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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 10000
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
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## Generate vaccination eligibility information
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 dummy data for study_definition - population_prelim
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 dates for all study cohorts
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 dummy data for study_definition - prevax
generate_study_population_prevax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax
--output-format csv.gz
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_prevax.csv.gz
## Generate dummy data for study_definition - vax
generate_study_population_vax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vax
--output-format csv.gz
needs:
- generate_index_dates
- vax_eligibility_inputs
outputs:
highly_sensitive:
cohort: output/input_vax.csv.gz
## Generate dummy data for study_definition - unvax
generate_study_population_unvax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax
--output-format csv.gz
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_unvax.csv.gz
## Preprocess data -prevax
preprocess_data_prevax:
run: r:latest analysis/preprocess/preprocess_data.R prevax
needs:
- generate_index_dates
- generate_study_population_prevax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_prevax_stage0.txt
describe_venn: output/not-for-review/describe_venn_prevax.txt
highly_sensitive:
cohort: output/input_prevax.rds
venn: output/venn_prevax.rds
## Preprocess data - vax
preprocess_data_vax:
run: r:latest analysis/preprocess/preprocess_data.R vax
needs:
- generate_index_dates
- generate_study_population_vax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_vax_stage0.txt
descrive_venn: output/not-for-review/describe_venn_vax.txt
highly_sensitive:
cohort: output/input_vax.rds
venn: output/venn_vax.rds
## Preprocess data -unvax
preprocess_data_unvax:
run: r:latest analysis/preprocess/preprocess_data.R unvax
needs:
- generate_index_dates
- generate_study_population_unvax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_unvax_stage0.txt
describe_venn: output/not-for-review/describe_venn_unvax.txt
highly_sensitive:
cohort: output/input_unvax.rds
venn: output/venn_unvax.rds
## Stage 1 - Data cleaning - all cohorts
stage1_data_cleaning_all:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R all
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- vax_eligibility_inputs
outputs:
moderately_sensitive:
refactoring: output/not-for-review/meta_data_factors_*.csv
QA_rules: output/review/descriptives/QA_summary_*.csv
IE_criteria: output/review/descriptives/Cohort_flow_*.csv
histograms: output/not-for-review/numeric_histograms_*.svg
highly_sensitive:
cohort: output/input_*.rds
describe_file-input_prevax_stage1:
run: r:latest analysis/describe_file.R input_prevax_stage1 rds
needs:
- stage1_data_cleaning_all
outputs:
moderately_sensitive:
describe_model_input: output/describe-input_prevax_stage1.txt
describe_file-input_vax_stage1:
run: r:latest analysis/describe_file.R input_vax_stage1 rds
needs:
- stage1_data_cleaning_all
outputs:
moderately_sensitive:
describe_model_input: output/describe-input_vax_stage1.txt
describe_file-input_unvax_stage1:
run: r:latest analysis/describe_file.R input_unvax_stage1 rds
needs:
- stage1_data_cleaning_all
outputs:
moderately_sensitive:
describe_model_input: output/describe-input_unvax_stage1.txt
## Stage 5 - Run models
make_model_input-cohort_prevax-main-asthma-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-asthma-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-asthma-no_preexisting.rds
cox_ipw-cohort_prevax-main-asthma-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_prevax-main-asthma-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
--total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
--age_spline=TRUE --df_output=model_output-cohort_prevax-main-asthma-no_preexisting.csv
needs:
- make_model_input-cohort_prevax-main-asthma-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-asthma-no_preexisting.csv
make_model_input-cohort_prevax-main-copd-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-copd-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-copd-no_preexisting.rds
cox_ipw-cohort_prevax-main-copd-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_prevax-main-copd-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
--total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
--age_spline=TRUE --df_output=model_output-cohort_prevax-main-copd-no_preexisting.csv
needs:
- make_model_input-cohort_prevax-main-copd-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-copd-no_preexisting.csv
make_model_input-cohort_prevax-main-pneumonia-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-pneumonia-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-pneumonia-no_preexisting.rds
cox_ipw-cohort_prevax-main-pneumonia-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_prevax-main-pneumonia-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
--total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
--age_spline=TRUE --df_output=model_output-cohort_prevax-main-pneumonia-no_preexisting.csv
needs:
- make_model_input-cohort_prevax-main-pneumonia-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-pneumonia-no_preexisting.csv
make_model_input-cohort_prevax-main-pneumonia-preexisting:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-pneumonia-preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-pneumonia-preexisting.rds
cox_ipw-cohort_prevax-main-pneumonia-preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_prevax-main-pneumonia-preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
--total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
--age_spline=TRUE --df_output=model_output-cohort_prevax-main-pneumonia-preexisting.csv
needs:
- make_model_input-cohort_prevax-main-pneumonia-preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-pneumonia-preexisting.csv
make_model_input-cohort_prevax-main-pulmonary_fibrosis-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-pulmonary_fibrosis-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-pulmonary_fibrosis-no_preexisting.rds
cox_ipw-cohort_prevax-main-pulmonary_fibrosis-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_prevax-main-pulmonary_fibrosis-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
--total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
--age_spline=TRUE --df_output=model_output-cohort_prevax-main-pulmonary_fibrosis-no_preexisting.csv
needs:
- make_model_input-cohort_prevax-main-pulmonary_fibrosis-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-pulmonary_fibrosis-no_preexisting.csv
make_model_input-cohort_prevax-main-pulmonary_fibrosis-preexisting:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-pulmonary_fibrosis-preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-pulmonary_fibrosis-preexisting.rds
cox_ipw-cohort_prevax-main-pulmonary_fibrosis-preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_prevax-main-pulmonary_fibrosis-preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
--total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
--age_spline=TRUE --df_output=model_output-cohort_prevax-main-pulmonary_fibrosis-preexisting.csv
needs:
- make_model_input-cohort_prevax-main-pulmonary_fibrosis-preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-pulmonary_fibrosis-preexisting.csv
make_model_input-cohort_unvax-main-asthma-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-asthma-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-asthma-no_preexisting.rds
cox_ipw-cohort_unvax-main-asthma-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_unvax-main-asthma-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-asthma-no_preexisting.csv
needs:
- make_model_input-cohort_unvax-main-asthma-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-asthma-no_preexisting.csv
make_model_input-cohort_unvax-main-copd-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-copd-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-copd-no_preexisting.rds
cox_ipw-cohort_unvax-main-copd-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_unvax-main-copd-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-copd-no_preexisting.csv
needs:
- make_model_input-cohort_unvax-main-copd-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-copd-no_preexisting.csv
make_model_input-cohort_unvax-main-pneumonia-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-pneumonia-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-pneumonia-no_preexisting.rds
cox_ipw-cohort_unvax-main-pneumonia-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_unvax-main-pneumonia-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-pneumonia-no_preexisting.csv
needs:
- make_model_input-cohort_unvax-main-pneumonia-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-pneumonia-no_preexisting.csv
make_model_input-cohort_unvax-main-pneumonia-preexisting:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-pneumonia-preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-pneumonia-preexisting.rds
cox_ipw-cohort_unvax-main-pneumonia-preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_unvax-main-pneumonia-preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-pneumonia-preexisting.csv
needs:
- make_model_input-cohort_unvax-main-pneumonia-preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-pneumonia-preexisting.csv
make_model_input-cohort_unvax-main-pulmonary_fibrosis-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-pulmonary_fibrosis-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-pulmonary_fibrosis-no_preexisting.rds
cox_ipw-cohort_unvax-main-pulmonary_fibrosis-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_unvax-main-pulmonary_fibrosis-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-pulmonary_fibrosis-no_preexisting.csv
needs:
- make_model_input-cohort_unvax-main-pulmonary_fibrosis-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-pulmonary_fibrosis-no_preexisting.csv
make_model_input-cohort_unvax-main-pulmonary_fibrosis-preexisting:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-pulmonary_fibrosis-preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-pulmonary_fibrosis-preexisting.rds
cox_ipw-cohort_unvax-main-pulmonary_fibrosis-preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_unvax-main-pulmonary_fibrosis-preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-pulmonary_fibrosis-preexisting.csv
needs:
- make_model_input-cohort_unvax-main-pulmonary_fibrosis-preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-pulmonary_fibrosis-preexisting.csv
make_model_input-cohort_vax-main-asthma-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-asthma-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-asthma-no_preexisting.rds
cox_ipw-cohort_vax-main-asthma-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_vax-main-asthma-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-asthma-no_preexisting.csv
needs:
- make_model_input-cohort_vax-main-asthma-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-asthma-no_preexisting.csv
make_model_input-cohort_vax-main-copd-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-copd-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-copd-no_preexisting.rds
cox_ipw-cohort_vax-main-copd-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_vax-main-copd-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-copd-no_preexisting.csv
needs:
- make_model_input-cohort_vax-main-copd-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-copd-no_preexisting.csv
make_model_input-cohort_vax-main-pneumonia-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-pneumonia-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-pneumonia-no_preexisting.rds
cox_ipw-cohort_vax-main-pneumonia-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_vax-main-pneumonia-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-pneumonia-no_preexisting.csv
needs:
- make_model_input-cohort_vax-main-pneumonia-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-pneumonia-no_preexisting.csv
make_model_input-cohort_vax-main-pneumonia-preexisting:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-pneumonia-preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-pneumonia-preexisting.rds
cox_ipw-cohort_vax-main-pneumonia-preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_vax-main-pneumonia-preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-pneumonia-preexisting.csv
needs:
- make_model_input-cohort_vax-main-pneumonia-preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-pneumonia-preexisting.csv
make_model_input-cohort_vax-main-pulmonary_fibrosis-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-pulmonary_fibrosis-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-pulmonary_fibrosis-no_preexisting.rds
cox_ipw-cohort_vax-main-pulmonary_fibrosis-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_vax-main-pulmonary_fibrosis-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-pulmonary_fibrosis-no_preexisting.csv
needs:
- make_model_input-cohort_vax-main-pulmonary_fibrosis-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-pulmonary_fibrosis-no_preexisting.csv
make_model_input-cohort_vax-main-pulmonary_fibrosis-preexisting:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-pulmonary_fibrosis-preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-pulmonary_fibrosis-preexisting.rds
cox_ipw-cohort_vax-main-pulmonary_fibrosis-preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_vax-main-pulmonary_fibrosis-preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-pulmonary_fibrosis-preexisting.csv
needs:
- make_model_input-cohort_vax-main-pulmonary_fibrosis-preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-pulmonary_fibrosis-preexisting.csv
make_model_input-cohort_prevax-sub_age_18_39-asthma-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-asthma-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-asthma-no_preexisting.rds
cox_ipw-cohort_prevax-sub_age_18_39-asthma-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_prevax-sub_age_18_39-asthma-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
--total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
--age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-asthma-no_preexisting.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-asthma-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-asthma-no_preexisting.csv
make_model_input-cohort_prevax-sub_age_18_39-copd-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-copd-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-copd-no_preexisting.rds
cox_ipw-cohort_prevax-sub_age_18_39-copd-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_prevax-sub_age_18_39-copd-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
--total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
--age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-copd-no_preexisting.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-copd-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-copd-no_preexisting.csv
make_model_input-cohort_prevax-sub_age_18_39-pneumonia-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-pneumonia-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-pneumonia-no_preexisting.rds
cox_ipw-cohort_prevax-sub_age_18_39-pneumonia-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_prevax-sub_age_18_39-pneumonia-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
--total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
--age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-pneumonia-no_preexisting.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-pneumonia-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-pneumonia-no_preexisting.csv
make_model_input-cohort_prevax-sub_age_18_39-pneumonia-preexisting:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-pneumonia-preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-pneumonia-preexisting.rds
cox_ipw-cohort_prevax-sub_age_18_39-pneumonia-preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_prevax-sub_age_18_39-pneumonia-preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
--total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
--age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-pneumonia-preexisting.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-pneumonia-preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-pneumonia-preexisting.csv
make_model_input-cohort_prevax-sub_age_18_39-pulmonary_fibrosis-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-pulmonary_fibrosis-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-pulmonary_fibrosis-no_preexisting.rds
cox_ipw-cohort_prevax-sub_age_18_39-pulmonary_fibrosis-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_prevax-sub_age_18_39-pulmonary_fibrosis-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
--total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
--age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-pulmonary_fibrosis-no_preexisting.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-pulmonary_fibrosis-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-pulmonary_fibrosis-no_preexisting.csv
make_model_input-cohort_prevax-sub_age_18_39-pulmonary_fibrosis-preexisting:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-pulmonary_fibrosis-preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-pulmonary_fibrosis-preexisting.rds
cox_ipw-cohort_prevax-sub_age_18_39-pulmonary_fibrosis-preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_prevax-sub_age_18_39-pulmonary_fibrosis-preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
--total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
--age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-pulmonary_fibrosis-preexisting.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-pulmonary_fibrosis-preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-pulmonary_fibrosis-preexisting.csv
make_model_input-cohort_unvax-sub_age_18_39-asthma-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-asthma-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-asthma-no_preexisting.rds
cox_ipw-cohort_unvax-sub_age_18_39-asthma-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_unvax-sub_age_18_39-asthma-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-asthma-no_preexisting.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-asthma-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-asthma-no_preexisting.csv
make_model_input-cohort_unvax-sub_age_18_39-copd-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-copd-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-copd-no_preexisting.rds
cox_ipw-cohort_unvax-sub_age_18_39-copd-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_unvax-sub_age_18_39-copd-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-copd-no_preexisting.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-copd-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-copd-no_preexisting.csv
make_model_input-cohort_unvax-sub_age_18_39-pneumonia-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-pneumonia-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-pneumonia-no_preexisting.rds
cox_ipw-cohort_unvax-sub_age_18_39-pneumonia-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_unvax-sub_age_18_39-pneumonia-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-pneumonia-no_preexisting.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-pneumonia-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-pneumonia-no_preexisting.csv
make_model_input-cohort_unvax-sub_age_18_39-pneumonia-preexisting:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-pneumonia-preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-pneumonia-preexisting.rds
cox_ipw-cohort_unvax-sub_age_18_39-pneumonia-preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_unvax-sub_age_18_39-pneumonia-preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-pneumonia-preexisting.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-pneumonia-preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-pneumonia-preexisting.csv
make_model_input-cohort_unvax-sub_age_18_39-pulmonary_fibrosis-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-pulmonary_fibrosis-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-pulmonary_fibrosis-no_preexisting.rds
cox_ipw-cohort_unvax-sub_age_18_39-pulmonary_fibrosis-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_unvax-sub_age_18_39-pulmonary_fibrosis-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-pulmonary_fibrosis-no_preexisting.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-pulmonary_fibrosis-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-pulmonary_fibrosis-no_preexisting.csv
make_model_input-cohort_unvax-sub_age_18_39-pulmonary_fibrosis-preexisting:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-pulmonary_fibrosis-preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-pulmonary_fibrosis-preexisting.rds
cox_ipw-cohort_unvax-sub_age_18_39-pulmonary_fibrosis-preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_unvax-sub_age_18_39-pulmonary_fibrosis-preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-pulmonary_fibrosis-preexisting.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-pulmonary_fibrosis-preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-pulmonary_fibrosis-preexisting.csv
make_model_input-cohort_vax-sub_age_18_39-asthma-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-asthma-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-asthma-no_preexisting.rds
cox_ipw-cohort_vax-sub_age_18_39-asthma-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_vax-sub_age_18_39-asthma-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-asthma-no_preexisting.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-asthma-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-asthma-no_preexisting.csv
make_model_input-cohort_vax-sub_age_18_39-copd-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-copd-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-copd-no_preexisting.rds
cox_ipw-cohort_vax-sub_age_18_39-copd-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_vax-sub_age_18_39-copd-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-copd-no_preexisting.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-copd-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-copd-no_preexisting.csv
make_model_input-cohort_vax-sub_age_18_39-pneumonia-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-pneumonia-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-pneumonia-no_preexisting.rds
cox_ipw-cohort_vax-sub_age_18_39-pneumonia-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_vax-sub_age_18_39-pneumonia-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-pneumonia-no_preexisting.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-pneumonia-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-pneumonia-no_preexisting.csv
make_model_input-cohort_vax-sub_age_18_39-pneumonia-preexisting:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-pneumonia-preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-pneumonia-preexisting.rds
cox_ipw-cohort_vax-sub_age_18_39-pneumonia-preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_vax-sub_age_18_39-pneumonia-preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-pneumonia-preexisting.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-pneumonia-preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-pneumonia-preexisting.csv
make_model_input-cohort_vax-sub_age_18_39-pulmonary_fibrosis-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-pulmonary_fibrosis-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-pulmonary_fibrosis-no_preexisting.rds
cox_ipw-cohort_vax-sub_age_18_39-pulmonary_fibrosis-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_vax-sub_age_18_39-pulmonary_fibrosis-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-pulmonary_fibrosis-no_preexisting.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-pulmonary_fibrosis-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-pulmonary_fibrosis-no_preexisting.csv
make_model_input-cohort_vax-sub_age_18_39-pulmonary_fibrosis-preexisting:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-pulmonary_fibrosis-preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-pulmonary_fibrosis-preexisting.rds
cox_ipw-cohort_vax-sub_age_18_39-pulmonary_fibrosis-preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_vax-sub_age_18_39-pulmonary_fibrosis-preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;28;197 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-pulmonary_fibrosis-preexisting.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-pulmonary_fibrosis-preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-pulmonary_fibrosis-preexisting.csv
make_model_input-cohort_prevax-sub_age_40_59-asthma-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-asthma-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_40_59-asthma-no_preexisting.rds
cox_ipw-cohort_prevax-sub_age_40_59-asthma-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_prevax-sub_age_40_59-asthma-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
--total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
--age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-asthma-no_preexisting.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-asthma-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-asthma-no_preexisting.csv
make_model_input-cohort_prevax-sub_age_40_59-copd-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-copd-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_40_59-copd-no_preexisting.rds
cox_ipw-cohort_prevax-sub_age_40_59-copd-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_prevax-sub_age_40_59-copd-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
--total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
--age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-copd-no_preexisting.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-copd-no_preexisting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-copd-no_preexisting.csv
make_model_input-cohort_prevax-sub_age_40_59-pneumonia-no_preexisting:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-pneumonia-no_preexisting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_40_59-pneumonia-no_preexisting.rds
cox_ipw-cohort_prevax-sub_age_40_59-pneumonia-no_preexisting:
run: cox-ipw:v0.0.21 --df_input=model_input-cohort_prevax-sub_age_40_59-pneumonia-no_preexisting.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_obesity;cov_bin_history_pneumonia_snomed;cov_bin_history_asthma_snomed;cov_bin_history_pulmonary_fibrosis_snomed;cov_bin_ami;cov_bin_all_stroke;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;28;197;365;714 --controls_per_case=20
--total_event_threshold=50 --episode_event_threshold=5 --covariate_threshold=5
--age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-pneumonia-no_preexisting.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-pneumonia-no_preexisting