generated from opensafely/research-template
/
project.yaml
6785 lines (6166 loc) · 420 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 200000
actions:
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml DIRECTLY
## This file is created by create_project_actions.R
## Edit and run create_project_actions.R to update the project.yaml
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
vax_eligibility_inputs:
run: r:latest analysis/metadates.R
outputs:
highly_sensitive:
study_dates_json: output/study_dates.json
vax_jcvi_groups: output/vax_jcvi_groups.csv
vax_eligible_dates: output/vax_eligible_dates.csv
generate_study_population_prelim:
run: cohortextractor:latest generate_cohort --study-definition study_definition_prelim
--output-format 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_prevax:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R prevax
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- vax_eligibility_inputs
outputs:
moderately_sensitive:
refactoring: output/not-for-review/meta_data_factors_prevax.csv
QA_rules: output/review/descriptives/QA_summary_prevax.csv
IE_criteria: output/review/descriptives/Cohort_flow_prevax.csv
histograms: output/not-for-review/numeric_histograms_prevax.svg
highly_sensitive:
cohort: output/input_prevax_*.rds
stage1_data_cleaning_vax:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R vax
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- vax_eligibility_inputs
outputs:
moderately_sensitive:
refactoring: output/not-for-review/meta_data_factors_vax.csv
QA_rules: output/review/descriptives/QA_summary_vax.csv
IE_criteria: output/review/descriptives/Cohort_flow_vax.csv
histograms: output/not-for-review/numeric_histograms_vax.svg
highly_sensitive:
cohort: output/input_vax_*.rds
stage1_data_cleaning_unvax:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R unvax
needs:
- preprocess_data_prevax
- preprocess_data_vax
- preprocess_data_unvax
- vax_eligibility_inputs
outputs:
moderately_sensitive:
refactoring: output/not-for-review/meta_data_factors_unvax.csv
QA_rules: output/review/descriptives/QA_summary_unvax.csv
IE_criteria: output/review/descriptives/Cohort_flow_unvax.csv
histograms: output/not-for-review/numeric_histograms_unvax.svg
highly_sensitive:
cohort: output/input_unvax_*.rds
describe_file-input_prevax_stage1:
run: r:latest analysis/describe_file.R input_prevax_stage1 rds
needs:
- stage1_data_cleaning_prevax
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_vax
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_unvax
outputs:
moderately_sensitive:
describe_model_input: output/describe-input_unvax_stage1.txt
## Stage 5 - Run models
make_model_input-cohort_prevax-main-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-alzheimer_disease
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-alzheimer_disease.rds
describe_model_input-cohort_prevax-main-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-alzheimer_disease
rds
needs:
- make_model_input-cohort_prevax-main-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-alzheimer_disease.txt
cox_ipw-cohort_prevax-main-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-alzheimer_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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
--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-alzheimer_disease.csv
needs:
- make_model_input-cohort_prevax-main-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-alzheimer_disease.csv
make_model_input-cohort_prevax-main-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-any_dementia
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-any_dementia.rds
describe_model_input-cohort_prevax-main-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-any_dementia
rds
needs:
- make_model_input-cohort_prevax-main-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-any_dementia.txt
cox_ipw-cohort_prevax-main-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-any_dementia.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
--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-any_dementia.csv
needs:
- make_model_input-cohort_prevax-main-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-any_dementia.csv
make_model_input-cohort_prevax-main-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-cognitive_impairment
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-cognitive_impairment.rds
describe_model_input-cohort_prevax-main-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-cognitive_impairment
rds
needs:
- make_model_input-cohort_prevax-main-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-cognitive_impairment.txt
cox_ipw-cohort_prevax-main-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-cognitive_impairment.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
--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-cognitive_impairment.csv
needs:
- make_model_input-cohort_prevax-main-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-cognitive_impairment.csv
make_model_input-cohort_prevax-main-migraine:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-migraine.rds
describe_model_input-cohort_prevax-main-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-migraine
rds
needs:
- make_model_input-cohort_prevax-main-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-migraine.txt
cox_ipw-cohort_prevax-main-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-migraine.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
--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-migraine.csv
needs:
- make_model_input-cohort_prevax-main-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-migraine.csv
make_model_input-cohort_prevax-main-motor_neurone_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-motor_neurone_disease
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-motor_neurone_disease.rds
describe_model_input-cohort_prevax-main-motor_neurone_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-motor_neurone_disease
rds
needs:
- make_model_input-cohort_prevax-main-motor_neurone_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-motor_neurone_disease.txt
cox_ipw-cohort_prevax-main-motor_neurone_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-motor_neurone_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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
--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-motor_neurone_disease.csv
needs:
- make_model_input-cohort_prevax-main-motor_neurone_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-motor_neurone_disease.csv
make_model_input-cohort_prevax-main-multiple_sclerosis:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-multiple_sclerosis
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-multiple_sclerosis.rds
describe_model_input-cohort_prevax-main-multiple_sclerosis:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-multiple_sclerosis
rds
needs:
- make_model_input-cohort_prevax-main-multiple_sclerosis
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-multiple_sclerosis.txt
cox_ipw-cohort_prevax-main-multiple_sclerosis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-multiple_sclerosis.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
--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-multiple_sclerosis.csv
needs:
- make_model_input-cohort_prevax-main-multiple_sclerosis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-multiple_sclerosis.csv
make_model_input-cohort_prevax-main-other_dementias:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-other_dementias
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-other_dementias.rds
describe_model_input-cohort_prevax-main-other_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-other_dementias
rds
needs:
- make_model_input-cohort_prevax-main-other_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-other_dementias.txt
cox_ipw-cohort_prevax-main-other_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-other_dementias.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
--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-other_dementias.csv
needs:
- make_model_input-cohort_prevax-main-other_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-other_dementias.csv
make_model_input-cohort_prevax-main-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-parkinson_disease
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-parkinson_disease.rds
describe_model_input-cohort_prevax-main-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-parkinson_disease
rds
needs:
- make_model_input-cohort_prevax-main-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-parkinson_disease.txt
cox_ipw-cohort_prevax-main-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-parkinson_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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
--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-parkinson_disease.csv
needs:
- make_model_input-cohort_prevax-main-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-parkinson_disease.csv
make_model_input-cohort_prevax-main-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-rem_sleep_disorder
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-rem_sleep_disorder.rds
describe_model_input-cohort_prevax-main-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_prevax-main-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-rem_sleep_disorder.txt
cox_ipw-cohort_prevax-main-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-rem_sleep_disorder.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
--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-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_prevax-main-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-rem_sleep_disorder.csv
make_model_input-cohort_prevax-main-restless_leg_syndrome:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-restless_leg_syndrome
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-restless_leg_syndrome.rds
describe_model_input-cohort_prevax-main-restless_leg_syndrome:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-restless_leg_syndrome
rds
needs:
- make_model_input-cohort_prevax-main-restless_leg_syndrome
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-restless_leg_syndrome.txt
cox_ipw-cohort_prevax-main-restless_leg_syndrome:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-restless_leg_syndrome.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
--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-restless_leg_syndrome.csv
needs:
- make_model_input-cohort_prevax-main-restless_leg_syndrome
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-restless_leg_syndrome.csv
make_model_input-cohort_prevax-main-unspecified_dementias:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-unspecified_dementias
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-unspecified_dementias.rds
describe_model_input-cohort_prevax-main-unspecified_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-unspecified_dementias
rds
needs:
- make_model_input-cohort_prevax-main-unspecified_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-unspecified_dementias.txt
cox_ipw-cohort_prevax-main-unspecified_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-unspecified_dementias.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
--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-unspecified_dementias.csv
needs:
- make_model_input-cohort_prevax-main-unspecified_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-unspecified_dementias.csv
make_model_input-cohort_prevax-main-vascular_dementia:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-vascular_dementia
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-vascular_dementia.rds
describe_model_input-cohort_prevax-main-vascular_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-vascular_dementia
rds
needs:
- make_model_input-cohort_prevax-main-vascular_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-main-vascular_dementia.txt
cox_ipw-cohort_prevax-main-vascular_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-vascular_dementia.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-18
--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-vascular_dementia.csv
needs:
- make_model_input-cohort_prevax-main-vascular_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-vascular_dementia.csv
make_model_input-cohort_unvax-main-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-alzheimer_disease
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-alzheimer_disease.rds
describe_model_input-cohort_unvax-main-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-alzheimer_disease
rds
needs:
- make_model_input-cohort_unvax-main-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-main-alzheimer_disease.txt
cox_ipw-cohort_unvax-main-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-alzheimer_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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--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-alzheimer_disease.csv
needs:
- make_model_input-cohort_unvax-main-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-alzheimer_disease.csv
make_model_input-cohort_unvax-main-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-any_dementia
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-any_dementia.rds
describe_model_input-cohort_unvax-main-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-any_dementia
rds
needs:
- make_model_input-cohort_unvax-main-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-main-any_dementia.txt
cox_ipw-cohort_unvax-main-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-any_dementia.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--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-any_dementia.csv
needs:
- make_model_input-cohort_unvax-main-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-any_dementia.csv
make_model_input-cohort_unvax-main-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-cognitive_impairment
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-cognitive_impairment.rds
describe_model_input-cohort_unvax-main-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-cognitive_impairment
rds
needs:
- make_model_input-cohort_unvax-main-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-main-cognitive_impairment.txt
cox_ipw-cohort_unvax-main-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-cognitive_impairment.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--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-cognitive_impairment.csv
needs:
- make_model_input-cohort_unvax-main-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-cognitive_impairment.csv
make_model_input-cohort_unvax-main-migraine:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-migraine.rds
describe_model_input-cohort_unvax-main-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-migraine
rds
needs:
- make_model_input-cohort_unvax-main-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-main-migraine.txt
cox_ipw-cohort_unvax-main-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-migraine.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--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-migraine.csv
needs:
- make_model_input-cohort_unvax-main-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-migraine.csv
make_model_input-cohort_unvax-main-motor_neurone_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-motor_neurone_disease
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-motor_neurone_disease.rds
describe_model_input-cohort_unvax-main-motor_neurone_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-motor_neurone_disease
rds
needs:
- make_model_input-cohort_unvax-main-motor_neurone_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-main-motor_neurone_disease.txt
cox_ipw-cohort_unvax-main-motor_neurone_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-motor_neurone_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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--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-motor_neurone_disease.csv
needs:
- make_model_input-cohort_unvax-main-motor_neurone_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-motor_neurone_disease.csv
make_model_input-cohort_unvax-main-multiple_sclerosis:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-multiple_sclerosis
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-multiple_sclerosis.rds
describe_model_input-cohort_unvax-main-multiple_sclerosis:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-multiple_sclerosis
rds
needs:
- make_model_input-cohort_unvax-main-multiple_sclerosis
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-main-multiple_sclerosis.txt
cox_ipw-cohort_unvax-main-multiple_sclerosis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-multiple_sclerosis.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--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-multiple_sclerosis.csv
needs:
- make_model_input-cohort_unvax-main-multiple_sclerosis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-multiple_sclerosis.csv
make_model_input-cohort_unvax-main-other_dementias:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-other_dementias
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-other_dementias.rds
describe_model_input-cohort_unvax-main-other_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-other_dementias
rds
needs:
- make_model_input-cohort_unvax-main-other_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-main-other_dementias.txt
cox_ipw-cohort_unvax-main-other_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-other_dementias.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--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-other_dementias.csv
needs:
- make_model_input-cohort_unvax-main-other_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-other_dementias.csv
make_model_input-cohort_unvax-main-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-parkinson_disease
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-parkinson_disease.rds
describe_model_input-cohort_unvax-main-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-parkinson_disease
rds
needs:
- make_model_input-cohort_unvax-main-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-main-parkinson_disease.txt
cox_ipw-cohort_unvax-main-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-parkinson_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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--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-parkinson_disease.csv
needs:
- make_model_input-cohort_unvax-main-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-parkinson_disease.csv
make_model_input-cohort_unvax-main-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-rem_sleep_disorder
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-rem_sleep_disorder.rds
describe_model_input-cohort_unvax-main-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_unvax-main-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-main-rem_sleep_disorder.txt
cox_ipw-cohort_unvax-main-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-rem_sleep_disorder.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--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-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_unvax-main-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-rem_sleep_disorder.csv
make_model_input-cohort_unvax-main-restless_leg_syndrome:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-restless_leg_syndrome
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-restless_leg_syndrome.rds
describe_model_input-cohort_unvax-main-restless_leg_syndrome:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-restless_leg_syndrome
rds
needs:
- make_model_input-cohort_unvax-main-restless_leg_syndrome
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-main-restless_leg_syndrome.txt
cox_ipw-cohort_unvax-main-restless_leg_syndrome:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-restless_leg_syndrome.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--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-restless_leg_syndrome.csv
needs:
- make_model_input-cohort_unvax-main-restless_leg_syndrome
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-restless_leg_syndrome.csv
make_model_input-cohort_unvax-main-unspecified_dementias:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-unspecified_dementias
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-unspecified_dementias.rds
describe_model_input-cohort_unvax-main-unspecified_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-unspecified_dementias
rds
needs:
- make_model_input-cohort_unvax-main-unspecified_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-main-unspecified_dementias.txt
cox_ipw-cohort_unvax-main-unspecified_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-unspecified_dementias.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--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-unspecified_dementias.csv
needs:
- make_model_input-cohort_unvax-main-unspecified_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-unspecified_dementias.csv
make_model_input-cohort_unvax-main-vascular_dementia:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-vascular_dementia
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-vascular_dementia.rds
describe_model_input-cohort_unvax-main-vascular_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-vascular_dementia
rds
needs:
- make_model_input-cohort_unvax-main-vascular_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-main-vascular_dementia.txt
cox_ipw-cohort_unvax-main-vascular_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-vascular_dementia.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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--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-vascular_dementia.csv
needs:
- make_model_input-cohort_unvax-main-vascular_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-vascular_dementia.csv
make_model_input-cohort_vax-main-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-alzheimer_disease
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-alzheimer_disease.rds
describe_model_input-cohort_vax-main-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-main-alzheimer_disease
rds
needs:
- make_model_input-cohort_vax-main-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-main-alzheimer_disease.txt
cox_ipw-cohort_vax-main-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-alzheimer_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_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_all_stroke;cov_bin_hypercholesterolaemia
--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_vax-main-alzheimer_disease.csv
needs:
- make_model_input-cohort_vax-main-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-alzheimer_disease.csv
make_model_input-cohort_vax-main-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-any_dementia
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-any_dementia.rds
describe_model_input-cohort_vax-main-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_vax-main-any_dementia
rds
needs:
- make_model_input-cohort_vax-main-any_dementia
outputs:
moderately_sensitive: