Job request: 17773
- Organisation:
- DataLab
- Workspace:
- long-covid-sick-notes
- ID:
- 5tzget27cxdac5k2
This page shows the technical details of what happened when authorised researcher Andrea Schaffer 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
-
- Job identifier:
-
6om3tuq6jo23mcmi
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 10000
actions:
generate_study_population_covid_2020:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_covid_2020
--output-dir=output/cohorts
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/cohorts/input_covid_2020.csv.gz
generate_study_population_covid_2021:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_covid_2021
--output-dir=output/cohorts
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/cohorts/input_covid_2021.csv.gz
generate_study_population_general_match_vars_2019:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_general_match_vars
--output-dir=output/cohorts
--output-format=csv.gz
--index-date-range="2019-02-01"
outputs:
highly_sensitive:
cohort: output/cohorts/input_general_match_vars_2019-02-01.csv.gz
generate_study_population_general_match_vars_2020:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_general_match_vars
--output-dir=output/cohorts
--output-format=csv.gz
--index-date-range="2020-02-01"
outputs:
highly_sensitive:
cohort: output/cohorts/input_general_match_vars_2020-02-01.csv.gz
generate_study_population_general_match_vars_2021:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_general_match_vars
--output-dir=output/cohorts
--output-format=csv.gz
--index-date-range="2021-02-01"
outputs:
highly_sensitive:
cohort: output/cohorts/input_general_match_vars_2021-02-01.csv.gz
generate_study_population_pneumonia_2019:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_pneumonia_2019
--output-dir=output/cohorts
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/cohorts/input_pneumonia_2019.csv.gz
matching_2019:
run: python:latest python analysis/match_running.py "2019" --output-dir=output/cohorts
needs: [generate_study_population_covid_2020, generate_study_population_general_match_vars_2019]
outputs:
moderately_sensitive:
matching_report: output/cohorts/matching_report_general_2019.txt
highly_sensitive:
matched_cohort: output/cohorts/matched_matches_general_2019.csv
matching_2020:
run: python:latest python analysis/match_running.py "2020" --output-dir=output/cohorts
needs: [generate_study_population_covid_2020, generate_study_population_general_match_vars_2020]
outputs:
moderately_sensitive:
matching_report: output/cohorts/matching_report_general_2020.txt
highly_sensitive:
matched_cohort: output/cohorts/matched_matches_general_2020.csv
matching_2021:
run: python:latest python analysis/match_running.py "2021" --output-dir=output/cohorts
needs: [generate_study_population_covid_2021, generate_study_population_general_match_vars_2021]
outputs:
moderately_sensitive:
matching_report: output/cohorts/matching_report_general_2021.txt
highly_sensitive:
matched_cohort: output/cohorts/matched_matches_general_2021.csv
generate_study_population_matched_2019:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_matched_2019
--output-dir=output/cohorts
--output-format=csv.gz
needs: [matching_2019]
outputs:
highly_sensitive:
cohort: output/cohorts/input_matched_2019.csv.gz
generate_study_population_matched_2020:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_matched_2020
--output-dir=output/cohorts
--output-format=csv.gz
needs: [matching_2020]
outputs:
highly_sensitive:
cohort: output/cohorts/input_matched_2020.csv.gz
generate_study_population_matched_2021:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_matched_2021
--output-dir=output/cohorts
--output-format=csv.gz
needs: [matching_2021]
outputs:
highly_sensitive:
cohort: output/cohorts/input_matched_2021.csv.gz
reconcile_sick_note_spells_covid_2020:
run: python:latest python analysis/reconcile_sick_note_spells.py "_covid_2020"
needs: [generate_study_population_covid_2020]
outputs:
highly_sensitive:
cohort_with_duration: output/cohorts/input_covid_2020_with_duration.csv
reconcile_sick_note_spells_covid_2021:
run: python:latest python analysis/reconcile_sick_note_spells.py "_covid_2021"
needs: [generate_study_population_covid_2021]
outputs:
highly_sensitive:
cohort_with_duration: output/cohorts/input_covid_2021_with_duration.csv
reconcile_sick_note_spells_general_2019:
run: python:latest python analysis/reconcile_sick_note_spells.py "_matched_2019"
needs: [generate_study_population_matched_2019]
outputs:
highly_sensitive:
cohort_with_duration: output/cohorts/input_matched_2019_with_duration.csv
reconcile_sick_note_spells_general_2020:
run: python:latest python analysis/reconcile_sick_note_spells.py "_matched_2020"
needs: [generate_study_population_matched_2020]
outputs:
highly_sensitive:
cohort_with_duration: output/cohorts/input_matched_2020_with_duration.csv
reconcile_sick_note_spells_general_2021:
run: python:latest python analysis/reconcile_sick_note_spells.py "_matched_2021"
needs: [generate_study_population_matched_2021]
outputs:
highly_sensitive:
cohort_with_duration: output/cohorts/input_matched_2021_with_duration.csv
reconcile_sick_note_spells_pneumonia_2019:
run: python:latest python analysis/reconcile_sick_note_spells.py "_pneumonia_2019"
needs: [generate_study_population_pneumonia_2019]
outputs:
highly_sensitive:
cohort_with_duration: output/cohorts/input_pneumonia_2019_with_duration.csv
covid_2020_rates_cohort:
run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "covid_2020" --output-dir=output/cohorts
needs: [reconcile_sick_note_spells_covid_2020]
outputs:
highly_sensitive:
analysis_dataset: output/cohorts/cohort_rates_*.dta
covid_2021_rates_cohort:
run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "covid_2021" --output-dir=output/cohorts
needs: [reconcile_sick_note_spells_covid_2021]
outputs:
highly_sensitive:
analysis_dataset: output/cohorts/cohort_rates*.dta
general_2019_rates_cohort:
run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "matched_2019" --output-dir=output/cohorts
needs: [reconcile_sick_note_spells_general_2019]
outputs:
highly_sensitive:
analysis_dataset: output/cohorts/cohort_rates_matched_2019.dta
general_2020_rates_cohort:
run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "matched_2020" --output-dir=output/cohorts
needs: [reconcile_sick_note_spells_general_2020]
outputs:
highly_sensitive:
analysis_dataset: output/cohorts/cohort_rates_matched_2020.dta
general_2021_rates_cohort:
run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "matched_2021" --output-dir=output/cohorts
needs: [reconcile_sick_note_spells_general_2021]
outputs:
highly_sensitive:
analysis_dataset: output/cohorts/cohort_rates_matched_2021.dta
pneumonia_2019_rates_cohort:
run: stata-mp:latest analysis/rates/000_cr_define_covariates_simple_rates.do "pneumonia_2019" --output-dir=output/cohorts
needs: [reconcile_sick_note_spells_pneumonia_2019]
outputs:
highly_sensitive:
analysis_dataset: output/cohorts/cohort_rates_pneumonia_2019.dta
covid_2020_rates:
run: stata-mp:latest analysis/rates/100_cr_simple_rates.do "covid_2020" --output-dir=output/tabfig
needs: [covid_2020_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_covid_2020.csv
covid_2021_rates:
run: stata-mp:latest analysis/rates/100_cr_simple_rates.do "covid_2021" --output-dir=output/tabfig
needs: [covid_2021_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_covid_2021.csv
general_2019_rates:
run: stata-mp:latest analysis/rates/100_cr_simple_rates.do "matched_2019" --output-dir=output/tabfig
needs: [general_2019_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_matched_2019.csv
general_2020_rates:
run: stata-mp:latest analysis/rates/100_cr_simple_rates.do "matched_2020" --output-dir=output/tabfig
needs: [general_2020_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_matched_2020.csv
general_2021_rates:
run: stata-mp:latest analysis/rates/100_cr_simple_rates.do "matched_2021" --output-dir=output/tabfig
needs: [general_2021_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_matched_2021.csv
pneumonia_2019_rates:
run: stata-mp:latest analysis/rates/100_cr_simple_rates_hosp.do "pneumonia_2019" --output-dir=output/tabfig
needs: [pneumonia_2019_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_hosp_pneumonia_2019.csv
covid_hosp_2020_rates:
run: stata-mp:latest analysis/rates/100_cr_simple_rates_hosp.do "covid_2020" --output-dir=output/tabfig
needs: [covid_2020_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_hosp_covid_2020.csv
covid_hosp_2021_rates:
run: stata-mp:latest analysis/rates/100_cr_simple_rates_hosp.do "covid_2021" --output-dir=output/tabfig
needs: [covid_2021_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_hosp_covid_2021.csv
append_cohorts:
run: stata-mp:latest analysis/cox_models/200_cr_data_management_matching.do --output-dir=output/cohorts
needs: [covid_2021_rates_cohort, covid_2020_rates_cohort, pneumonia_2019_rates_cohort, general_2021_rates_cohort, general_2020_rates_cohort, general_2019_rates_cohort]
outputs:
moderately_sensitive:
log: output/cohorts/append_cohorts.txt
highly_sensitive:
dataset: output/cohorts/combined_covid_2020_pneumonia.dta
dataset2: output/cohorts/combined_covid_2021_pneumonia.dta
dataset3: output/cohorts/combined_covid_2020_general_2019.dta
dataset4: output/cohorts/combined_covid_2021_general_2019.dta
dataset5: output/cohorts/combined_covid_general_2020.dta
dataset6: output/cohorts/combined_covid_general_2021.dta
cox_models:
run: stata-mp:latest analysis/cox_models/201_cox_models.do
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models.txt
dataset: output/tabfig/cox_model_summary.csv
# Cox model overall stratified by age
cox_models_age:
run: stata-mp:latest analysis/cox_models/203_cox_models_stratified.do "age_group"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_summary_age_group.txt
dataset: output/tabfig/cox_model_summary_age_group*.csv
# Cox model overall stratified by ethnicity
cox_models_ethnicity:
run: stata-mp:latest analysis/cox_models/203_cox_models_stratified.do "ethnicity"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_summary_ethnicity.txt
dataset: output/tabfig/cox_model_summary_ethnicity.csv
# Cox model overall stratified by IMD
cox_models_imd:
run: stata-mp:latest analysis/cox_models/203_cox_models_stratified.do "imd"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_summary_imd.txt
dataset: output/tabfig/cox_model_summary_imd.csv
# Cox model overall stratified by region
cox_models_region:
run: stata-mp:latest analysis/cox_models/203_cox_models_stratified.do "region_9"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_summary_region_9.txt
dataset: output/tabfig/cox_model_summary_region_9.csv
# Cox model overall stratified by sex
cox_models_sex:
run: stata-mp:latest analysis/cox_models/203_cox_models_stratified.do "male"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_summary_male.txt
dataset: output/tabfig/cox_model_summary_male.csv
# Cox modes split by follow-up time
cox_models_split_2020_pneumo:
run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "2020_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_pneumonia.txt
dataset: output/tabfig/cox_model_split_summary_2020_pneumonia.csv
cox_models_split_2021_pneumo:
run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "2021_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_pneumonia.txt
dataset: output/tabfig/cox_model_split_summary_2021_pneumonia.csv
cox_models_split_2020_gen_2019:
run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "2020_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_general_2019.txt
dataset: output/tabfig/cox_model_split_summary_2020_general_2019.csv
cox_models_split_2021_gen_2019:
run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "2021_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_general_2019.txt
dataset: output/tabfig/cox_model_split_summary_2021_general_2019.csv
cox_models_split_gen_2020:
run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "general_2020"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2020.txt
dataset: output/tabfig/cox_model_split_summary_general_2020.csv
cox_models_split_gen_2021:
run: stata-mp:latest analysis/cox_models/202_cox_models_split.do "general_2021"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2021.txt
dataset: output/tabfig/cox_model_split_summary_general_2021.csv
# Cox modes split by follow-up time - stratified by age
cox_models_split_2020_pneumo_age:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "2020_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_pneumonia_age_group.txt
dataset: output/tabfig/cox_model_split_summary_2020_pneumonia_age_group.csv
cox_models_split_2021_pneumo_age:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "2021_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_pneumonia_age_group.txt
dataset: output/tabfig/cox_model_split_summary_2021_pneumonia_age_group.csv
cox_models_split_2020_gen_2019_age:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "2020_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_general_2019_age_group.txt
dataset: output/tabfig/cox_model_split_summary_2020_general_2019_age_group.csv
cox_models_split_2021_gen_2019_age:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "2021_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_general_2019_age_group.txt
dataset: output/tabfig/cox_model_split_summary_2021_general_2019_age_group.csv
cox_models_split_gen_2020_age:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "general_2020"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2020_age_group.txt
dataset: output/tabfig/cox_model_split_summary_general_2020_age_group.csv
cox_models_split_gen_2021_age:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_age.do "general_2021"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2021_age_group.txt
dataset: output/tabfig/cox_model_split_summary_general_2021_age_group.csv
# Cox models split by follow-up time - stratified by ethnicity
cox_models_split_2020_pneumo_ethnicity:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "2020_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_pneumonia_ethnicity.txt
dataset: output/tabfig/cox_model_split_summary_2020_pneumonia_ethnicity.csv
cox_models_split_2021_pneumo_ethnicity:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "2021_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_pneumonia_ethnicity.txt
dataset: output/tabfig/cox_model_split_summary_2021_pneumonia_ethnicity.csv
cox_models_split_2020_gen_2019_ethnicity:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "2020_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_general_2019_ethnicity.txt
dataset: output/tabfig/cox_model_split_summary_2020_general_2019_ethnicity.csv
cox_models_split_2021_gen_2019_ethnicity:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "2021_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_general_2019_ethnicity.txt
dataset: output/tabfig/cox_model_split_summary_2021_general_2019_ethnicity.csv
cox_models_split_gen_2020_ethnicity:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "general_2020"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2020_ethnicity.txt
dataset: output/tabfig/cox_model_split_summary_general_2020_ethnicity.csv
cox_models_split_gen_2021_ethnicity:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_ethnicity.do "general_2021"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2021_ethnicity.txt
dataset: output/tabfig/cox_model_split_summary_general_2021_ethnicity.csv
# Cox models split by follow-up time - stratified by IMD
cox_models_split_2020_pneumo_imd:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "2020_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_pneumonia_imd.txt
dataset: output/tabfig/cox_model_split_summary_2020_pneumonia_imd.csv
cox_models_split_2021_pneumo_imd:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "2021_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_pneumonia_imd.txt
dataset: output/tabfig/cox_model_split_summary_2021_pneumonia_imd.csv
cox_models_split_2020_gen_2019_imd:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "2020_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_general_2019_imd.txt
dataset: output/tabfig/cox_model_split_summary_2020_general_2019_imd.csv
cox_models_split_2021_gen_2019_imd:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "2021_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_general_2019_imd.txt
dataset: output/tabfig/cox_model_split_summary_2021_general_2019_imd.csv
cox_models_split_gen_2020_imd:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "general_2020"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2020_imd.txt
dataset: output/tabfig/cox_model_split_summary_general_2020_imd.csv
cox_models_split_gen_2021_imd:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_imd.do "general_2021"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2021_imd.txt
dataset: output/tabfig/cox_model_split_summary_general_2021_imd.csv
# Cox models split by follow-up time - stratified by region
cox_models_split_2020_pneumo_region:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "2020_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_pneumonia_region.txt
dataset: output/tabfig/cox_model_split_summary_2020_pneumonia_region.csv
cox_models_split_2021_pneumo_region:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "2021_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_pneumonia_region.txt
dataset: output/tabfig/cox_model_split_summary_2021_pneumonia_region.csv
cox_models_split_2020_gen_2019_region:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "2020_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_general_2019_region.txt
dataset: output/tabfig/cox_model_split_summary_2020_general_2019_region.csv
cox_models_split_2021_gen_2019_region:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "2021_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_general_2019_region.txt
dataset: output/tabfig/cox_model_split_summary_2021_general_2019_region.csv
cox_models_split_gen_2020_region:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "general_2020"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2020_region.txt
dataset: output/tabfig/cox_model_split_summary_general_2020_region.csv
cox_models_split_gen_2021_region:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_region.do "general_2021"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2021_region.txt
dataset: output/tabfig/cox_model_split_summary_general_2021_region.csv
# Cox models split by follow-up time - stratified by sex
cox_models_split_2020_pneumo_sex:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "2020_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_pneumonia_sex.txt
dataset: output/tabfig/cox_model_split_summary_2020_pneumonia_sex.csv
cox_models_split_2021_pneumo_sex:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "2021_pneumonia"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_pneumonia_sex.txt
dataset: output/tabfig/cox_model_split_summary_2021_pneumonia_sex.csv
cox_models_split_2020_gen_2019_sex:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "2020_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2020_general_2019_sex.txt
dataset: output/tabfig/cox_model_split_summary_2020_general_2019_sex.csv
cox_models_split_2021_gen_2019_sex:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "2021_general_2019"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_2021_general_2019_sex.txt
dataset: output/tabfig/cox_model_split_summary_2021_general_2019_sex.csv
cox_models_split_gen_2020_sex:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "general_2020"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2020_sex.txt
dataset: output/tabfig/cox_model_split_summary_general_2020_sex.csv
cox_models_split_gen_2021_sex:
run: stata-mp:latest analysis/cox_models/204_cox_models_split_stratified_sex.do "general_2021"
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cohorts/cox_models_split_general_2021_sex.txt
dataset: output/tabfig/cox_model_split_summary_general_2021_sex.csv
# describe_duration_diagnoses:
# run: jupyter:latest jupyter nbconvert /workspace/notebooks/describe_duration_diagnoses.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# needs: [covid_2021_rates_cohort, covid_2020_rates_cohort, general_2019_rates_cohort, general_2020_rates_cohort, general_2021_rates_cohort, pneumonia_2019_rates_cohort]
# outputs:
# moderately_sensitive:
# notebook: output/describe_duration_diagnoses.html
# table: output/tabfig/med_mean_overall.csv
# table2: output/tabfig/med_mean_age_group.csv
# table3: output/tabfig/med_mean_sex.csv
# table4: output/tabfig/med_mean_ethnicity.csv
# table5: output/tabfig/med_mean_imd.csv
# table6: output/tabfig/med_mean_region.csv
# subplots: output/tabfig/diag_*.png
table1:
run: r:latest analysis/descriptive/1_table1_demo_clinical.R
needs: [append_cohorts]
outputs:
moderately_sensitive:
table: output/tabfig/table1_*.csv
visualise_diagnoses:
run: r:latest analysis/descriptive/2_visualise_diagnoses.R
needs: [append_cohorts]
outputs:
moderately_sensitive:
table: output/tabfig/diag_by_cohort.csv
plot: output/tabfig/diag_all.png
check_died:
run: r:latest analysis/descriptive/3_check_died.R
needs: [covid_2020_rates_cohort, covid_2021_rates_cohort, general_2019_rates_cohort,
general_2020_rates_cohort, general_2021_rates_cohort, pneumonia_2019_rates_cohort,
reconcile_sick_note_spells_general_2020, reconcile_sick_note_spells_general_2019,
reconcile_sick_note_spells_general_2021]
outputs:
moderately_sensitive:
table1: output/tabfig/check_died_*.csv
# table3: output/tabfig/check_ons*.csv
table4: output/tabfig/check_index*.csv
table5: output/tabfig/check_deregister*.csv
Timeline
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Created:
-
Started:
-
Finished:
-
Runtime: 00:14:06
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- long-covid-sick-notes
- Requested by
- Andrea Schaffer
- Branch
- master
- Force run dependencies
- No
- Git commit hash
- 880013e
- Requested actions
-
-
check_died
-