generated from opensafely/research-template
/
project.yaml
2557 lines (2315 loc) · 170 KB
/
project.yaml
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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_original_follow_up_any_position_events:
run: r:latest analysis/descriptives/table_2.R original_follow_up any_position
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
table_2: output/review/descriptives/table2_pre_vaccination_original_follow_up_any_position_events.csv
table_2_extended_follow_up_any_position_events:
run: r:latest analysis/descriptives/table_2.R extended_follow_up any_position
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
table_2: output/review/descriptives/table2_pre_vaccination_extended_follow_up_any_position_events.csv
table_2_original_follow_up_primary_position_events:
run: r:latest analysis/descriptives/table_2.R original_follow_up primary_position
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
table_2: output/review/descriptives/table2_pre_vaccination_original_follow_up_primary_position_events.csv
table_2_extended_follow_up_primary_position_events:
run: r:latest analysis/descriptives/table_2.R extended_follow_up primary_position
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
table_2: output/review/descriptives/table2_pre_vaccination_extended_follow_up_primary_position_events.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_original_follow_up:
run: r:latest analysis/descriptives/histogram_data_post_exposure_days_to_event.R
original_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
histogram_data: output/review/descriptives/histogram_data_pre_vaccination_original_follow_up.csv
days_to_event_histogram_extended_follow_up:
run: r:latest analysis/descriptives/histogram_data_post_exposure_days_to_event.R
extended_follow_up
needs:
- stage1_data_cleaning
- stage1_end_date_table
outputs:
moderately_sensitive:
histogram_data: output/review/descriptives/histogram_data_pre_vaccination_extended_follow_up.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_day0_FALSE_extf_FALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_ami
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_day0_FALSE_extf_FALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
FALSE FALSE
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_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_day0_FALSE_extf_FALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_dvt
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_pe_covid_pheno_hospitalised_pre_vaccination_reduced_day0_FALSE_extf_FALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_pe
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_tia_covid_pheno_hospitalised_pre_vaccination_reduced_day0_FALSE_extf_FALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_tia
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_day0_FALSE_extf_FALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
FALSE FALSE
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_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_hf_covid_pheno_hospitalised_pre_vaccination_reduced_day0_FALSE_extf_FALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_hf
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_angina_covid_pheno_hospitalised_pre_vaccination_reduced_day0_FALSE_extf_FALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_angina
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_ate_covid_pheno_hospitalised_pre_vaccination_reduced_day0_FALSE_extf_FALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_ate
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_vte_covid_pheno_hospitalised_pre_vaccination_reduced_day0_FALSE_extf_FALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_vte
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt