Job request: 9997
- Organisation:
- University of Bristol
- Workspace:
- post-covid-vaccinated
- ID:
- njczhkryistecqf4
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
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- Job identifier:
-
h67tz4uf6qmoykxu
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- Job identifier:
-
6bglkvocjfuroeh4
-
- Job identifier:
-
nd3qiown2lzm4ps2
-
- Job identifier:
-
24dcrjvyapxzlwjs
-
- Job identifier:
-
j7m5rooqyj6qbi4j
-
- Job identifier:
-
4qpevo6mnmf27g53
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- Job identifier:
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bnrczw4uprnhivfj
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_electively_unvaccinated:
run: cohortextractor:latest generate_cohort --study-definition study_definition_electively_unvaccinated
--output-format feather
needs:
- vax_eligibility_inputs
outputs:
highly_sensitive:
cohort: output/input_electively_unvaccinated.feather
generate_study_population_vaccinated:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccinated
--output-format feather
outputs:
highly_sensitive:
cohort: output/input_vaccinated.feather
generate_study_population_index:
run: cohortextractor:latest generate_cohort --study-definition study_definition_index
--output-format feather
outputs:
highly_sensitive:
cohort: output/input_index.feather
preprocess_data_vaccinated:
run: r:latest analysis/preprocess/preprocess_data.R vaccinated
needs:
- generate_study_population_index
- generate_study_population_vaccinated
- generate_study_population_electively_unvaccinated
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_vaccinated_*.txt
describe_index: output/not-for-review/describe_tmp_index_vaccinated.txt
describe_cohort: output/not-for-review/describe_tmp_vaccinated.txt
descrive_venn: output/not-for-review/describe_venn_vaccinated.txt
highly_sensitive:
cohort: output/input_vaccinated.rds
venn: output/venn_vaccinated.rds
preprocess_data_electively_unvaccinated:
run: r:latest analysis/preprocess/preprocess_data.R electively_unvaccinated
needs:
- generate_study_population_index
- generate_study_population_vaccinated
- generate_study_population_electively_unvaccinated
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_electively_unvaccinated_*.txt
describe_index: output/not-for-review/describe_tmp_index_electively_unvaccinated.txt
describe_cohort: output/not-for-review/describe_tmp_electively_unvaccinated.txt
descrive_venn: output/not-for-review/describe_venn_electively_unvaccinated.txt
highly_sensitive:
cohort: output/input_electively_unvaccinated.rds
venn: output/venn_electively_unvaccinated.rds
stage1_data_cleaning_both:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R both
needs:
- preprocess_data_vaccinated
- preprocess_data_electively_unvaccinated
outputs:
moderately_sensitive:
refactoring: output/not-for-review/meta_data_factors_*.csv
QA_rules: output/review/descriptives/QA_summary_*.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_vaccinated:
run: r:latest analysis/preprocess/create_follow_up_end_date.R vaccinated
needs:
- preprocess_data_vaccinated
- preprocess_data_electively_unvaccinated
- stage1_data_cleaning_both
outputs:
highly_sensitive:
end_date_table: output/follow_up_end_dates_vaccinated.rds
stage1_end_date_table_electively_unvaccinated:
run: r:latest analysis/preprocess/create_follow_up_end_date.R electively_unvaccinated
needs:
- preprocess_data_vaccinated
- preprocess_data_electively_unvaccinated
- stage1_data_cleaning_both
outputs:
highly_sensitive:
end_date_table: output/follow_up_end_dates_electively_unvaccinated.rds
stage2_missing_table1_both:
run: r:latest analysis/descriptives/Stage2_missing_table1.R both
needs:
- stage1_data_cleaning_both
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_*.csv
stage3_diabetes_flow_vaccinated:
run: r:latest analysis/descriptives/diabetes_flowchart.R vaccinated
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
flow_df: output/review/figure-data/diabetes_flow_values_vaccinated.csv
stage3_diabetes_flow_electively_unvaccinated:
run: r:latest analysis/descriptives/diabetes_flowchart.R electively_unvaccinated
needs:
- stage1_data_cleaning_both
outputs:
moderately_sensitive:
flow_df: output/review/figure-data/diabetes_flow_values_electively_unvaccinated.csv
## Stage 4 - Table 2 - vaccinated cohort
stage4_table_2_vaccinated:
run: r:latest analysis/descriptives/table_2.R vaccinated
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
outputs:
moderately_sensitive:
input_table_2: output/review/descriptives/table2_vaccinated.csv
## Stage 4 - Table 2 - electively_unvaccinated cohort
stage4_table_2_electively_unvaccinated:
run: r:latest analysis/descriptives/table_2.R electively_unvaccinated
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
outputs:
moderately_sensitive:
input_table_2: output/review/descriptives/table2_electively_unvaccinated.csv
stage4_venn_diagram_both:
run: r:latest analysis/descriptives/venn_diagram.R both
needs:
- preprocess_data_vaccinated
- preprocess_data_electively_unvaccinated
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- stage1_end_date_table_electively_unvaccinated
outputs:
moderately_sensitive:
venn_diagram: output/review/venn-diagrams/venn_diagram_*
reusableaction_input:
run: r:latest analysis/reusableaction_input.R ami vaccinated
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
outputs:
highly_sensitive:
cohort: output/reusableaction_input_*
reusableaction_model:
run: cox-ipw:v0.0.4 --df_input=reusableaction_input_vaccinated_ami.csv --outcome=out_date_ami
--covariate_other=cov_num_consulation_rate;cov_bin_healthcare_worker;cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_lipid_medications;cov_bin_antiplatelet_medications;cov_bin_anticoagulation_medications;cov_bin_combined_oral_contraceptive_pill;cov_bin_hormone_replacement_therapy;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease
--covariate_protect=cov_cat_sex;cov_num_age;cov_cat_region --cox_start=index_date
--cox_stop=follow_up_end --controls_per_case=20 --df_output=results_vaccinated_hospitalised_ami.csv
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- reusableaction_input
outputs:
moderately_sensitive:
arguments: output/args-results_vaccinated_hospitalised_ami.csv
estimates: output/results_vaccinated_hospitalised_ami.csv
## Cox model for ami - vaccinated
Analysis_cox_ami_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R ami vaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ami_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_ami_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for ami - electively_unvaccinated
Analysis_cox_ami_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R ami electively_unvaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ami_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_ami_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for stroke_isch - vaccinated
Analysis_cox_stroke_isch_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R stroke_isch vaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_isch_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for stroke_isch - electively_unvaccinated
Analysis_cox_stroke_isch_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R stroke_isch electively_unvaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_isch_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for dvt - vaccinated
Analysis_cox_dvt_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R dvt vaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_dvt_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_dvt_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for dvt - electively_unvaccinated
Analysis_cox_dvt_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R dvt electively_unvaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_dvt_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_dvt_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for pe - vaccinated
Analysis_cox_pe_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R pe vaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_pe_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_pe_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for pe - electively_unvaccinated
Analysis_cox_pe_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R pe electively_unvaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_pe_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_pe_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for tia - vaccinated
Analysis_cox_tia_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R tia vaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_tia_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_tia_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for tia - electively_unvaccinated
Analysis_cox_tia_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R tia electively_unvaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_tia_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_tia_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for stroke_sah_hs - vaccinated
Analysis_cox_stroke_sah_hs_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs vaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for stroke_sah_hs - electively_unvaccinated
Analysis_cox_stroke_sah_hs_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs electively_unvaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for hf - vaccinated
Analysis_cox_hf_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R hf vaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_hf_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_hf_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for hf - electively_unvaccinated
Analysis_cox_hf_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R hf electively_unvaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_hf_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_hf_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for angina - vaccinated
Analysis_cox_angina_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R angina vaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_angina_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_angina_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for angina - electively_unvaccinated
Analysis_cox_angina_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R angina electively_unvaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_angina_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_angina_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for ate - vaccinated
Analysis_cox_ate_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R ate vaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ate_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_ate_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for ate - electively_unvaccinated
Analysis_cox_ate_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R ate electively_unvaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ate_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_ate_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for vte - vaccinated
Analysis_cox_vte_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R vte vaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_vte_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_vte_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for vte - electively_unvaccinated
Analysis_cox_vte_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R vte electively_unvaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_vte_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_vte_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for ami_primary_position - vaccinated
Analysis_cox_ami_primary_position_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R ami_primary_position vaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ami_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_primary_position_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_primary_position_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_primary_position_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_ami_primary_position_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for ami_primary_position - electively_unvaccinated
Analysis_cox_ami_primary_position_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R ami_primary_position electively_unvaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ami_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_primary_position_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_primary_position_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_ami_primary_position_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for stroke_isch_primary_position - vaccinated
Analysis_cox_stroke_isch_primary_position_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_primary_position vaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_isch_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_primary_position_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_primary_position_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_primary_position_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for stroke_isch_primary_position - electively_unvaccinated
Analysis_cox_stroke_isch_primary_position_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_primary_position electively_unvaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_isch_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_primary_position_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_primary_position_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for dvt_primary_position - vaccinated
Analysis_cox_dvt_primary_position_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R dvt_primary_position vaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_dvt_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_primary_position_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_primary_position_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_dvt_primary_position_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for dvt_primary_position - electively_unvaccinated
Analysis_cox_dvt_primary_position_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R dvt_primary_position electively_unvaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_dvt_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_primary_position_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_dvt_primary_position_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for pe_primary_position - vaccinated
Analysis_cox_pe_primary_position_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R pe_primary_position vaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_pe_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_primary_position_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_primary_position_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_primary_position_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_pe_primary_position_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for pe_primary_position - electively_unvaccinated
Analysis_cox_pe_primary_position_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R pe_primary_position electively_unvaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_pe_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_primary_position_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_primary_position_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_pe_primary_position_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for tia_primary_position - vaccinated
Analysis_cox_tia_primary_position_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R tia_primary_position vaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_tia_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_primary_position_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_primary_position_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_primary_position_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_tia_primary_position_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for tia_primary_position - electively_unvaccinated
Analysis_cox_tia_primary_position_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R tia_primary_position electively_unvaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_tia_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_primary_position_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_primary_position_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_tia_primary_position_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for stroke_sah_hs_primary_position - vaccinated
Analysis_cox_stroke_sah_hs_primary_position_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_primary_position
vaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_primary_position_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_primary_position_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_primary_position_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for stroke_sah_hs_primary_position - electively_unvaccinated
Analysis_cox_stroke_sah_hs_primary_position_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_primary_position
electively_unvaccinated normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_primary_position_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_primary_position_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for hf_primary_position - vaccinated
Analysis_cox_hf_primary_position_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R hf_primary_position vaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_hf_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_primary_position_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_primary_position_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_primary_position_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_hf_primary_position_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for hf_primary_position - electively_unvaccinated
Analysis_cox_hf_primary_position_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R hf_primary_position electively_unvaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_hf_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_primary_position_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_primary_position_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_hf_primary_position_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for angina_primary_position - vaccinated
Analysis_cox_angina_primary_position_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R angina_primary_position vaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_angina_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_primary_position_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_primary_position_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_primary_position_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_angina_primary_position_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for angina_primary_position - electively_unvaccinated
Analysis_cox_angina_primary_position_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R angina_primary_position electively_unvaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_angina_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_primary_position_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_primary_position_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_angina_primary_position_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for ate_primary_position - vaccinated
Analysis_cox_ate_primary_position_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R ate_primary_position vaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ate_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_primary_position_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_primary_position_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_primary_position_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_ate_primary_position_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for ate_primary_position - electively_unvaccinated
Analysis_cox_ate_primary_position_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R ate_primary_position electively_unvaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ate_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_primary_position_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_primary_position_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_ate_primary_position_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model for vte_primary_position - vaccinated
Analysis_cox_vte_primary_position_vaccinated:
run: r:latest analysis/model/01_cox_pipeline.R vte_primary_position vaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_vte_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_primary_position_vaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_primary_position_vaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_primary_position_vaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_primary_position_vaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_vte_primary_position_*_vaccinated_*_covariate_testing_normal.txt
## Cox model for vte_primary_position - electively_unvaccinated
Analysis_cox_vte_primary_position_electively_unvaccinated:
run: r:latest analysis/model/01_cox_pipeline.R vte_primary_position electively_unvaccinated
normal
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_vte_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_primary_position_electively_unvaccinated_covariate_testing_normal_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_primary_position_electively_unvaccinated_covariate_testing_normal.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_primary_position_electively_unvaccinated_covariate_testing_normal.csv
describe_data_surv: output/not-for-review/describe_data_surv_vte_primary_position_*_electively_unvaccinated_*_covariate_testing_normal.txt
## Cox model ami - vaccinated, covariate_testing
Analysis_cox_ami_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R ami vaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ami_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_ami_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model ami - electively_unvaccinated, covariate_testing
Analysis_cox_ami_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R ami electively_unvaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ami_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_ami_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model stroke_isch - vaccinated, covariate_testing
Analysis_cox_stroke_isch_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R stroke_isch vaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_isch_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model stroke_isch - electively_unvaccinated, covariate_testing
Analysis_cox_stroke_isch_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R stroke_isch electively_unvaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_isch_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model dvt - vaccinated, covariate_testing
Analysis_cox_dvt_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R dvt vaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_dvt_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_dvt_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model dvt - electively_unvaccinated, covariate_testing
Analysis_cox_dvt_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R dvt electively_unvaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_dvt_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_dvt_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model pe - vaccinated, covariate_testing
Analysis_cox_pe_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R pe vaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_pe_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_pe_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model pe - electively_unvaccinated, covariate_testing
Analysis_cox_pe_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R pe electively_unvaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_pe_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_pe_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model tia - vaccinated, covariate_testing
Analysis_cox_tia_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R tia vaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_tia_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_tia_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model tia - electively_unvaccinated, covariate_testing
Analysis_cox_tia_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R tia electively_unvaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_tia_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_tia_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model stroke_sah_hs - vaccinated, covariate_testing
Analysis_cox_stroke_sah_hs_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs vaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model stroke_sah_hs - electively_unvaccinated, covariate_testing
Analysis_cox_stroke_sah_hs_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs electively_unvaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model hf - vaccinated, covariate_testing
Analysis_cox_hf_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R hf vaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_hf_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_hf_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model hf - electively_unvaccinated, covariate_testing
Analysis_cox_hf_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R hf electively_unvaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_hf_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_hf_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model angina - vaccinated, covariate_testing
Analysis_cox_angina_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R angina vaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_angina_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_angina_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model angina - electively_unvaccinated, covariate_testing
Analysis_cox_angina_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R angina electively_unvaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_angina_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_angina_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model ate - vaccinated, covariate_testing
Analysis_cox_ate_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R ate vaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ate_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_ate_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model ate - electively_unvaccinated, covariate_testing
Analysis_cox_ate_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R ate electively_unvaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ate_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_ate_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model vte - vaccinated, covariate_testing
Analysis_cox_vte_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R vte vaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_vte_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_vte_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model vte - electively_unvaccinated, covariate_testing
Analysis_cox_vte_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R vte electively_unvaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_vte_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_vte_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model ami_primary_position - vaccinated, covariate_testing
Analysis_cox_ami_primary_position_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R ami_primary_position vaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ami_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_primary_position_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_primary_position_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_ami_primary_position_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model ami_primary_position - electively_unvaccinated, covariate_testing
Analysis_cox_ami_primary_position_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R ami_primary_position electively_unvaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ami_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_primary_position_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_ami_primary_position_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model stroke_isch_primary_position - vaccinated, covariate_testing
Analysis_cox_stroke_isch_primary_position_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_primary_position vaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_isch_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_primary_position_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_primary_position_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model stroke_isch_primary_position - electively_unvaccinated, covariate_testing
Analysis_cox_stroke_isch_primary_position_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_primary_position electively_unvaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_isch_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_primary_position_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model dvt_primary_position - vaccinated, covariate_testing
Analysis_cox_dvt_primary_position_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R dvt_primary_position vaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_dvt_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_primary_position_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_dvt_primary_position_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model dvt_primary_position - electively_unvaccinated, covariate_testing
Analysis_cox_dvt_primary_position_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R dvt_primary_position electively_unvaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_dvt_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_dvt_primary_position_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model pe_primary_position - vaccinated, covariate_testing
Analysis_cox_pe_primary_position_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R pe_primary_position vaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_pe_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_primary_position_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_primary_position_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_pe_primary_position_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model pe_primary_position - electively_unvaccinated, covariate_testing
Analysis_cox_pe_primary_position_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R pe_primary_position electively_unvaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_pe_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_primary_position_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_pe_primary_position_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model tia_primary_position - vaccinated, covariate_testing
Analysis_cox_tia_primary_position_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R tia_primary_position vaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_tia_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_primary_position_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_primary_position_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_tia_primary_position_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model tia_primary_position - electively_unvaccinated, covariate_testing
Analysis_cox_tia_primary_position_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R tia_primary_position electively_unvaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_tia_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_primary_position_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_tia_primary_position_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model stroke_sah_hs_primary_position - vaccinated, covariate_testing
Analysis_cox_stroke_sah_hs_primary_position_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_primary_position
vaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_primary_position_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_primary_position_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model stroke_sah_hs_primary_position - electively_unvaccinated, covariate_testing
Analysis_cox_stroke_sah_hs_primary_position_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_primary_position
electively_unvaccinated test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_primary_position_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model hf_primary_position - vaccinated, covariate_testing
Analysis_cox_hf_primary_position_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R hf_primary_position vaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_hf_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_primary_position_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_primary_position_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_hf_primary_position_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model hf_primary_position - electively_unvaccinated, covariate_testing
Analysis_cox_hf_primary_position_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R hf_primary_position electively_unvaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_hf_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_primary_position_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_hf_primary_position_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model angina_primary_position - vaccinated, covariate_testing
Analysis_cox_angina_primary_position_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R angina_primary_position vaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_angina_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_primary_position_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_primary_position_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_angina_primary_position_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model angina_primary_position - electively_unvaccinated, covariate_testing
Analysis_cox_angina_primary_position_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R angina_primary_position electively_unvaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_angina_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_primary_position_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_angina_primary_position_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model ate_primary_position - vaccinated, covariate_testing
Analysis_cox_ate_primary_position_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R ate_primary_position vaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ate_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_primary_position_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_primary_position_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_ate_primary_position_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model ate_primary_position - electively_unvaccinated, covariate_testing
Analysis_cox_ate_primary_position_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R ate_primary_position electively_unvaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_ate_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_primary_position_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_ate_primary_position_*_electively_unvaccinated_*_covariate_testing_test_all.txt
## Cox model vte_primary_position - vaccinated, covariate_testing
Analysis_cox_vte_primary_position_vaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R vte_primary_position vaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_vte_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_primary_position_vaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_primary_position_vaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_primary_position_vaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_vte_primary_position_*_vaccinated_*_covariate_testing_test_all.txt
## Cox model vte_primary_position - electively_unvaccinated, covariate_testing
Analysis_cox_vte_primary_position_electively_unvaccinated_covariate_testing:
run: r:latest analysis/model/01_cox_pipeline.R vte_primary_position electively_unvaccinated
test_all
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
- select_covariates_for_hosp_covid
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/analyses_not_run_vte_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_primary_position_electively_unvaccinated_covariate_testing_test_all_to_release.csv
compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_primary_position_electively_unvaccinated_covariate_testing_test_all.csv
describe_data_surv: output/not-for-review/describe_data_surv_vte_primary_position_*_electively_unvaccinated_*_covariate_testing_test_all.txt
split_hosp_covid_by_region_vaccinated:
run: r:latest analysis/descriptives/hospitalised_covid_events_by_region.R vaccinated
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
outputs:
moderately_sensitive:
hosp_events_by_region_non_suppressed: output/not-for-review/hospitalised_covid_event_counts_by_region_vaccinated_non_suppressed.csv
hosp_events_by_region_suppressed: output/not-for-review/hospitalised_covid_event_counts_by_region_vaccinated_suppressed.csv
split_hosp_covid_by_region_electively_unvaccinated:
run: r:latest analysis/descriptives/hospitalised_covid_events_by_region.R electively_unvaccinated
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
outputs:
moderately_sensitive:
hosp_events_by_region_non_suppressed: output/not-for-review/hospitalised_covid_event_counts_by_region_electively_unvaccinated_non_suppressed.csv
hosp_events_by_region_suppressed: output/not-for-review/hospitalised_covid_event_counts_by_region_electively_unvaccinated_suppressed.csv
## Hospitalised event counts by covariate - vaccinated
hosp_event_counts_by_covariate_level_vaccinated:
run: r:latest analysis/descriptives/hospitalised_events_split_by_time_period_and_covariate_level.R
vaccinated
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_vaccinated
outputs:
moderately_sensitive:
hosp_counts_by_covariate: output/not-for-review/hospitalised_event_counts_by_covariate_level_vaccinated.csv
## Hospitalised event counts by covariate - electively_unvaccinated
hosp_event_counts_by_covariate_level_electively_unvaccinated:
run: r:latest analysis/descriptives/hospitalised_events_split_by_time_period_and_covariate_level.R
electively_unvaccinated
needs:
- stage1_data_cleaning_both
- stage1_end_date_table_electively_unvaccinated
outputs:
moderately_sensitive:
hosp_counts_by_covariate: output/not-for-review/hospitalised_event_counts_by_covariate_level_electively_unvaccinated.csv
select_covariates_for_hosp_covid:
run: r:latest analysis/descriptives/determine_covariates_for_hosp_covid.R both
needs:
- hosp_event_counts_by_covariate_level_vaccinated
- hosp_event_counts_by_covariate_level_electively_unvaccinated
outputs:
moderately_sensitive:
covariates_for_hosp_covid_vacc: output/not-for-review/covariates_to_adjust_for_hosp_covid_vaccinated.csv
covariates_for_hosp_covid_electively_unvacc: output/not-for-review/covariates_to_adjust_for_hosp_covid_electively_unvaccinated.csv
Timeline
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Created:
-
Started:
-
Finished:
-
Runtime: 06:17:49
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- post-covid-vaccinated
- Requested by
- Rochelle Knight
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 1feddf6
- Requested actions
-
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Analysis_cox_ami_electively_unvaccinated
-
Analysis_cox_stroke_isch_electively_unvaccinated
-
Analysis_cox_dvt_electively_unvaccinated
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Analysis_cox_hf_electively_unvaccinated
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Analysis_cox_angina_electively_unvaccinated
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Analysis_cox_ate_electively_unvaccinated
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Analysis_cox_vte_electively_unvaccinated
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