This page shows the technical details of what happened when authorised researcher Rochelle Knight requested one or more actions to be run against real patient data in the project, within a secure environment.
By cross-referencing the indicated Requested Actions with the
Pipeline section below, you can infer what
security level
various outputs were written to. Outputs marked as
highly_sensitive
can never be viewed directly by a researcher; they can only
request that code runs against them. Outputs marked as
moderately_sensitive
can be viewed by an approved researcher by logging into a highly
secure environment. Only outputs marked as
moderately_sensitive
can be requested for release to the public, via a controlled
output review service.
Jobs
-
- Job identifier:
-
gfpiuefc5iiemmxy
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 200000
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/metadates.R
outputs:
highly_sensitive:
study_dates_json: output/study_dates.json
vax_jcvi_groups: output/vax_jcvi_groups.csv
vax_eligible_dates: output/vax_eligible_dates.csv
generate_study_population_prelim:
run: cohortextractor:latest generate_cohort --study-definition study_definition_prelim
--output-format feather
needs:
- vax_eligibility_inputs
outputs:
highly_sensitive:
cohort: output/input_prelim.feather
generate_index_dates:
run: r:latest analysis/prelim.R
needs:
- vax_eligibility_inputs
- generate_study_population_prelim
outputs:
highly_sensitive:
index_dates: output/index_dates.csv
generate_study_population_prevax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax
--output-format feather
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_prevax.feather
generate_study_population_vax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vax
--output-format feather
needs:
- generate_index_dates
- vax_eligibility_inputs
outputs:
highly_sensitive:
cohort: output/input_vax.feather
generate_study_population_unvax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax
--output-format feather
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_unvax.feather
preprocess_data_prevax:
run: r:latest analysis/preprocess/preprocess_data.R prevax
needs:
- generate_index_dates
- generate_study_population_prelim
- generate_study_population_prevax
- generate_study_population_vax
- generate_study_population_unvax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_prevax_*.txt
highly_sensitive:
cohort: output/input_prevax.rds
venn: output/venn_prevax.rds
preprocess_data_vax:
run: r:latest analysis/preprocess/preprocess_data.R vax
needs:
- generate_index_dates
- generate_study_population_prelim
- generate_study_population_prevax
- generate_study_population_vax
- generate_study_population_unvax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_vax_*.txt
highly_sensitive:
cohort: output/input_vax.rds
venn: output/venn_vax.rds
preprocess_data_unvax:
run: r:latest analysis/preprocess/preprocess_data.R unvax
needs:
- generate_index_dates
- generate_study_population_prelim
- generate_study_population_prevax
- generate_study_population_vax
- generate_study_population_unvax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_unvax_*.txt
highly_sensitive:
cohort: output/input_unvax.rds
venn: output/venn_unvax.rds
stage1_data_cleaning_prevax:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R prevax
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- vax_eligibility_inputs
outputs:
moderately_sensitive:
refactoring: output/not-for-review/meta_data_factors_prevax.csv
QA_rules: output/review/descriptives/QA_summary_prevax_*.csv
IE_criteria: output/review/descriptives/Cohort_flow_prevax_*.csv
histograms: output/not-for-review/numeric_histograms_prevax_*.svg
highly_sensitive:
cohort: output/input_prevax_*.rds
cohort_csv: output/input_prevax_*.csv.gz
stage1_data_cleaning_vax:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R vax
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- vax_eligibility_inputs
outputs:
moderately_sensitive:
refactoring: output/not-for-review/meta_data_factors_vax.csv
QA_rules: output/review/descriptives/QA_summary_vax_*.csv
IE_criteria: output/review/descriptives/Cohort_flow_vax_*.csv
histograms: output/not-for-review/numeric_histograms_vax_*.svg
highly_sensitive:
cohort: output/input_vax_*.rds
cohort_csv: output/input_vax_*.csv.gz
stage1_data_cleaning_unvax:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R unvax
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- vax_eligibility_inputs
outputs:
moderately_sensitive:
refactoring: output/not-for-review/meta_data_factors_unvax.csv
QA_rules: output/review/descriptives/QA_summary_unvax_*.csv
IE_criteria: output/review/descriptives/Cohort_flow_unvax_*.csv
histograms: output/not-for-review/numeric_histograms_unvax_*.svg
highly_sensitive:
cohort: output/input_unvax_*.rds
cohort_csv: output/input_unvax_*.csv.gz
stage1_end_date_table_prevax:
run: r:latest analysis/preprocess/create_follow_up_end_date.R prevax
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- stage1_data_cleaning_prevax
- vax_eligibility_inputs
outputs:
highly_sensitive:
end_date_table: output/follow_up_end_dates_prevax_*.rds
end_date_table_csv: output/follow_up_end_dates_prevax_*.csv.gz
stage1_end_date_table_vax:
run: r:latest analysis/preprocess/create_follow_up_end_date.R vax
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- stage1_data_cleaning_vax
- vax_eligibility_inputs
outputs:
highly_sensitive:
end_date_table: output/follow_up_end_dates_vax_*.rds
end_date_table_csv: output/follow_up_end_dates_vax_*.csv.gz
stage1_end_date_table_unvax:
run: r:latest analysis/preprocess/create_follow_up_end_date.R unvax
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- stage1_data_cleaning_unvax
- vax_eligibility_inputs
outputs:
highly_sensitive:
end_date_table: output/follow_up_end_dates_unvax_*.rds
end_date_table_csv: output/follow_up_end_dates_unvax_*.csv.gz
generate_study_population_prevax_diabetes_analyis:
run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax_diabetes_analysis
--output-format feather
needs:
- vax_eligibility_inputs
- stage1_data_cleaning_prevax
- stage1_end_date_table_prevax
outputs:
highly_sensitive:
cohort: output/input_prevax_diabetes_analysis.feather
generate_study_population_vax_diabetes_analyis:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vax_diabetes_analysis
--output-format feather
needs:
- vax_eligibility_inputs
- stage1_data_cleaning_vax
- stage1_end_date_table_vax
outputs:
highly_sensitive:
cohort: output/input_vax_diabetes_analysis.feather
generate_study_population_unvax_diabetes_analyis:
run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax_diabetes_analysis
--output-format feather
needs:
- vax_eligibility_inputs
- stage1_data_cleaning_unvax
- stage1_end_date_table_unvax
outputs:
highly_sensitive:
cohort: output/input_unvax_diabetes_analysis.feather
diabetes_post_hoc_prevax:
run: r:latest analysis/descriptives/diabetes-follow-up-analysis.R prevax
needs:
- generate_study_population_prevax_diabetes_analyis
- generate_study_population_vax_diabetes_analyis
- generate_study_population_unvax_diabetes_analyis
- vax_eligibility_inputs
- stage1_data_cleaning_prevax
outputs:
moderately_sensitive:
res_table: output/review/descriptives/diabetes_posthoc_analysis_res_*_prevax.csv
histograms: output/review/descriptives/days_*_prevax.png
highly_sensitive:
cohort_new: output/input_prevax_stage1_diabetes.rds
diabetes_post_hoc_vax:
run: r:latest analysis/descriptives/diabetes-follow-up-analysis.R vax
needs:
- generate_study_population_prevax_diabetes_analyis
- generate_study_population_vax_diabetes_analyis
- generate_study_population_unvax_diabetes_analyis
- vax_eligibility_inputs
- stage1_data_cleaning_vax
outputs:
moderately_sensitive:
res_table: output/review/descriptives/diabetes_posthoc_analysis_res_*_vax.csv
histograms: output/review/descriptives/days_*_vax.png
highly_sensitive:
cohort_new: output/input_vax_stage1_diabetes.rds
diabetes_post_hoc_unvax:
run: r:latest analysis/descriptives/diabetes-follow-up-analysis.R unvax
needs:
- generate_study_population_prevax_diabetes_analyis
- generate_study_population_vax_diabetes_analyis
- generate_study_population_unvax_diabetes_analyis
- vax_eligibility_inputs
- stage1_data_cleaning_unvax
outputs:
moderately_sensitive:
res_table: output/review/descriptives/diabetes_posthoc_analysis_res_*_unvax.csv
histograms: output/review/descriptives/days_*_unvax.png
highly_sensitive:
cohort_new: output/input_unvax_stage1_diabetes.rds
diabetes_post_hoc_prevax_extended_follow_up:
run: r:latest analysis/descriptives/diabetes-follow-up-analysis-extended-follow-up.R
prevax
needs:
- generate_study_population_prevax_diabetes_analyis
- generate_study_population_vax_diabetes_analyis
- generate_study_population_unvax_diabetes_analyis
- vax_eligibility_inputs
- stage1_data_cleaning_prevax
outputs:
moderately_sensitive:
res_table: output/review/descriptives/diabetes_posthoc_analysis_res_EXTENDED_*_prevax.csv
stage2_missing_table1_all:
run: r:latest analysis/descriptives/Stage2_missing_table1.R all
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
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_prevax:
run: r:latest analysis/descriptives/diabetes_flowchart.R prevax
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
moderately_sensitive:
flow_df: output/review/figure-data/diabetes_flow_values_prevax_*.csv
stage3_diabetes_flow_vax:
run: r:latest analysis/descriptives/diabetes_flowchart.R vax
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
moderately_sensitive:
flow_df: output/review/figure-data/diabetes_flow_values_vax_*.csv
stage3_diabetes_flow_unvax:
run: r:latest analysis/descriptives/diabetes_flowchart.R unvax
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
moderately_sensitive:
flow_df: output/review/figure-data/diabetes_flow_values_unvax_*.csv
## Stage 4 - Table 2 - prevax cohort
stage4_table_2_prevax:
run: r:latest analysis/descriptives/table_2.R prevax
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
- diabetes_post_hoc_vax
- diabetes_post_hoc_unvax
- diabetes_post_hoc_prevax_extended_follow_up
outputs:
moderately_sensitive:
input_table_2: output/review/descriptives/table2_prevax_*.csv
## Stage 4 - Table 2 - vax cohort
stage4_table_2_vax:
run: r:latest analysis/descriptives/table_2.R vax
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_vax
- diabetes_post_hoc_prevax
- diabetes_post_hoc_vax
- diabetes_post_hoc_unvax
- diabetes_post_hoc_prevax_extended_follow_up
outputs:
moderately_sensitive:
input_table_2: output/review/descriptives/table2_vax_*.csv
## Stage 4 - Table 2 - unvax cohort
stage4_table_2_unvax:
run: r:latest analysis/descriptives/table_2.R unvax
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_unvax
- diabetes_post_hoc_prevax
- diabetes_post_hoc_vax
- diabetes_post_hoc_unvax
- diabetes_post_hoc_prevax_extended_follow_up
outputs:
moderately_sensitive:
input_table_2: output/review/descriptives/table2_unvax_*.csv
## Cox model for t1dm - prevax
Analysis_cox_t1dm_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t1dm prevax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t1dm_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t1dm_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t1dm_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t1dm_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t1dm_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t1dm_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t1dm_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t1dm_*_prevax_*_time_periods.csv
## Cox model for t1dm - vax
Analysis_cox_t1dm_vax:
run: r:latest analysis/model/01_cox_pipeline.R t1dm vax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_vax
- diabetes_post_hoc_vax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t1dm_vax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t1dm_vax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t1dm_vax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t1dm_vax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t1dm_vax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t1dm_*_vax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t1dm_*_vax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t1dm_*_vax_*_time_periods.csv
## Cox model for t1dm - unvax
Analysis_cox_t1dm_unvax:
run: r:latest analysis/model/01_cox_pipeline.R t1dm unvax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_unvax
- diabetes_post_hoc_unvax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t1dm_unvax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t1dm_unvax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t1dm_unvax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t1dm_unvax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t1dm_unvax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t1dm_*_unvax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t1dm_*_unvax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t1dm_*_unvax_*_time_periods.csv
## Cox model for t2dm - prevax
Analysis_cox_t2dm_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm prevax TRUE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_*_prevax_*_time_periods.csv
## Cox model for t2dm - vax
Analysis_cox_t2dm_vax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm vax TRUE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_vax
- diabetes_post_hoc_vax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_vax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_vax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_vax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_vax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_vax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_*_vax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_*_vax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_*_vax_*_time_periods.csv
## Cox model for t2dm - unvax
Analysis_cox_t2dm_unvax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm unvax TRUE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_unvax
- diabetes_post_hoc_unvax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_unvax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_unvax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_unvax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_unvax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_unvax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_*_unvax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_*_unvax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_*_unvax_*_time_periods.csv
## Cox model for t2dm_rec - prevax
Analysis_cox_t2dm_rec_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_rec prevax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_rec_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_rec_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_rec_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_rec_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_rec_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_rec_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_rec_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_rec_*_prevax_*_time_periods.csv
## Cox model for t2dm_pre_rec - prevax
Analysis_cox_t2dm_pre_rec_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_pre_rec prevax TRUE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pre_rec_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pre_rec_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pre_rec_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pre_rec_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_pre_rec_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_pre_rec_*_prevax_*_time_periods.csv
## Cox model for t2dm_pre_rec - vax
Analysis_cox_t2dm_pre_rec_vax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_pre_rec vax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_vax
- diabetes_post_hoc_vax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pre_rec_vax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_vax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_vax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pre_rec_vax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pre_rec_vax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pre_rec_*_vax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_pre_rec_*_vax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_pre_rec_*_vax_*_time_periods.csv
## Cox model for t2dm_pre_rec - unvax
Analysis_cox_t2dm_pre_rec_unvax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_pre_rec unvax TRUE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_unvax
- diabetes_post_hoc_unvax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pre_rec_unvax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_unvax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_unvax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pre_rec_unvax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pre_rec_unvax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pre_rec_*_unvax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_pre_rec_*_unvax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_pre_rec_*_unvax_*_time_periods.csv
## Cox model for t2dm_post_rec - prevax
Analysis_cox_t2dm_post_rec_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_post_rec prevax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_post_rec_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_post_rec_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_post_rec_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_post_rec_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_post_rec_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_post_rec_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_post_rec_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_post_rec_*_prevax_*_time_periods.csv
## Cox model for t2dm_follow - prevax
Analysis_cox_t2dm_follow_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_follow prevax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_follow_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_follow_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_follow_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_follow_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_follow_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_follow_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_follow_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_follow_*_prevax_*_time_periods.csv
## Cox model for t2dm_pd - prevax
Analysis_cox_t2dm_pd_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd prevax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_pd_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_pd_*_prevax_*_time_periods.csv
## Cox model for t2dm_pd - vax
Analysis_cox_t2dm_pd_vax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd vax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_vax
- diabetes_post_hoc_vax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_vax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_vax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_vax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_vax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_vax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_*_vax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_pd_*_vax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_pd_*_vax_*_time_periods.csv
## Cox model for t2dm_pd - unvax
Analysis_cox_t2dm_pd_unvax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd unvax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_unvax
- diabetes_post_hoc_unvax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_unvax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_unvax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_unvax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_unvax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_unvax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_*_unvax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_pd_*_unvax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_pd_*_unvax_*_time_periods.csv
## Cox model for t2dm_pd_no - prevax
Analysis_cox_t2dm_pd_no_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd_no prevax TRUE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_no_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_no_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_no_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_no_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_pd_no_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_pd_no_*_prevax_*_time_periods.csv
## Cox model for t2dm_pd_no - vax
Analysis_cox_t2dm_pd_no_vax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd_no vax TRUE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_vax
- diabetes_post_hoc_vax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_no_vax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_vax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_vax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_no_vax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_no_vax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_no_*_vax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_pd_no_*_vax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_pd_no_*_vax_*_time_periods.csv
## Cox model for t2dm_pd_no - unvax
Analysis_cox_t2dm_pd_no_unvax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd_no unvax TRUE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_unvax
- diabetes_post_hoc_unvax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_no_unvax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_unvax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_unvax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_no_unvax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_no_unvax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_no_*_unvax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_pd_no_*_unvax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_pd_no_*_unvax_*_time_periods.csv
## Cox model for t2dm_obes - prevax
Analysis_cox_t2dm_obes_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes prevax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_obes_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_obes_*_prevax_*_time_periods.csv
## Cox model for t2dm_obes - vax
Analysis_cox_t2dm_obes_vax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes vax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_vax
- diabetes_post_hoc_vax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_vax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_vax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_vax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_vax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_vax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_*_vax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_obes_*_vax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_obes_*_vax_*_time_periods.csv
## Cox model for t2dm_obes - unvax
Analysis_cox_t2dm_obes_unvax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes unvax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_unvax
- diabetes_post_hoc_unvax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_unvax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_unvax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_unvax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_unvax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_unvax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_*_unvax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_obes_*_unvax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_obes_*_unvax_*_time_periods.csv
## Cox model for t2dm_obes_no - prevax
Analysis_cox_t2dm_obes_no_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes_no prevax TRUE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_no_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_no_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_no_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_no_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_obes_no_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_obes_no_*_prevax_*_time_periods.csv
## Cox model for t2dm_obes_no - vax
Analysis_cox_t2dm_obes_no_vax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes_no vax TRUE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_vax
- diabetes_post_hoc_vax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_no_vax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_vax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_vax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_no_vax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_no_vax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_no_*_vax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_obes_no_*_vax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_obes_no_*_vax_*_time_periods.csv
## Cox model for t2dm_obes_no - unvax
Analysis_cox_t2dm_obes_no_unvax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes_no unvax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_unvax
- diabetes_post_hoc_unvax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_no_unvax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_unvax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_unvax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_no_unvax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_no_unvax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_no_*_unvax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_obes_no_*_unvax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_obes_no_*_unvax_*_time_periods.csv
## Cox model for otherdm - prevax
Analysis_cox_otherdm_prevax:
run: r:latest analysis/model/01_cox_pipeline.R otherdm prevax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_otherdm_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_otherdm_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_otherdm_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_otherdm_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_otherdm_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_otherdm_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_otherdm_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_otherdm_*_prevax_*_time_periods.csv
## Cox model for otherdm - vax
Analysis_cox_otherdm_vax:
run: r:latest analysis/model/01_cox_pipeline.R otherdm vax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_vax
- diabetes_post_hoc_vax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_otherdm_vax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_otherdm_vax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_otherdm_vax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_otherdm_vax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_otherdm_vax.csv
describe_data_surv: output/not-for-review/describe_data_surv_otherdm_*_vax_*_time_periods.txt
highly_sensitive:
dataset: output/input_otherdm_*_vax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_otherdm_*_vax_*_time_periods.csv
## Cox model for otherdm - unvax
Analysis_cox_otherdm_unvax:
run: r:latest analysis/model/01_cox_pipeline.R otherdm unvax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_unvax
- diabetes_post_hoc_unvax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_otherdm_unvax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_otherdm_unvax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_otherdm_unvax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_otherdm_unvax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_otherdm_unvax.csv
describe_data_surv: output/not-for-review/describe_data_surv_otherdm_*_unvax_*_time_periods.txt
highly_sensitive:
dataset: output/input_otherdm_*_unvax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_otherdm_*_unvax_*_time_periods.csv
## Cox model for gestationaldm - prevax
Analysis_cox_gestationaldm_prevax:
run: r:latest analysis/model/01_cox_pipeline.R gestationaldm prevax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_gestationaldm_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_gestationaldm_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_gestationaldm_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_gestationaldm_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_gestationaldm_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_gestationaldm_*_prevax_*_time_periods.csv
## Cox model for gestationaldm - vax
Analysis_cox_gestationaldm_vax:
run: r:latest analysis/model/01_cox_pipeline.R gestationaldm vax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_vax
- diabetes_post_hoc_vax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_gestationaldm_vax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_vax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_vax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_gestationaldm_vax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_gestationaldm_vax.csv
describe_data_surv: output/not-for-review/describe_data_surv_gestationaldm_*_vax_*_time_periods.txt
highly_sensitive:
dataset: output/input_gestationaldm_*_vax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_gestationaldm_*_vax_*_time_periods.csv
## Cox model for gestationaldm - unvax
Analysis_cox_gestationaldm_unvax:
run: r:latest analysis/model/01_cox_pipeline.R gestationaldm unvax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_unvax
- diabetes_post_hoc_unvax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_gestationaldm_unvax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_unvax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_unvax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_gestationaldm_unvax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_gestationaldm_unvax.csv
describe_data_surv: output/not-for-review/describe_data_surv_gestationaldm_*_unvax_*_time_periods.txt
highly_sensitive:
dataset: output/input_gestationaldm_*_unvax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_gestationaldm_*_unvax_*_time_periods.csv
## Cox model for t1dm_extended_follow_up - prevax
Analysis_cox_t1dm_extended_follow_up_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t1dm_extended_follow_up prevax
FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t1dm_extended_follow_up_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t1dm_extended_follow_up_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t1dm_extended_follow_up_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t1dm_extended_follow_up_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t1dm_extended_follow_up_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t1dm_extended_follow_up_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t1dm_extended_follow_up_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t1dm_extended_follow_up_*_prevax_*_time_periods.csv
## Cox model for t2dm_extended_follow_up - prevax
Analysis_cox_t2dm_extended_follow_up_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_extended_follow_up prevax
TRUE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_extended_follow_up_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_extended_follow_up_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_extended_follow_up_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_extended_follow_up_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_extended_follow_up_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_extended_follow_up_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_extended_follow_up_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_extended_follow_up_*_prevax_*_time_periods.csv
## Cox model for otherdm_extended_follow_up - prevax
Analysis_cox_otherdm_extended_follow_up_prevax:
run: r:latest analysis/model/01_cox_pipeline.R otherdm_extended_follow_up prevax
FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_otherdm_extended_follow_up_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_otherdm_extended_follow_up_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_otherdm_extended_follow_up_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_otherdm_extended_follow_up_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_otherdm_extended_follow_up_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_otherdm_extended_follow_up_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_otherdm_extended_follow_up_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_otherdm_extended_follow_up_*_prevax_*_time_periods.csv
## Cox model for gestationaldm_extended_follow_up - prevax
Analysis_cox_gestationaldm_extended_follow_up_prevax:
run: r:latest analysis/model/01_cox_pipeline.R gestationaldm_extended_follow_up
prevax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_gestationaldm_extended_follow_up_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_extended_follow_up_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_extended_follow_up_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_gestationaldm_extended_follow_up_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_gestationaldm_extended_follow_up_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_gestationaldm_extended_follow_up_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_gestationaldm_extended_follow_up_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_gestationaldm_extended_follow_up_*_prevax_*_time_periods.csv
## Cox model for t2dm_follow_extended_follow_up - prevax
Analysis_cox_t2dm_follow_extended_follow_up_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_follow_extended_follow_up
prevax TRUE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_follow_extended_follow_up_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_follow_extended_follow_up_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_follow_extended_follow_up_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_follow_extended_follow_up_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_follow_extended_follow_up_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_follow_extended_follow_up_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_follow_extended_follow_up_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_follow_extended_follow_up_*_prevax_*_time_periods.csv
## Cox model for t2dm_pd_extended_follow_up - prevax
Analysis_cox_t2dm_pd_extended_follow_up_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd_extended_follow_up prevax
FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_extended_follow_up_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_extended_follow_up_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_extended_follow_up_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_extended_follow_up_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_extended_follow_up_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_extended_follow_up_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_pd_extended_follow_up_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_pd_extended_follow_up_*_prevax_*_time_periods.csv
## Cox model for t2dm_pd_no_extended_follow_up - prevax
Analysis_cox_t2dm_pd_no_extended_follow_up_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd_no_extended_follow_up prevax
FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_no_extended_follow_up_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_extended_follow_up_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_extended_follow_up_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_no_extended_follow_up_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_no_extended_follow_up_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_no_extended_follow_up_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_pd_no_extended_follow_up_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_pd_no_extended_follow_up_*_prevax_*_time_periods.csv
## Cox model for t2dm_obes_extended_follow_up - prevax
Analysis_cox_t2dm_obes_extended_follow_up_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes_extended_follow_up prevax
FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_extended_follow_up_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_extended_follow_up_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_extended_follow_up_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_extended_follow_up_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_extended_follow_up_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_extended_follow_up_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_obes_extended_follow_up_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_obes_extended_follow_up_*_prevax_*_time_periods.csv
## Cox model for t2dm_obes_no_extended_follow_up - prevax
Analysis_cox_t2dm_obes_no_extended_follow_up_prevax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes_no_extended_follow_up
prevax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_prevax
- diabetes_post_hoc_prevax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_no_extended_follow_up_prevax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_extended_follow_up_prevax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_extended_follow_up_prevax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_no_extended_follow_up_prevax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_no_extended_follow_up_prevax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_no_extended_follow_up_*_prevax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_obes_no_extended_follow_up_*_prevax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_obes_no_extended_follow_up_*_prevax_*_time_periods.csv
## Cox model for t2dm_unvax_sens - unvax
Analysis_cox_t2dm_unvax_sens_unvax:
run: r:latest analysis/model/01_cox_pipeline.R t2dm_unvax_sens unvax TRUE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_unvax
- diabetes_post_hoc_unvax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t2dm_unvax_sens_unvax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_unvax_sens_unvax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_unvax_sens_unvax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_unvax_sens_unvax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_unvax_sens_unvax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t2dm_unvax_sens_*_unvax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t2dm_unvax_sens_*_unvax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t2dm_unvax_sens_*_unvax_*_time_periods.csv
## Cox model for t1dm_unvax_sens - unvax
Analysis_cox_t1dm_unvax_sens_unvax:
run: r:latest analysis/model/01_cox_pipeline.R t1dm_unvax_sens unvax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_unvax
- diabetes_post_hoc_unvax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_t1dm_unvax_sens_unvax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t1dm_unvax_sens_unvax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t1dm_unvax_sens_unvax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t1dm_unvax_sens_unvax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t1dm_unvax_sens_unvax.csv
describe_data_surv: output/not-for-review/describe_data_surv_t1dm_unvax_sens_*_unvax_*_time_periods.txt
highly_sensitive:
dataset: output/input_t1dm_unvax_sens_*_unvax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_t1dm_unvax_sens_*_unvax_*_time_periods.csv
## Cox model for otherdm_unvax_sens - unvax
Analysis_cox_otherdm_unvax_sens_unvax:
run: r:latest analysis/model/01_cox_pipeline.R otherdm_unvax_sens unvax FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_unvax
- diabetes_post_hoc_unvax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_otherdm_unvax_sens_unvax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_otherdm_unvax_sens_unvax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_otherdm_unvax_sens_unvax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_otherdm_unvax_sens_unvax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_otherdm_unvax_sens_unvax.csv
describe_data_surv: output/not-for-review/describe_data_surv_otherdm_unvax_sens_*_unvax_*_time_periods.txt
highly_sensitive:
dataset: output/input_otherdm_unvax_sens_*_unvax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_otherdm_unvax_sens_*_unvax_*_time_periods.csv
## Cox model for gestationaldm_unvax_sens - unvax
Analysis_cox_gestationaldm_unvax_sens_unvax:
run: r:latest analysis/model/01_cox_pipeline.R gestationaldm_unvax_sens unvax
FALSE
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
- stage1_end_date_table_unvax
- diabetes_post_hoc_unvax
outputs:
moderately_sensitive:
analyses_not_run: output/review/model/*/analyses_not_run_gestationaldm_unvax_sens_unvax.csv
compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_unvax_sens_unvax.csv
compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_unvax_sens_unvax_to_release.csv
compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_gestationaldm_unvax_sens_unvax.csv
compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_gestationaldm_unvax_sens_unvax.csv
describe_data_surv: output/not-for-review/describe_data_surv_gestationaldm_unvax_sens_*_unvax_*_time_periods.txt
highly_sensitive:
dataset: output/input_gestationaldm_unvax_sens_*_unvax_*_time_periods.csv
sampled_dataset: output/input_sampled_data_gestationaldm_unvax_sens_*_unvax_*_time_periods.csv
stata_cox_model_t2dm_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_covid_pheno_hospitalised_vax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_vax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_vax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_vax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_vax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_covid_pheno_hospitalised_unvax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_unvax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_main_prevax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_prevax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_main_vax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_vax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_vax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_main_vax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_main_vax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_main_unvax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_unvax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_unvax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_main_unvax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_main_unvax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_covid_pheno_non_hospitalised_vax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_vax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_covid_pheno_non_hospitalised_unvax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_unvax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_follow_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_follow_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_follow_main_prevax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_main_prevax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_follow_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_follow_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_follow_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_follow_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_follow_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_rec_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_pre_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_pre_rec_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_post_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_post_rec_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_rec_main_prevax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_rec_main_prevax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_rec_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_rec_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_rec_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_pre_rec_main_prevax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_pre_rec_main_prevax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_pre_rec_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_pre_rec_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_pre_rec_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_post_rec_main_prevax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_post_rec_main_prevax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_post_rec_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_post_rec_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_post_rec_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_extended_follow_up_main_prevax_reduced_time_periods
TRUE TRUE
needs:
- Analysis_cox_t2dm_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
stata_output: output/input_sampled_data_t2dm_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt
stata_cox_model_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0TRUE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods
TRUE TRUE
needs:
- Analysis_cox_t2dm_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
stata_output: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt
stata_cox_model_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0TRUE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods
TRUE TRUE
needs:
- Analysis_cox_t2dm_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
stata_output: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt
stata_cox_model_t2dm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_extended_follow_up_main_prevax_reduced_time_periods
FALSE TRUE
needs:
- Analysis_cox_t2dm_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
stata_output: output/input_sampled_data_t2dm_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt
stata_cox_model_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods
FALSE TRUE
needs:
- Analysis_cox_t2dm_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
stata_output: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt
stata_cox_model_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods
FALSE TRUE
needs:
- Analysis_cox_t2dm_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
stata_output: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt
stata_cox_model_t2dm_follow_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_extended_follow_up_main_prevax_reduced_time_periods
TRUE TRUE
needs:
- Analysis_cox_t2dm_follow_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_follow_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
stata_output: output/input_sampled_data_t2dm_follow_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt
stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0TRUE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods
TRUE TRUE
needs:
- Analysis_cox_t2dm_follow_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
stata_output: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt
stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0TRUE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods
TRUE TRUE
needs:
- Analysis_cox_t2dm_follow_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
stata_output: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt
stata_cox_model_t2dm_follow_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_extended_follow_up_main_prevax_reduced_time_periods
FALSE TRUE
needs:
- Analysis_cox_t2dm_follow_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_follow_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
stata_output: output/input_sampled_data_t2dm_follow_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt
stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods
FALSE TRUE
needs:
- Analysis_cox_t2dm_follow_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
stata_output: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt
stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods
FALSE TRUE
needs:
- Analysis_cox_t2dm_follow_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
stata_output: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt
stata_cox_model_t1dm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t1dm_extended_follow_up_main_prevax_reduced_time_periods
TRUE TRUE
needs:
- Analysis_cox_t1dm_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t1dm_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
stata_output: output/input_sampled_data_t1dm_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt
stata_cox_model_otherdm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_otherdm_extended_follow_up_main_prevax_reduced_time_periods
TRUE TRUE
needs:
- Analysis_cox_otherdm_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_otherdm_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
stata_output: output/input_sampled_data_otherdm_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt
stata_cox_model_gestationaldm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_gestationaldm_extended_follow_up_main_prevax_reduced_time_periods
TRUE TRUE
needs:
- Analysis_cox_gestationaldm_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_gestationaldm_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
stata_output: output/input_sampled_data_gestationaldm_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt
stata_cox_model_t1dm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t1dm_extended_follow_up_main_prevax_reduced_time_periods
FALSE TRUE
needs:
- Analysis_cox_t1dm_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t1dm_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
stata_output: output/input_sampled_data_t1dm_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt
stata_cox_model_otherdm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_otherdm_extended_follow_up_main_prevax_reduced_time_periods
FALSE TRUE
needs:
- Analysis_cox_otherdm_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_otherdm_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
stata_output: output/input_sampled_data_otherdm_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt
stata_cox_model_gestationaldm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_gestationaldm_extended_follow_up_main_prevax_reduced_time_periods
FALSE TRUE
needs:
- Analysis_cox_gestationaldm_extended_follow_up_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_gestationaldm_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
stata_output: output/input_sampled_data_gestationaldm_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt
stata_cox_model_t2dm_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_covid_pheno_hospitalised_vax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_vax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_vax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_vax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_vax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_covid_pheno_hospitalised_unvax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_unvax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_main_prevax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_prevax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_main_vax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_vax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_vax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_main_vax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_main_vax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_main_unvax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_unvax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_unvax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_main_unvax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_main_unvax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_covid_pheno_non_hospitalised_vax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_vax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_covid_pheno_non_hospitalised_unvax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_unvax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_follow_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_follow_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_follow_main_prevax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_main_prevax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_follow_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_follow_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_follow_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_follow_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_follow_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_rec_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_pre_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_pre_rec_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_post_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_post_rec_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_rec_main_prevax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_rec_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_rec_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_rec_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_pre_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_pre_rec_main_prevax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_pre_rec_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_pre_rec_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_pre_rec_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_post_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_post_rec_main_prevax_day_zero_reduced_time_periods
TRUE FALSE
needs:
- Analysis_cox_t2dm_post_rec_prevax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_post_rec_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_post_rec_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt
stata_cox_model_t2dm_unvax_sens_covid_pheno_hospitalised_unvax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_unvax_sens_covid_pheno_hospitalised_unvax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_unvax_sens_unvax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_unvax_sens_covid_pheno_hospitalised_unvax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_unvax_sens_covid_pheno_hospitalised_unvax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_unvax_sens_main_unvax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_unvax_sens_main_unvax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_unvax_sens_unvax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_unvax_sens_main_unvax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_unvax_sens_main_unvax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
stata_cox_model_t2dm_unvax_sens_covid_pheno_non_hospitalised_unvax_reduced_day0FALSE_extfFALSE:
run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_unvax_sens_covid_pheno_non_hospitalised_unvax_reduced_time_periods
FALSE FALSE
needs:
- Analysis_cox_t2dm_unvax_sens_unvax
outputs:
moderately_sensitive:
medianfup: output/input_sampled_data_t2dm_unvax_sens_covid_pheno_non_hospitalised_unvax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
stata_output: output/input_sampled_data_t2dm_unvax_sens_covid_pheno_non_hospitalised_unvax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt
format_stata_output:
run: r:latest analysis/format_stata_output.R
needs:
- stata_cox_model_t2dm_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_hospitalised_vax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_hospitalised_unvax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_main_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_main_vax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_main_unvax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_non_hospitalised_vax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_non_hospitalised_unvax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_follow_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_follow_main_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_follow_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_pre_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_post_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_rec_main_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_pre_rec_main_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_post_rec_main_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_t2dm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_t2dm_follow_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_t2dm_follow_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_t1dm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_otherdm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_gestationaldm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_t1dm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_otherdm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_gestationaldm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_t2dm_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_hospitalised_vax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_hospitalised_unvax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_main_vax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_main_unvax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_non_hospitalised_vax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_non_hospitalised_unvax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_follow_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_follow_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_follow_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_pre_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_post_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_pre_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_post_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_unvax_sens_covid_pheno_hospitalised_unvax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_unvax_sens_main_unvax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_unvax_sens_covid_pheno_non_hospitalised_unvax_reduced_day0FALSE_extfFALSE
outputs:
moderately_sensitive:
stata_output: output/stata_output.csv
format_stata_output_new:
run: r:latest analysis/mediantte_and_events.R
needs:
- stata_cox_model_t2dm_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_hospitalised_vax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_hospitalised_unvax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_main_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_main_vax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_main_unvax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_non_hospitalised_vax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_non_hospitalised_unvax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_follow_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_follow_main_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_follow_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_pre_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_post_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_rec_main_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_pre_rec_main_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_post_rec_main_prevax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_t2dm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_t2dm_follow_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_t2dm_follow_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_t1dm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_otherdm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_gestationaldm_extended_follow_up_main_prevax_reduced_day0TRUE_extfTRUE
- stata_cox_model_t1dm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_otherdm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_gestationaldm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE
- stata_cox_model_t2dm_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_hospitalised_vax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_hospitalised_unvax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_main_vax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_main_unvax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_non_hospitalised_vax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_covid_pheno_non_hospitalised_unvax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_follow_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_follow_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_follow_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_pre_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_post_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_pre_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_post_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
- stata_cox_model_t2dm_unvax_sens_covid_pheno_hospitalised_unvax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_unvax_sens_main_unvax_reduced_day0FALSE_extfFALSE
- stata_cox_model_t2dm_unvax_sens_covid_pheno_non_hospitalised_unvax_reduced_day0FALSE_extfFALSE
outputs:
moderately_sensitive:
stata_output: output/mediantte_and_events.csv
format_hazard_ratios:
run: r:latest analysis/model/format_hazard_ratio_outputs.R
needs:
- format_stata_output
- stage4_table_2_prevax
- stage4_table_2_vax
- stage4_table_2_unvax
- Analysis_cox_t1dm_prevax
- Analysis_cox_t1dm_vax
- Analysis_cox_t1dm_unvax
- Analysis_cox_t2dm_prevax
- Analysis_cox_t2dm_vax
- Analysis_cox_t2dm_unvax
- Analysis_cox_t2dm_pre_rec_prevax
- Analysis_cox_t2dm_pre_rec_vax
- Analysis_cox_t2dm_pre_rec_unvax
- Analysis_cox_t2dm_pd_prevax
- Analysis_cox_t2dm_pd_vax
- Analysis_cox_t2dm_pd_unvax
- Analysis_cox_t2dm_pd_no_prevax
- Analysis_cox_t2dm_pd_no_vax
- Analysis_cox_t2dm_pd_no_unvax
- Analysis_cox_t2dm_obes_prevax
- Analysis_cox_t2dm_obes_vax
- Analysis_cox_t2dm_obes_unvax
- Analysis_cox_t2dm_obes_no_prevax
- Analysis_cox_t2dm_obes_no_vax
- Analysis_cox_t2dm_obes_no_unvax
- Analysis_cox_otherdm_prevax
- Analysis_cox_otherdm_vax
- Analysis_cox_otherdm_unvax
- Analysis_cox_gestationaldm_prevax
- Analysis_cox_gestationaldm_vax
- Analysis_cox_gestationaldm_unvax
- Analysis_cox_t2dm_rec_prevax
- Analysis_cox_t2dm_post_rec_prevax
- Analysis_cox_t2dm_follow_prevax
- Analysis_cox_t1dm_extended_follow_up_prevax
- Analysis_cox_t2dm_extended_follow_up_prevax
- Analysis_cox_otherdm_extended_follow_up_prevax
- Analysis_cox_gestationaldm_extended_follow_up_prevax
- Analysis_cox_t2dm_follow_extended_follow_up_prevax
- Analysis_cox_t2dm_pd_extended_follow_up_prevax
- Analysis_cox_t2dm_pd_no_extended_follow_up_prevax
- Analysis_cox_t2dm_obes_extended_follow_up_prevax
- Analysis_cox_t2dm_obes_no_extended_follow_up_prevax
- Analysis_cox_t2dm_unvax_sens_unvax
- Analysis_cox_t1dm_unvax_sens_unvax
- Analysis_cox_otherdm_unvax_sens_unvax
- Analysis_cox_gestationaldm_unvax_sens_unvax
outputs:
moderately_sensitive:
hr_output: output/review/model/hr_output_formatted.csv
hr_output_no_events: output/review/model/hr_output_formatted_no_event_counts.csv
table2_output: output/review/model/table2_output_formatted_no_hrs.csv
R_event_counts: output/review/model/R_event_count_output.csv
R_event_counts_day_zero: output/review/model/R_event_count_day_zero_output.csv
check_table2_matches_cox_event_counts:
run: r:latest analysis/descriptives/check_table2_matches_cox_event_counts.R
needs:
- stage4_table_2_prevax
- stage4_table_2_vax
- stage4_table_2_unvax
- Analysis_cox_t1dm_prevax
- Analysis_cox_t1dm_vax
- Analysis_cox_t1dm_unvax
- Analysis_cox_t2dm_prevax
- Analysis_cox_t2dm_vax
- Analysis_cox_t2dm_unvax
- Analysis_cox_t2dm_rec_prevax
- Analysis_cox_t2dm_pre_rec_prevax
- Analysis_cox_t2dm_pre_rec_vax
- Analysis_cox_t2dm_pre_rec_unvax
- Analysis_cox_t2dm_post_rec_prevax
- Analysis_cox_t2dm_follow_prevax
- Analysis_cox_t2dm_pd_prevax
- Analysis_cox_t2dm_pd_vax
- Analysis_cox_t2dm_pd_unvax
- Analysis_cox_t2dm_pd_no_prevax
- Analysis_cox_t2dm_pd_no_vax
- Analysis_cox_t2dm_pd_no_unvax
- Analysis_cox_t2dm_obes_prevax
- Analysis_cox_t2dm_obes_vax
- Analysis_cox_t2dm_obes_unvax
- Analysis_cox_t2dm_obes_no_prevax
- Analysis_cox_t2dm_obes_no_vax
- Analysis_cox_t2dm_obes_no_unvax
- Analysis_cox_otherdm_prevax
- Analysis_cox_otherdm_vax
- Analysis_cox_otherdm_unvax
- Analysis_cox_gestationaldm_prevax
- Analysis_cox_gestationaldm_vax
- Analysis_cox_gestationaldm_unvax
- Analysis_cox_t1dm_extended_follow_up_prevax
- Analysis_cox_t2dm_extended_follow_up_prevax
- Analysis_cox_otherdm_extended_follow_up_prevax
- Analysis_cox_gestationaldm_extended_follow_up_prevax
- Analysis_cox_t2dm_follow_extended_follow_up_prevax
- Analysis_cox_t2dm_pd_extended_follow_up_prevax
- Analysis_cox_t2dm_pd_no_extended_follow_up_prevax
- Analysis_cox_t2dm_obes_extended_follow_up_prevax
- Analysis_cox_t2dm_obes_no_extended_follow_up_prevax
- Analysis_cox_t2dm_unvax_sens_unvax
- Analysis_cox_t1dm_unvax_sens_unvax
- Analysis_cox_otherdm_unvax_sens_unvax
- Analysis_cox_gestationaldm_unvax_sens_unvax
outputs:
moderately_sensitive:
check_table2_cox_event_counts: output/not-for-review/descriptives/table2_cox_model_event_counts_comparison.csv
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:01:00
These timestamps are generated and stored using the UTC timezone on the backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- post-covid-diabetes
- Requested by
- Rochelle Knight
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- dc11eae
- Requested actions
-
-
format_stata_output
-