LD main analysis: Cox regression (adults)  #
###############################################

# Outcome = COVID-19 hospital admission

  cox_lda1:
    run: stata-mp:latest analysis/AL004_cox_regression.do 1 covidadmission ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave1_covidadmission_ldr.log
        hrs: output/ldcox_wave1_covidadmission_ldr.out

  cox_lda2:
    run: stata-mp:latest analysis/AL004_cox_regression.do 2 covidadmission ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave2_covidadmission_ldr.log
        hrs: output/ldcox_wave2_covidadmission_ldr.out

  cox_lda3:
    run: stata-mp:latest analysis/AL004_cox_regression.do 1 covidadmission ldr_cat
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave1_covidadmission_ldr_cat.log
        hrs: output/ldcox_wave1_covidadmission_ldr_cat.out

  cox_lda4:
    run: stata-mp:latest analysis/AL004_cox_regression.do 2 covidadmission ldr_cat
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave2_covidadmission_ldr_cat.log
        hrs: output/ldcox_wave2_covidadmission_ldr_cat.out

  cox_lda5:
    run: stata-mp:latest analysis/AL004_cox_regression.do 1 covidadmission ldr_carecat
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave1_covidadmission_ldr_carecat.log
        hrs: output/ldcox_wave1_covidadmission_ldr_carecat.out

  cox_lda6:
    run: stata-mp:latest analysis/AL004_cox_regression.do 2 covidadmission ldr_carecat
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave2_covidadmission_ldr_carecat.log
        hrs: output/ldcox_wave2_covidadmission_ldr_carecat.out

  cox_lda7:
    run: stata-mp:latest analysis/AL004_cox_regression.do 1 covidadmission ds
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave1_covidadmission_ds.log
        hrs: output/ldcox_wave1_covidadmission_ds.out

  cox_lda8:
    run: stata-mp:latest analysis/AL004_cox_regression.do 2 covidadmission ds
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave2_covidadmission_ds.log
        hrs: output/ldcox_wave2_covidadmission_ds.out

  cox_lda9:
    run: stata-mp:latest analysis/AL004_cox_regression.do 1 covidadmission cp
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave1_covidadmission_cp.log
        hrs: output/ldcox_wave1_covidadmission_cp.out

  cox_lda10:
    run: stata-mp:latest analysis/AL004_cox_regression.do 2 covidadmission cp
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave2_covidadmission_cp.log
        hrs: output/ldcox_wave2_covidadmission_cp.out

  cox_lda11:
    run: stata-mp:latest analysis/AL004_cox_regression.do 1 covidadmission ldr_group
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave1_covidadmission_ldr_group.log
        hrs: output/ldcox_wave1_covidadmission_ldr_group.out

  cox_lda12:
    run: stata-mp:latest analysis/AL004_cox_regression.do 2 covidadmission ldr_group
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave2_covidadmission_ldr_group.log
        hrs: output/ldcox_wave2_covidadmission_ldr_group.out

# Outcome = COVID-19 death

  cox_ldd1:
    run: stata-mp:latest analysis/AL004_cox_regression.do 1 coviddeath ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave1_coviddeath_ldr.log
        hrs: output/ldcox_wave1_coviddeath_ldr.out

  cox_ldd2:
    run: stata-mp:latest analysis/AL004_cox_regression.do 2 coviddeath ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave2_coviddeath_ldr.log
        hrs: output/ldcox_wave2_coviddeath_ldr.out

  cox_ldd3:
    run: stata-mp:latest analysis/AL004_cox_regression.do 1 coviddeath ldr_cat
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave1_coviddeath_ldr_cat.log
        hrs: output/ldcox_wave1_coviddeath_ldr_cat.out

  cox_ldd4:
    run: stata-mp:latest analysis/AL004_cox_regression.do 2 coviddeath ldr_cat
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave2_coviddeath_ldr_cat.log
        hrs: output/ldcox_wave2_coviddeath_ldr_cat.out

  cox_ldd5:
    run: stata-mp:latest analysis/AL004_cox_regression.do 1 coviddeath ldr_carecat
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave1_coviddeath_ldr_carecat.log
        hrs: output/ldcox_wave1_coviddeath_ldr_carecat.out

  cox_ldd6:
    run: stata-mp:latest analysis/AL004_cox_regression.do 2 coviddeath ldr_carecat
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave2_coviddeath_ldr_carecat.log
        hrs: output/ldcox_wave2_coviddeath_ldr_carecat.out

  cox_ldd7:
    run: stata-mp:latest analysis/AL004_cox_regression.do 1 coviddeath ds
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave1_coviddeath_ds.log
        hrs: output/ldcox_wave1_coviddeath_ds.out

  cox_ldd8:
    run: stata-mp:latest analysis/AL004_cox_regression.do 2 coviddeath ds
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave2_coviddeath_ds.log
        hrs: output/ldcox_wave2_coviddeath_ds.out

  cox_ldd9:
    run: stata-mp:latest analysis/AL004_cox_regression.do 1 coviddeath cp
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave1_coviddeath_cp.log
        hrs: output/ldcox_wave1_coviddeath_cp.out

  cox_ldd10:
    run: stata-mp:latest analysis/AL004_cox_regression.do 2 coviddeath cp
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave2_coviddeath_cp.log
        hrs: output/ldcox_wave2_coviddeath_cp.out

  cox_ldd11:
    run: stata-mp:latest analysis/AL004_cox_regression.do 1 coviddeath ldr_group
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave1_coviddeath_ldr_group.log
        hrs: output/ldcox_wave1_coviddeath_ldr_group.out

  cox_ldd12:
    run: stata-mp:latest analysis/AL004_cox_regression.do 2 coviddeath ldr_group
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL004_cox_regression_wave2_coviddeath_ldr_group.log
        hrs: output/ldcox_wave2_coviddeath_ldr_group.out


#################################################
#  LD main analysis: Cox regression (children)  #
#################################################

  cox_regression_child:
    run: stata-mp:latest analysis/AL005_cox_regression_child.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL005_cox_regression_child.log
        hrs: output/ldcox_covidadmission_child.out


#####################################
#  LD main analysis: Interactions   #
#####################################

# Interactions with age

  cox_ldint_age_a1:
    run: stata-mp:latest analysis/AL006a_cox_regression_interactions_age.do 1 covidadmission ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL006a_cox_regression_inter_age_wave1_covidadmission_ldr.log
        hrs: output/ldcox_inter_age_wave1_covidadmission_ldr.out

  cox_ldint_age_a2:
    run: stata-mp:latest analysis/AL006a_cox_regression_interactions_age.do 2 covidadmission ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL006a_cox_regression_inter_age_wave2_covidadmission_ldr.log
        hrs: output/ldcox_inter_age_wave2_covidadmission_ldr.out

  cox_ldint_age_d1:
    run: stata-mp:latest analysis/AL006a_cox_regression_interactions_age.do 1 coviddeath ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL006a_cox_regression_inter_age_wave1_coviddeath_ldr.log
        hrs: output/ldcox_inter_age_wave1_coviddeath_ldr.out

  cox_ldint_age_d2:
    run: stata-mp:latest analysis/AL006a_cox_regression_interactions_age.do 2 coviddeath ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL006a_cox_regression_inter_age_wave2_coviddeath_ldr.log
        hrs: output/ldcox_inter_age_wave2_coviddeath_ldr.out


# Interactions with sex

  cox_ldint_sex_a1:
    run: stata-mp:latest analysis/AL006b_cox_regression_interactions_sex.do 1 covidadmission ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL006b_cox_regression_inter_sex_wave1_covidadmission_ldr.log
        hrs: output/ldcox_inter_sex_wave1_covidadmission_ldr.out

  cox_ldint_sex_a2:
    run: stata-mp:latest analysis/AL006b_cox_regression_interactions_sex.do 2 covidadmission ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL006b_cox_regression_inter_sex_wave2_covidadmission_ldr.log
        hrs: output/ldcox_inter_sex_wave2_covidadmission_ldr.out

  cox_ldint_sex_d1:
    run: stata-mp:latest analysis/AL006b_cox_regression_interactions_sex.do 1 coviddeath ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL006b_cox_regression_inter_sex_wave1_coviddeath_ldr.log
        hrs: output/ldcox_inter_sex_wave1_coviddeath_ldr.out

  cox_ldint_sex_d2:
    run: stata-mp:latest analysis/AL006b_cox_regression_interactions_sex.do 2 coviddeath ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL006b_cox_regression_inter_sex_wave2_coviddeath_ldr.log
        hrs: output/ldcox_inter_sex_wave2_coviddeath_ldr.out

# Interactions with deprivation (IMD)

  cox_ldint_imd_a1:
    run: stata-mp:latest analysis/AL006c_cox_regression_interactions_imd.do 1 covidadmission ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL006c_cox_regression_inter_imd_wave1_covidadmission_ldr.log
        hrs: output/ldcox_inter_imd_wave1_covidadmission_ldr.out

  cox_ldint_imd_a2:
    run: stata-mp:latest analysis/AL006c_cox_regression_interactions_imd.do 2 covidadmission ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL006c_cox_regression_inter_imd_wave2_covidadmission_ldr.log
        hrs: output/ldcox_inter_imd_wave2_covidadmission_ldr.out

  cox_ldint_imd_d1:
    run: stata-mp:latest analysis/AL006c_cox_regression_interactions_imd.do 1 coviddeath ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL006c_cox_regression_inter_imd_wave1_coviddeath_ldr.log
        hrs: output/ldcox_inter_imd_wave1_coviddeath_ldr.out

  cox_ldint_imd_d2:
    run: stata-mp:latest analysis/AL006c_cox_regression_interactions_imd.do 2 coviddeath ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL006c_cox_regression_inter_imd_wave2_coviddeath_ldr.log
        hrs: output/ldcox_inter_imd_wave2_coviddeath_ldr.out

# Interactions with ethnicity

  cox_ldint_ethnicity_a1:
    run: stata-mp:latest analysis/AL006d_cox_regression_interactions_ethnicity.do 1 covidadmission ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL006d_cox_regression_inter_ethnicity_wave1_covidadmission_ldr.log
        hrs: output/ldcox_inter_ethnicity_wave1_covidadmission_ldr.out

  cox_ldint_ethnicity_a2:
    run: stata-mp:latest analysis/AL006d_cox_regression_interactions_ethnicity.do 2 covidadmission ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL006d_cox_regression_inter_ethnicity_wave2_covidadmission_ldr.log
        hrs: output/ldcox_inter_ethnicity_wave2_covidadmission_ldr.out

  cox_ldint_ethnicity_d1:
    run: stata-mp:latest analysis/AL006d_cox_regression_interactions_ethnicity.do 1 coviddeath ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL006d_cox_regression_inter_ethnicity_wave1_coviddeath_ldr.log
        hrs: output/ldcox_inter_ethnicity_wave1_coviddeath_ldr.out

  cox_ldint_ethnicity_d2:
    run: stata-mp:latest analysis/AL006d_cox_regression_interactions_ethnicity.do 2 coviddeath ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL006d_cox_regression_inter_ethnicity_wave2_coviddeath_ldr.log
        hrs: output/ldcox_inter_ethnicity_wave2_coviddeath_ldr.out


#############################################################
#  LD main analysis: Restricting population to "low risk"   #
#############################################################

  cox_ldresta1:
    run: stata-mp:latest analysis/AL007_cox_regression_restrict.do 1 covidadmission ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL007_cox_regression_restrict_wave1_covidadmission_ldr.log
        hrs: output/ldcox_restrict_wave1_covidadmission_ldr.out

  cox_ldresta2:
    run: stata-mp:latest analysis/AL007_cox_regression_restrict.do 2 covidadmission ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL007_cox_regression_restrict_wave2_covidadmission_ldr.log
        hrs: output/ldcox_restrict_wave2_covidadmission_ldr.out


#########################################
#  LD main analysis: Non-COVID deaths   #
#########################################

  cox_ldnoncovid1:
    run: stata-mp:latest analysis/AL008_cox_regression_noncovid.do 1 ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL008_cox_regression_noncovid_wave1_ldr.log
        hrs: output/ldcox_noncovid_wave1_ldr.out

  cox_ldnoncovid2:
    run: stata-mp:latest analysis/AL008_cox_regression_noncovid.do 2 ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL008_cox_regression_noncovid_wave2_ldr.log
        hrs: output/ldcox_noncovid_wave2_ldr.out

  cox_ldnoncovid3:
    run: stata-mp:latest analysis/AL008_cox_regression_noncovid.do 1 ldr_cat
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL008_cox_regression_noncovid_wave1_ldr_cat.log
        hrs: output/ldcox_noncovid_wave1_ldr_cat.out

  cox_ldnoncovid4:
    run: stata-mp:latest analysis/AL008_cox_regression_noncovid.do 2 ldr_cat
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL008_cox_regression_noncovid_wave2_ldr_cat.log
        hrs: output/ldcox_noncovid_wave2_ldr_cat.out

  cox_ldnoncovid5:
    run: stata-mp:latest analysis/AL008_cox_regression_noncovid.do 1 ldr_carecat
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL008_cox_regression_noncovid_wave1_ldr_carecat.log
        hrs: output/ldcox_noncovid_wave1_ldr_carecat.out

  cox_ldnoncovid6:
    run: stata-mp:latest analysis/AL008_cox_regression_noncovid.do 2 ldr_carecat
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL008_cox_regression_noncovid_wave2_ldr_carecat.log
        hrs: output/ldcox_noncovid_wave2_ldr_carecat.out

  cox_ldnoncovid7:
    run: stata-mp:latest analysis/AL008_cox_regression_noncovid.do 1 ds
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL008_cox_regression_noncovid_wave1_ds.log
        hrs: output/ldcox_noncovid_wave1_ds.out

  cox_ldnoncovid8:
    run: stata-mp:latest analysis/AL008_cox_regression_noncovid.do 2 ds
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL008_cox_regression_noncovid_wave2_ds.log
        hrs: output/ldcox_noncovid_wave2_ds.out

  cox_ldnoncovid9:
    run: stata-mp:latest analysis/AL008_cox_regression_noncovid.do 1 cp
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL008_cox_regression_noncovid_wave1_cp.log
        hrs: output/ldcox_noncovid_wave1_cp.out

  cox_ldnoncovid10:
    run: stata-mp:latest analysis/AL008_cox_regression_noncovid.do 2 cp
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL008_cox_regression_noncovid_wave2_cp.log
        hrs: output/ldcox_noncovid_wave2_cp.out

  cox_ldnoncovid11:
    run: stata-mp:latest analysis/AL008_cox_regression_noncovid.do 1 ldr_group
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL008_cox_regression_noncovid_wave1_ldr_group.log
        hrs: output/ldcox_noncovid_wave1_ldr_group.out

  cox_ldnoncovid12:
    run: stata-mp:latest analysis/AL008_cox_regression_noncovid.do 2 ldr_group
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL008_cox_regression_noncovid_wave2_ldr_group.log
        hrs: output/ldcox_noncovid_wave2_ldr_group.out



#############################
#  Model checking: PH test  #
#############################

  cox_phtest:
    run: stata-mp:latest analysis/AL009_phtest.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL009_phtest.log




###############################
#  Models for absolute risks  #
###############################

  cox_ar1:
    run: stata-mp:latest analysis/AAR001_cox_regression.do 1 covidadmission
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR001_cox_regression_wave1_covidadmission.log
        hrs: output/hr_wave1_male*_covidadmission.txt

  cox_ar2:
    run: stata-mp:latest analysis/AAR001_cox_regression.do 2 covidadmission
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR001_cox_regression_wave2_covidadmission.log
        hrs: output/hr_wave2_male*_covidadmission.txt

  cox_ar3:
    run: stata-mp:latest analysis/AAR001_cox_regression.do 1 coviddeath
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR001_cox_regression_wave1_coviddeath.log
        hrs: output/hr_wave1_male*_coviddeath.txt

  cox_ar4:
    run: stata-mp:latest analysis/AAR001_cox_regression.do 2 coviddeath
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR001_cox_regression_wave2_coviddeath.log
        hrs: output/hr_wave2_male*_coviddeath.txt


  ar_1:
    run: stata-mp:latest analysis/AAR002_risk_by_age.do 1 0 covidadmission
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR002_risk_by_age_wave1_male0_covidadmission.log
        absrisk: output/ar_wave1_male0_covidadmission.out
        graph: output/ar_wave1_male0_covidadmission.svg

  ar_2:
    run: stata-mp:latest analysis/AAR002_risk_by_age.do 1 1 covidadmission
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR002_risk_by_age_wave1_male1_covidadmission.log
        absrisk: output/ar_wave1_male1_covidadmission.out
        graph: output/ar_wave1_male1_covidadmission.svg

  ar_3:
    run: stata-mp:latest analysis/AAR002_risk_by_age.do 2 0 covidadmission
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR002_risk_by_age_wave2_male0_covidadmission.log
        absrisk: output/ar_wave2_male0_covidadmission.out
        graph: output/ar_wave2_male0_covidadmission.svg

  ar_4:
    run: stata-mp:latest analysis/AAR002_risk_by_age.do 2 1 covidadmission
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR002_risk_by_age_wave2_male1_covidadmission.log
        absrisk: output/ar_wave2_male1_covidadmission.out
        graph: output/ar_wave2_male1_covidadmission.svg

  ar_5:
    run: stata-mp:latest analysis/AAR002_risk_by_age.do 1 0 coviddeath
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR002_risk_by_age_wave1_male0_coviddeath.log
        absrisk: output/ar_wave1_male0_coviddeath.out
        graph: output/ar_wave1_male0_coviddeath.svg

  ar_6:
    run: stata-mp:latest analysis/AAR002_risk_by_age.do 1 1 coviddeath
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR002_risk_by_age_wave1_male1_coviddeath.log
        absrisk: output/ar_wave1_male1_coviddeath.out
        graph: output/ar_wave1_male1_coviddeath.svg

  ar_7:
    run: stata-mp:latest analysis/AAR002_risk_by_age.do 2 0 coviddeath
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR002_risk_by_age_wave2_male0_coviddeath.log
        absrisk: output/ar_wave2_male0_coviddeath.out
        graph: output/ar_wave2_male0_coviddeath.svg

  ar_8:
    run: stata-mp:latest analysis/AAR002_risk_by_age.do 2 1 coviddeath
    needs: [create_analysis_ar]
    outputs:
      moderately_sensitive:
        log: logs/AAR002_risk_by_age_wave2_male1_coviddeath.log
        absrisk: output/ar_wave2_male1_coviddeath.out
        graph: output/ar_wave2_male1_coviddeath.svg


  x_risk_by_age:
    run: stata-mp:latest analysis/X_covid_outcomes_by_at_risk.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/X_covid_outcomes_by_at_risk.log
        risk: output/X_covid_outcomes_by_at_risk.out


#################################################
#  Sensitivity anaysis:  Multiple Imputation    #
#################################################

  impute_ethnicity:
    run: stata-mp:latest analysis/AL010_MI.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL010_MI.log
      highly_sensitive:
        clean1: analysis/data_ldanalysis_cohort1_MI.dta
        clean2: analysis/data_ldanalysis_cohort2_MI.dta

  impute_ethnicity_child:
    run: stata-mp:latest analysis/AL010_MI_child.do
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL010_MI_child.log
      highly_sensitive:
        clean1: analysis/data_ldanalysis_cohort1_MI_child.dta
        clean2: analysis/data_ldanalysis_cohort2_MI_child.dta

  cox_lda1_MI:
    run: stata-mp:latest analysis/AL011_cox_regression_MI.do 1 covidadmission
    needs: [create_analysis, impute_ethnicity]
    outputs:
      moderately_sensitive:
        log: logs/AL011_cox_regression_wave1_covidadmission_MI.log
        hrs: output/ldcox_wave1_covidadmission_mi.out

  cox_lda2_MI:
    run: stata-mp:latest analysis/AL011_cox_regression_MI.do 2 covidadmission
    needs: [create_analysis, impute_ethnicity]
    outputs:
      moderately_sensitive:
        log: logs/AL011_cox_regression_wave2_covidadmission_MI.log
        hrs: output/ldcox_wave2_covidadmission_mi.out

  cox_ldd1_MI:
    run: stata-mp:latest analysis/AL011_cox_regression_MI.do 1 coviddeath
    needs: [create_analysis, impute_ethnicity]
    outputs:
      moderately_sensitive:
        log: logs/AL011_cox_regression_wave1_coviddeath_MI.log
        hrs: output/ldcox_wave1_coviddeath_mi.out

  cox_ldd2_MI:
    run: stata-mp:latest analysis/AL011_cox_regression_MI.do 2 coviddeath
    needs: [create_analysis, impute_ethnicity]
    outputs:
      moderately_sensitive:
        log: logs/AL011_cox_regression_wave2_coviddeath_MI.log
        hrs: output/ldcox_wave2_coviddeath_mi.out

  cox_MI_child:
    run: stata-mp:latest analysis/AL011_cox_regression_MI_child.do
    needs: [create_analysis, impute_ethnicity_child]
    outputs:
      moderately_sensitive:
        log: logs/AL011_cox_regression_MI_child.log
        hrs: output/ldcox_covidadmission_child_mi.out


############################################################
#  Sensitivity anaysis:  Complete case analysis for BMI    #
############################################################

  cox_lda1_CC_BMI:
    run: stata-mp:latest analysis/AL012_cox_regression_CC_BMI.do 1 covidadmission ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL012_cox_regression_CC_BMI_wave1_covidadmission_ldr.log
        hrs: output/ldcox_wave1_covidadmission_ldr_CC_BMI.out

  cox_lda2_CC_BMI:
    run: stata-mp:latest analysis/AL012_cox_regression_CC_BMI.do 2 covidadmission ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL012_cox_regression_CC_BMI_wave2_covidadmission_ldr.log
        hrs: output/ldcox_wave2_covidadmission_ldr_CC_BMI.out

  cox_ldd1_CC_BMI:
    run: stata-mp:latest analysis/AL012_cox_regression_CC_BMI.do 1 coviddeath ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL012_cox_regression_CC_BMI_wave1_coviddeath_ldr.log
        hrs: output/ldcox_wave1_coviddeath_ldr_CC_BMI.out

  cox_ldd2_CC_BMI:
    run: stata-mp:latest analysis/AL012_cox_regression_CC_BMI.do 2 coviddeath ldr
    needs: [create_analysis]
    outputs:
      moderately_sensitive:
        log: logs/AL012_cox_regression_CC_BMI_wave2_coviddeath_ldr.log
        hrs: output/ldcox_wave2_coviddeath_ldr_CC_BMI.out

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:09:22

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

Job information

Status
Failed
Backend
TPP
Workspace
learning-disabilities-full
Requested by
Elizabeth (Fizz) Williamson
Branch
master
Force run dependencies
No
Git commit hash
58ec07b
Requested actions
  • cox_MI_child