Job request: 14022
- Organisation:
- University of Bristol
- Workspace:
- post-covid-pre-vaccinated-cardiovascular
- ID:
- atk4zlezl4uwhlcw
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 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:
-
gek7jo6pb342gsgb
Pipeline
Show 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
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_*
days_to_event_histogram:
run: r:latest analysis/descriptives/histogram_data_post_exposure_days_to_event.R
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
histogram_data: output/review/descriptives/histogram_data_pre_vaccination.csv
## 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
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_ami_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_ami_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_ami_*_pre_vaccination_*_time_periods.csv
## 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
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_stroke_isch_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_stroke_isch_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_stroke_isch_*_pre_vaccination_*_time_periods.csv
## 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
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_dvt_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_dvt_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_dvt_*_pre_vaccination_*_time_periods.csv
## 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
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_pe_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_pe_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_pe_*_pre_vaccination_*_time_periods.csv
## 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
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_tia_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_tia_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_tia_*_pre_vaccination_*_time_periods.csv
## 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
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_stroke_sah_hs_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_stroke_sah_hs_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_stroke_sah_hs_*_pre_vaccination_*_time_periods.csv
## 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
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_hf_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_hf_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_hf_*_pre_vaccination_*_time_periods.csv
## 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
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_angina_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_angina_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_angina_*_pre_vaccination_*_time_periods.csv
## Apply cox model for ami_extended_follow_up
Analysis_cox_ami_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R ami_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ami_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_ami_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_ami_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_ami_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## Apply cox model for stroke_isch_extended_follow_up
Analysis_cox_stroke_isch_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_isch_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_stroke_isch_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_stroke_isch_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_stroke_isch_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## Apply cox model for dvt_extended_follow_up
Analysis_cox_dvt_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R dvt_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_dvt_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_dvt_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_dvt_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_dvt_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## Apply cox model for pe_extended_follow_up
Analysis_cox_pe_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R pe_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_pe_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_pe_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_pe_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_pe_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## Apply cox model for tia_extended_follow_up
Analysis_cox_tia_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R tia_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_tia_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_tia_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_tia_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_tia_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## Apply cox model for stroke_sah_hs_extended_follow_up
Analysis_cox_stroke_sah_hs_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_stroke_sah_hs_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_stroke_sah_hs_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_stroke_sah_hs_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## Apply cox model for hf_extended_follow_up
Analysis_cox_hf_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R hf_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_hf_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_hf_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_hf_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_hf_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## Apply cox model for angina_extended_follow_up
Analysis_cox_angina_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R angina_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_angina_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_angina_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_angina_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_angina_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## 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
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_ate_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_ate_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_ate_*_pre_vaccination_*_time_periods.csv
## 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
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_vte_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_vte_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_vte_*_pre_vaccination_*_time_periods.csv
## Apply cox model for ate_extended_follow_up
Analysis_cox_ate_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R ate_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ate_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_ate_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_ate_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_ate_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## Apply cox model for vte_extended_follow_up
Analysis_cox_vte_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R vte_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_vte_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_vte_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_vte_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_vte_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## 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
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_ami_primary_position_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_ami_primary_position_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_ami_primary_position_*_pre_vaccination_*_time_periods.csv
## 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
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_stroke_isch_primary_position_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_stroke_isch_primary_position_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_stroke_isch_primary_position_*_pre_vaccination_*_time_periods.csv
## 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
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_dvt_primary_position_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_dvt_primary_position_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_dvt_primary_position_*_pre_vaccination_*_time_periods.csv
## 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
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_pe_primary_position_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_pe_primary_position_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_pe_primary_position_*_pre_vaccination_*_time_periods.csv
## 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
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_tia_primary_position_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_tia_primary_position_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_tia_primary_position_*_pre_vaccination_*_time_periods.csv
## 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
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_stroke_sah_hs_primary_position_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_stroke_sah_hs_primary_position_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_stroke_sah_hs_primary_position_*_pre_vaccination_*_time_periods.csv
## 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
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_hf_primary_position_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_hf_primary_position_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_hf_primary_position_*_pre_vaccination_*_time_periods.csv
## 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
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_angina_primary_position_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_angina_primary_position_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_angina_primary_position_*_pre_vaccination_*_time_periods.csv
## Apply cox model for ami_primary_position_extended_follow_up
Analysis_cox_ami_primary_position_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R ami_primary_position_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ami_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_primary_position_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_primary_position_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_primary_position_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_ami_primary_position_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_ami_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_ami_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## Apply cox model for stroke_isch_primary_position_extended_follow_up
Analysis_cox_stroke_isch_primary_position_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_primary_position_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_isch_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_primary_position_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_primary_position_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_stroke_isch_primary_position_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_stroke_isch_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_stroke_isch_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## Apply cox model for dvt_primary_position_extended_follow_up
Analysis_cox_dvt_primary_position_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R dvt_primary_position_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_dvt_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_primary_position_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_primary_position_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_dvt_primary_position_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_dvt_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_dvt_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## Apply cox model for pe_primary_position_extended_follow_up
Analysis_cox_pe_primary_position_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R pe_primary_position_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_pe_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_primary_position_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_primary_position_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_primary_position_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_pe_primary_position_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_pe_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_pe_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## Apply cox model for tia_primary_position_extended_follow_up
Analysis_cox_tia_primary_position_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R tia_primary_position_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_tia_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_primary_position_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_primary_position_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_primary_position_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_tia_primary_position_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_tia_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_tia_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## Apply cox model for stroke_sah_hs_primary_position_extended_follow_up
Analysis_cox_stroke_sah_hs_primary_position_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_primary_position_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_primary_position_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_primary_position_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_stroke_sah_hs_primary_position_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_stroke_sah_hs_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_stroke_sah_hs_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## Apply cox model for hf_primary_position_extended_follow_up
Analysis_cox_hf_primary_position_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R hf_primary_position_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_hf_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_primary_position_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_primary_position_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_primary_position_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_hf_primary_position_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_hf_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_hf_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## Apply cox model for angina_primary_position_extended_follow_up
Analysis_cox_angina_primary_position_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R angina_primary_position_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_angina_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_primary_position_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_primary_position_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_primary_position_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_angina_primary_position_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_angina_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_angina_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## 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
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_ate_primary_position_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_ate_primary_position_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_ate_primary_position_*_pre_vaccination_*_time_periods.csv
## 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
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_vte_primary_position_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_vte_primary_position_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_vte_primary_position_*_pre_vaccination_*_time_periods.csv
## Apply cox model for ate_primary_position_extended_follow_up
Analysis_cox_ate_primary_position_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R ate_primary_position_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ate_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_primary_position_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_primary_position_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_primary_position_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_ate_primary_position_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_ate_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_ate_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
## Apply cox model for vte_primary_position_extended_follow_up
Analysis_cox_vte_primary_position_extended_follow_up:
run: r:latest analysis/model/01_cox_pipeline.R vte_primary_position_extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_vte_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_primary_position_extended_follow_up_pre_vaccination.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_primary_position_extended_follow_up_pre_vaccination_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_primary_position_extended_follow_up_pre_vaccination.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_primary_position_extended_follow_up_pre_vaccination.csv
describe_data_surv: output/not-for-review/describe_vte_primary_position_extended_follow_up_*_time_periods.txt
highly_sensitive:
sampled_data: output/input_sampled_data_vte_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
cox_input_data: output/input_vte_primary_position_extended_follow_up_*_pre_vaccination_*_time_periods.csv
stata_cox_model_ami_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ami
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_stroke_isch
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_dvt_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_dvt
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_pe_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_pe
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_tia_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_tia
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_stroke_sah_hs
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_hf_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_hf
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_angina_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_angina
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_ate_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ate
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_vte_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_vte
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ami_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_stroke_isch_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_dvt_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_pe_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_tia_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_hf_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_angina_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ate_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_vte_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_vte_agegp_60_79_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_agegp_60_79_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_vte
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_vte_agegp_60_79_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_vte_agegp_60_79_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_vte_ethnicity_Other_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_ethnicity_Other_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_vte
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_vte_ethnicity_Other_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_vte_ethnicity_Other_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_model_vte_aer_Male_60_79_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_aer_Male_60_79_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_vte
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_vte_aer_Male_60_79_pre_vaccination_reduced_time_periods_stata_median_fup.csv
stata_output: output/input_sampled_data_vte_aer_Male_60_79_pre_vaccination_reduced_time_periods_cox_model.txt
stata_cox_day_zero_ami_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ami
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_stroke_isch
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_dvt_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_dvt
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_pe_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_pe
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_tia_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_tia
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_stroke_sah_hs
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_hf_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_hf
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_angina_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_angina
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_ate_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ate
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_vte_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_vte
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ami_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_stroke_isch_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_dvt_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_pe_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_tia_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_hf_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_angina_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ate_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_vte_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_ami_main_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ami_main_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ami
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ami_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_ami_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_stroke_isch_main_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_isch_main_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_stroke_isch
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_stroke_isch_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_stroke_isch_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_dvt_main_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_dvt_main_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_dvt
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_dvt_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_dvt_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_pe_main_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_pe_main_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_pe
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_pe_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_pe_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_tia_main_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_tia_main_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_tia
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_tia_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_tia_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_stroke_sah_hs_main_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_sah_hs_main_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_stroke_sah_hs
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_stroke_sah_hs_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_stroke_sah_hs_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_hf_main_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_hf_main_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_hf
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_hf_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_hf_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_angina_main_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_angina_main_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_angina
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_angina_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_angina_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_ate_main_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ate_main_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ate
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ate_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_ate_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_vte_main_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_vte_main_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_vte
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_vte_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_vte_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_ami_primary_position_main_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ami_primary_position_main_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ami_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ami_primary_position_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_ami_primary_position_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_stroke_isch_primary_position_main_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_isch_primary_position_main_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_stroke_isch_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_stroke_isch_primary_position_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_stroke_isch_primary_position_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_pe_primary_position_main_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_pe_primary_position_main_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_pe_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_pe_primary_position_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_pe_primary_position_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_hf_primary_position_main_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_hf_primary_position_main_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_hf_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_hf_primary_position_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_hf_primary_position_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_ate_primary_position_main_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ate_primary_position_main_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ate_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ate_primary_position_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_ate_primary_position_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_vte_primary_position_main_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_vte_primary_position_main_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_vte_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_vte_primary_position_main_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_vte_primary_position_main_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_ami_covid_pheno_non_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ami_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ami
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ami_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_ami_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_stroke_isch_covid_pheno_non_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_isch_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_stroke_isch
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_stroke_isch_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_stroke_isch_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_dvt_covid_pheno_non_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_dvt_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_dvt
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_dvt_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_dvt_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_pe_covid_pheno_non_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_pe_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_pe
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_pe_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_pe_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_stroke_sah_hs_covid_pheno_non_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_sah_hs_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_stroke_sah_hs
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_stroke_sah_hs_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_stroke_sah_hs_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_hf_covid_pheno_non_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_hf_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_hf
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_hf_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_hf_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_angina_covid_pheno_non_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_angina_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_angina
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_angina_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_angina_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_ate_covid_pheno_non_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ate_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ate
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ate_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_ate_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_vte_covid_pheno_non_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_vte_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_vte
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_vte_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_vte_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_ami_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ami_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ami_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ami_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_ami_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_stroke_isch_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_isch_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_stroke_isch_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_pe_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_pe_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_pe_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_pe_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_pe_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_stroke_sah_hs_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_stroke_sah_hs_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_stroke_sah_hs_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_stroke_sah_hs_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_stroke_sah_hs_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_hf_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_hf_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_hf_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_hf_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_hf_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_ate_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_ate_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ate_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ate_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_ate_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_day_zero_vte_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_day0.do input_sampled_data_vte_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_vte_primary_position
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_vte_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day_zero.csv
stata_output: output/input_sampled_data_vte_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day_zero.txt
stata_cox_extended_ami_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_ami_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ami_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ami_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_ami_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_stroke_isch_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_stroke_isch_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_stroke_isch_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_stroke_isch_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_stroke_isch_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_dvt_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_dvt_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_dvt_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_dvt_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_dvt_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_pe_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_pe_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_pe_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_pe_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_pe_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_tia_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_tia_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_tia_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_tia_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_tia_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_stroke_sah_hs_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_stroke_sah_hs_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_stroke_sah_hs_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_stroke_sah_hs_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_stroke_sah_hs_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_hf_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_hf_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_hf_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_hf_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_hf_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_angina_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_angina_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_angina_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_angina_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_angina_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_ate_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_ate_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ate_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ate_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_ate_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_vte_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_vte_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_vte_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_vte_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_vte_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_ami_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_ami_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ami_primary_position_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ami_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_ami_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_stroke_isch_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_stroke_isch_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_stroke_isch_primary_position_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_stroke_isch_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_stroke_isch_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_dvt_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_dvt_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_dvt_primary_position_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_dvt_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_dvt_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_pe_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_pe_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_pe_primary_position_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_pe_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_pe_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_tia_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_tia_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_tia_primary_position_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_tia_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_tia_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_hf_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_hf_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_hf_primary_position_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_hf_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_hf_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_angina_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_angina_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_angina_primary_position_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_angina_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_angina_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_ate_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_ate_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_ate_primary_position_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ate_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_ate_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
stata_cox_extended_vte_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced:
run: stata-mp:latest analysis/cox_model_extended_follow_up.do input_sampled_data_vte_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
needs:
- Analysis_cox_vte_primary_position_extended_follow_up
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_vte_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_extended_follow_up.csv
stata_output: output/input_sampled_data_vte_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_extended_follow_up.txt
format_stata_output:
run: r:latest analysis/format_stata_output.R
needs:
- stata_cox_model_ami_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_dvt_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_pe_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_tia_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_hf_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_angina_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_ate_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_vte_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_model_vte_agegp_60_79_pre_vaccination_reduced
- stata_cox_model_vte_ethnicity_Other_pre_vaccination_reduced
- stata_cox_model_vte_aer_Male_60_79_pre_vaccination_reduced
- stata_cox_day_zero_ami_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_dvt_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_pe_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_tia_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_hf_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_angina_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_ate_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_vte_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_ami_main_pre_vaccination_reduced
- stata_cox_day_zero_stroke_isch_main_pre_vaccination_reduced
- stata_cox_day_zero_dvt_main_pre_vaccination_reduced
- stata_cox_day_zero_pe_main_pre_vaccination_reduced
- stata_cox_day_zero_tia_main_pre_vaccination_reduced
- stata_cox_day_zero_stroke_sah_hs_main_pre_vaccination_reduced
- stata_cox_day_zero_hf_main_pre_vaccination_reduced
- stata_cox_day_zero_angina_main_pre_vaccination_reduced
- stata_cox_day_zero_ate_main_pre_vaccination_reduced
- stata_cox_day_zero_vte_main_pre_vaccination_reduced
- stata_cox_day_zero_ami_primary_position_main_pre_vaccination_reduced
- stata_cox_day_zero_stroke_isch_primary_position_main_pre_vaccination_reduced
- stata_cox_day_zero_pe_primary_position_main_pre_vaccination_reduced
- stata_cox_day_zero_hf_primary_position_main_pre_vaccination_reduced
- stata_cox_day_zero_ate_primary_position_main_pre_vaccination_reduced
- stata_cox_day_zero_vte_primary_position_main_pre_vaccination_reduced
- stata_cox_day_zero_ami_covid_pheno_non_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_stroke_isch_covid_pheno_non_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_dvt_covid_pheno_non_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_pe_covid_pheno_non_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_stroke_sah_hs_covid_pheno_non_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_hf_covid_pheno_non_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_angina_covid_pheno_non_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_ate_covid_pheno_non_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_vte_covid_pheno_non_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_ami_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_stroke_isch_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_pe_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_stroke_sah_hs_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_hf_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_ate_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced
- stata_cox_day_zero_vte_primary_position_covid_pheno_non_hospitalised_pre_vaccination_reduced
- stata_cox_extended_ami_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_stroke_isch_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_dvt_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_pe_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_tia_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_stroke_sah_hs_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_hf_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_angina_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_ate_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_vte_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_ami_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_stroke_isch_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_dvt_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_pe_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_tia_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_hf_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_angina_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_ate_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
- stata_cox_extended_vte_primary_position_extended_follow_up_covid_pheno_hospitalised_pre_vaccination_reduced
outputs:
moderately_sensitive:
stata_output: output/stata_output.csv
format_R_output:
run: r:latest analysis/model/07_combine_HRs_to_one_file.R
needs:
- Analysis_cox_ami
- Analysis_cox_stroke_isch
- Analysis_cox_dvt
- Analysis_cox_pe
- Analysis_cox_tia
- Analysis_cox_stroke_sah_hs
- Analysis_cox_hf
- Analysis_cox_angina
- Analysis_cox_ami_extended_follow_up
- Analysis_cox_stroke_isch_extended_follow_up
- Analysis_cox_dvt_extended_follow_up
- Analysis_cox_pe_extended_follow_up
- Analysis_cox_tia_extended_follow_up
- Analysis_cox_stroke_sah_hs_extended_follow_up
- Analysis_cox_hf_extended_follow_up
- Analysis_cox_angina_extended_follow_up
- Analysis_cox_ate
- Analysis_cox_vte
- Analysis_cox_ate_extended_follow_up
- Analysis_cox_vte_extended_follow_up
- Analysis_cox_ami_primary_position
- Analysis_cox_stroke_isch_primary_position
- Analysis_cox_dvt_primary_position
- Analysis_cox_pe_primary_position
- Analysis_cox_tia_primary_position
- Analysis_cox_stroke_sah_hs_primary_position
- Analysis_cox_hf_primary_position
- Analysis_cox_angina_primary_position
- Analysis_cox_ami_primary_position_extended_follow_up
- Analysis_cox_stroke_isch_primary_position_extended_follow_up
- Analysis_cox_dvt_primary_position_extended_follow_up
- Analysis_cox_pe_primary_position_extended_follow_up
- Analysis_cox_tia_primary_position_extended_follow_up
- Analysis_cox_stroke_sah_hs_primary_position_extended_follow_up
- Analysis_cox_hf_primary_position_extended_follow_up
- Analysis_cox_angina_primary_position_extended_follow_up
- Analysis_cox_ate_primary_position
- Analysis_cox_vte_primary_position
- Analysis_cox_ate_primary_position_extended_follow_up
- Analysis_cox_vte_primary_position_extended_follow_up
outputs:
moderately_sensitive:
R_output: output/review/model/R_HR_output.csv
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:09:41
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Workspace
- post-covid-pre-vaccinated-cardiovascular
- Requested by
- Rochelle Knight
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 55e6808
- Requested actions
-
-
days_to_event_histogram
-