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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
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
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 csv.gz
needs:
- vax_eligibility_inputs
outputs:
highly_sensitive:
cohort: output/input_prelim.csv.gz
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.gz
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_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_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:
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:
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:
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
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
## Stage 4a - Venn diagrams prevax
stage4_venn_diagram_prevax:
run: r:latest analysis/descriptives/venn_diagram.R prevax
needs:
- preprocess_data_prevax
- make_model_input-cohort_prevax-main-
- make_model_input-cohort_prevax-main-abdominal_distension
- make_model_input-cohort_prevax-main-abdominal_paindiscomfort
- make_model_input-cohort_prevax-main-acute_pancreatitis
- make_model_input-cohort_prevax-main-appendicitis
- make_model_input-cohort_prevax-main-belching
- make_model_input-cohort_prevax-main-bloody_stools
- make_model_input-cohort_prevax-main-bowel_ischaemia
- make_model_input-cohort_prevax-main-diarrhoea
- make_model_input-cohort_prevax-main-dyspepsia
- make_model_input-cohort_prevax-main-gallstones_disease
- make_model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease
- make_model_input-cohort_prevax-main-ibs
- make_model_input-cohort_prevax-main-intestinal_obstruction
- make_model_input-cohort_prevax-main-lower_gi_bleeding
- make_model_input-cohort_prevax-main-nausea
- make_model_input-cohort_prevax-main-nonalcoholic_steatohepatitis
- make_model_input-cohort_prevax-main-nonvariceal_gi_bleeding
- make_model_input-cohort_prevax-main-peptic_ulcer
- make_model_input-cohort_prevax-main-upper_gi_bleeding
- make_model_input-cohort_prevax-main-variceal_gi_bleeding
- make_model_input-cohort_prevax-main-vomiting
outputs:
moderately_sensitive:
venn_diagram: output/review/venn-diagrams/venn_diagram_number_check_prevax.csv
## Stage 4b - Venn diagrams vax
stage4_venn_diagram_vax:
run: r:latest analysis/descriptives/venn_diagram.R vax
needs:
- preprocess_data_vax
- make_model_input-cohort_vax-main-
- make_model_input-cohort_vax-main-abdominal_distension
- make_model_input-cohort_vax-main-abdominal_paindiscomfort
- make_model_input-cohort_vax-main-acute_pancreatitis
- make_model_input-cohort_vax-main-appendicitis
- make_model_input-cohort_vax-main-belching
- make_model_input-cohort_vax-main-bloody_stools
- make_model_input-cohort_vax-main-bowel_ischaemia
- make_model_input-cohort_vax-main-diarrhoea
- make_model_input-cohort_vax-main-dyspepsia
- make_model_input-cohort_vax-main-gallstones_disease
- make_model_input-cohort_vax-main-gastro_oesophageal_reflux_disease
- make_model_input-cohort_vax-main-ibs
- make_model_input-cohort_vax-main-intestinal_obstruction
- make_model_input-cohort_vax-main-lower_gi_bleeding
- make_model_input-cohort_vax-main-nausea
- make_model_input-cohort_vax-main-nonalcoholic_steatohepatitis
- make_model_input-cohort_vax-main-nonvariceal_gi_bleeding
- make_model_input-cohort_vax-main-peptic_ulcer
- make_model_input-cohort_vax-main-upper_gi_bleeding
- make_model_input-cohort_vax-main-variceal_gi_bleeding
- make_model_input-cohort_vax-main-vomiting
outputs:
moderately_sensitive:
venn_diagram: output/review/venn-diagrams/venn_diagram_number_check_vax.csv
## Stage 4c - Venn diagrams unvax
stage4_venn_diagram_unvax:
run: r:latest analysis/descriptives/venn_diagram.R unvax
needs:
- preprocess_data_unvax
- make_model_input-cohort_unvax-main-
- make_model_input-cohort_unvax-main-abdominal_distension
- make_model_input-cohort_unvax-main-abdominal_paindiscomfort
- make_model_input-cohort_unvax-main-acute_pancreatitis
- make_model_input-cohort_unvax-main-appendicitis
- make_model_input-cohort_unvax-main-belching
- make_model_input-cohort_unvax-main-bloody_stools
- make_model_input-cohort_unvax-main-bowel_ischaemia
- make_model_input-cohort_unvax-main-diarrhoea
- make_model_input-cohort_unvax-main-dyspepsia
- make_model_input-cohort_unvax-main-gallstones_disease
- make_model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease
- make_model_input-cohort_unvax-main-ibs
- make_model_input-cohort_unvax-main-intestinal_obstruction
- make_model_input-cohort_unvax-main-lower_gi_bleeding
- make_model_input-cohort_unvax-main-nausea
- make_model_input-cohort_unvax-main-nonalcoholic_steatohepatitis
- make_model_input-cohort_unvax-main-nonvariceal_gi_bleeding
- make_model_input-cohort_unvax-main-peptic_ulcer
- make_model_input-cohort_unvax-main-upper_gi_bleeding
- make_model_input-cohort_unvax-main-variceal_gi_bleeding
- make_model_input-cohort_unvax-main-vomiting
outputs:
moderately_sensitive:
venn_diagram: output/review/venn-diagrams/venn_diagram_number_check_unvax.csv
## Stage 5 - Run models
make_model_input-cohort_prevax-main-:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-.rds
describe_model_input-cohort_prevax-main-:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main- rds
needs:
- make_model_input-cohort_prevax-main-
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-.txt
cox_ipw-cohort_prevax-main-:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-.csv
needs:
- make_model_input-cohort_prevax-main-
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-.csv
make_model_input-cohort_prevax-main-abdominal_distension:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-abdominal_distension
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-abdominal_distension.rds
describe_model_input-cohort_prevax-main-abdominal_distension:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-abdominal_distension
rds
needs:
- make_model_input-cohort_prevax-main-abdominal_distension
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-abdominal_distension.txt
cox_ipw-cohort_prevax-main-abdominal_distension:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-abdominal_distension.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-abdominal_distension.csv
needs:
- make_model_input-cohort_prevax-main-abdominal_distension
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-abdominal_distension.csv
make_model_input-cohort_prevax-main-abdominal_paindiscomfort:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-abdominal_paindiscomfort
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-abdominal_paindiscomfort.rds
describe_model_input-cohort_prevax-main-abdominal_paindiscomfort:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-abdominal_paindiscomfort
rds
needs:
- make_model_input-cohort_prevax-main-abdominal_paindiscomfort
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-abdominal_paindiscomfort.txt
cox_ipw-cohort_prevax-main-abdominal_paindiscomfort:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-abdominal_paindiscomfort.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-abdominal_paindiscomfort.csv
needs:
- make_model_input-cohort_prevax-main-abdominal_paindiscomfort
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-abdominal_paindiscomfort.csv
make_model_input-cohort_prevax-main-acute_pancreatitis:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-acute_pancreatitis
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-acute_pancreatitis.rds
describe_model_input-cohort_prevax-main-acute_pancreatitis:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-acute_pancreatitis
rds
needs:
- make_model_input-cohort_prevax-main-acute_pancreatitis
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-acute_pancreatitis.txt
cox_ipw-cohort_prevax-main-acute_pancreatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-acute_pancreatitis.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-acute_pancreatitis.csv
needs:
- make_model_input-cohort_prevax-main-acute_pancreatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-acute_pancreatitis.csv
make_model_input-cohort_prevax-main-appendicitis:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-appendicitis
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-appendicitis.rds
describe_model_input-cohort_prevax-main-appendicitis:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-appendicitis
rds
needs:
- make_model_input-cohort_prevax-main-appendicitis
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-appendicitis.txt
cox_ipw-cohort_prevax-main-appendicitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-appendicitis.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-appendicitis.csv
needs:
- make_model_input-cohort_prevax-main-appendicitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-appendicitis.csv
make_model_input-cohort_prevax-main-belching:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-belching
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-belching.rds
describe_model_input-cohort_prevax-main-belching:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-belching
rds
needs:
- make_model_input-cohort_prevax-main-belching
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-belching.txt
cox_ipw-cohort_prevax-main-belching:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-belching.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-belching.csv
needs:
- make_model_input-cohort_prevax-main-belching
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-belching.csv
make_model_input-cohort_prevax-main-bloody_stools:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-bloody_stools
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-bloody_stools.rds
describe_model_input-cohort_prevax-main-bloody_stools:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-bloody_stools
rds
needs:
- make_model_input-cohort_prevax-main-bloody_stools
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-bloody_stools.txt
cox_ipw-cohort_prevax-main-bloody_stools:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-bloody_stools.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-bloody_stools.csv
needs:
- make_model_input-cohort_prevax-main-bloody_stools
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-bloody_stools.csv
make_model_input-cohort_prevax-main-bowel_ischaemia:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-bowel_ischaemia
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-bowel_ischaemia.rds
describe_model_input-cohort_prevax-main-bowel_ischaemia:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-bowel_ischaemia
rds
needs:
- make_model_input-cohort_prevax-main-bowel_ischaemia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-bowel_ischaemia.txt
cox_ipw-cohort_prevax-main-bowel_ischaemia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-bowel_ischaemia.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-bowel_ischaemia.csv
needs:
- make_model_input-cohort_prevax-main-bowel_ischaemia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-bowel_ischaemia.csv
make_model_input-cohort_prevax-main-diarrhoea:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-diarrhoea
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-diarrhoea.rds
describe_model_input-cohort_prevax-main-diarrhoea:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-diarrhoea
rds
needs:
- make_model_input-cohort_prevax-main-diarrhoea
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-diarrhoea.txt
cox_ipw-cohort_prevax-main-diarrhoea:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-diarrhoea.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-diarrhoea.csv
needs:
- make_model_input-cohort_prevax-main-diarrhoea
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-diarrhoea.csv
make_model_input-cohort_prevax-main-dyspepsia:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-dyspepsia
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-dyspepsia.rds
describe_model_input-cohort_prevax-main-dyspepsia:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-dyspepsia
rds
needs:
- make_model_input-cohort_prevax-main-dyspepsia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-dyspepsia.txt
cox_ipw-cohort_prevax-main-dyspepsia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-dyspepsia.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-dyspepsia.csv
needs:
- make_model_input-cohort_prevax-main-dyspepsia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-dyspepsia.csv
make_model_input-cohort_prevax-main-gallstones_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-gallstones_disease
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-gallstones_disease.rds
describe_model_input-cohort_prevax-main-gallstones_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-gallstones_disease
rds
needs:
- make_model_input-cohort_prevax-main-gallstones_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-gallstones_disease.txt
cox_ipw-cohort_prevax-main-gallstones_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-gallstones_disease.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-gallstones_disease.csv
needs:
- make_model_input-cohort_prevax-main-gallstones_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-gallstones_disease.csv
make_model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-gastro_oesophageal_reflux_disease
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease.rds
describe_model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease
rds
needs:
- make_model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease.txt
cox_ipw-cohort_prevax-main-gastro_oesophageal_reflux_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-gastro_oesophageal_reflux_disease.csv
needs:
- make_model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-gastro_oesophageal_reflux_disease.csv
make_model_input-cohort_prevax-main-ibs:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-ibs
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-ibs.rds
describe_model_input-cohort_prevax-main-ibs:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-ibs rds
needs:
- make_model_input-cohort_prevax-main-ibs
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-ibs.txt
cox_ipw-cohort_prevax-main-ibs:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-ibs.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-ibs.csv
needs:
- make_model_input-cohort_prevax-main-ibs
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-ibs.csv
make_model_input-cohort_prevax-main-intestinal_obstruction:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-intestinal_obstruction
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-intestinal_obstruction.rds
describe_model_input-cohort_prevax-main-intestinal_obstruction:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-intestinal_obstruction
rds
needs:
- make_model_input-cohort_prevax-main-intestinal_obstruction
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-intestinal_obstruction.txt
cox_ipw-cohort_prevax-main-intestinal_obstruction:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-intestinal_obstruction.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-intestinal_obstruction.csv
needs:
- make_model_input-cohort_prevax-main-intestinal_obstruction
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-intestinal_obstruction.csv
make_model_input-cohort_prevax-main-lower_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-lower_gi_bleeding
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-lower_gi_bleeding.rds
describe_model_input-cohort_prevax-main-lower_gi_bleeding:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-lower_gi_bleeding
rds
needs:
- make_model_input-cohort_prevax-main-lower_gi_bleeding
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-lower_gi_bleeding.txt
cox_ipw-cohort_prevax-main-lower_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-lower_gi_bleeding.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-lower_gi_bleeding.csv
needs:
- make_model_input-cohort_prevax-main-lower_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-lower_gi_bleeding.csv
make_model_input-cohort_prevax-main-nausea:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-nausea
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-nausea.rds
describe_model_input-cohort_prevax-main-nausea:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-nausea rds
needs:
- make_model_input-cohort_prevax-main-nausea
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-nausea.txt
cox_ipw-cohort_prevax-main-nausea:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-nausea.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-nausea.csv
needs:
- make_model_input-cohort_prevax-main-nausea
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-nausea.csv
make_model_input-cohort_prevax-main-nonalcoholic_steatohepatitis:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-nonalcoholic_steatohepatitis
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-nonalcoholic_steatohepatitis.rds
describe_model_input-cohort_prevax-main-nonalcoholic_steatohepatitis:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-nonalcoholic_steatohepatitis
rds
needs:
- make_model_input-cohort_prevax-main-nonalcoholic_steatohepatitis
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-nonalcoholic_steatohepatitis.txt
cox_ipw-cohort_prevax-main-nonalcoholic_steatohepatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-nonalcoholic_steatohepatitis.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-nonalcoholic_steatohepatitis.csv
needs:
- make_model_input-cohort_prevax-main-nonalcoholic_steatohepatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-nonalcoholic_steatohepatitis.csv
make_model_input-cohort_prevax-main-nonvariceal_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-nonvariceal_gi_bleeding
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-nonvariceal_gi_bleeding.rds
describe_model_input-cohort_prevax-main-nonvariceal_gi_bleeding:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-nonvariceal_gi_bleeding
rds
needs:
- make_model_input-cohort_prevax-main-nonvariceal_gi_bleeding
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-nonvariceal_gi_bleeding.txt
cox_ipw-cohort_prevax-main-nonvariceal_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-nonvariceal_gi_bleeding.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-nonvariceal_gi_bleeding.csv
needs:
- make_model_input-cohort_prevax-main-nonvariceal_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-nonvariceal_gi_bleeding.csv
make_model_input-cohort_prevax-main-peptic_ulcer:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-peptic_ulcer
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-peptic_ulcer.rds
describe_model_input-cohort_prevax-main-peptic_ulcer:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-peptic_ulcer
rds
needs:
- make_model_input-cohort_prevax-main-peptic_ulcer
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-peptic_ulcer.txt
cox_ipw-cohort_prevax-main-peptic_ulcer:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-peptic_ulcer.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-peptic_ulcer.csv
needs:
- make_model_input-cohort_prevax-main-peptic_ulcer
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-peptic_ulcer.csv
make_model_input-cohort_prevax-main-upper_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-upper_gi_bleeding
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-upper_gi_bleeding.rds
describe_model_input-cohort_prevax-main-upper_gi_bleeding:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-upper_gi_bleeding
rds
needs:
- make_model_input-cohort_prevax-main-upper_gi_bleeding
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-upper_gi_bleeding.txt
cox_ipw-cohort_prevax-main-upper_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-upper_gi_bleeding.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-upper_gi_bleeding.csv
needs:
- make_model_input-cohort_prevax-main-upper_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-upper_gi_bleeding.csv
make_model_input-cohort_prevax-main-variceal_gi_bleeding:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-variceal_gi_bleeding
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-variceal_gi_bleeding.rds
describe_model_input-cohort_prevax-main-variceal_gi_bleeding:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-variceal_gi_bleeding
rds
needs:
- make_model_input-cohort_prevax-main-variceal_gi_bleeding
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-variceal_gi_bleeding.txt
cox_ipw-cohort_prevax-main-variceal_gi_bleeding:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-variceal_gi_bleeding.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-variceal_gi_bleeding.csv
needs:
- make_model_input-cohort_prevax-main-variceal_gi_bleeding
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-variceal_gi_bleeding.csv
make_model_input-cohort_prevax-main-vomiting:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-vomiting
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-vomiting.rds
describe_model_input-cohort_prevax-main-vomiting:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-vomiting
rds
needs:
- make_model_input-cohort_prevax-main-vomiting
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-vomiting.txt
cox_ipw-cohort_prevax-main-vomiting:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-vomiting.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
--cut_points=28;197;535 --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-vomiting.csv
needs:
- make_model_input-cohort_prevax-main-vomiting
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-vomiting.csv
make_model_input-cohort_unvax-main-:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-.rds
describe_model_input-cohort_unvax-main-:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-main- rds
needs:
- make_model_input-cohort_unvax-main-
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-main-.txt
cox_ipw-cohort_unvax-main-:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
--cut_points=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-.csv
needs:
- make_model_input-cohort_unvax-main-
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-.csv
make_model_input-cohort_unvax-main-abdominal_distension:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-abdominal_distension
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-abdominal_distension.rds
describe_model_input-cohort_unvax-main-abdominal_distension:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-abdominal_distension
rds
needs:
- make_model_input-cohort_unvax-main-abdominal_distension
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-main-abdominal_distension.txt
cox_ipw-cohort_unvax-main-abdominal_distension:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-abdominal_distension.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
--cut_points=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-abdominal_distension.csv
needs:
- make_model_input-cohort_unvax-main-abdominal_distension
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-abdominal_distension.csv
make_model_input-cohort_unvax-main-abdominal_paindiscomfort:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-abdominal_paindiscomfort
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-abdominal_paindiscomfort.rds
describe_model_input-cohort_unvax-main-abdominal_paindiscomfort:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-abdominal_paindiscomfort
rds
needs:
- make_model_input-cohort_unvax-main-abdominal_paindiscomfort
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-main-abdominal_paindiscomfort.txt
cox_ipw-cohort_unvax-main-abdominal_paindiscomfort:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-abdominal_paindiscomfort.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
--cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
--cut_points=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-abdominal_paindiscomfort.csv
needs:
- make_model_input-cohort_unvax-main-abdominal_paindiscomfort
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-abdominal_paindiscomfort.csv
make_model_input-cohort_unvax-main-acute_pancreatitis:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-acute_pancreatitis
needs:
- stage1_data_cleaning_all
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-acute_pancreatitis.rds
describe_model_input-cohort_unvax-main-acute_pancreatitis:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-acute_pancreatitis
rds
needs:
- make_model_input-cohort_unvax-main-acute_pancreatitis
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-main-acute_pancreatitis.txt
cox_ipw-cohort_unvax-main-acute_pancreatitis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-acute_pancreatitis.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_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp;
--cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
--cut_points=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-acute_pancreatitis.csv
needs:
- make_model_input-cohort_unvax-main-acute_pancreatitis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-acute_pancreatitis.csv
make_model_input-cohort_unvax-main-appendicitis: