Job request: 15953
- Organisation:
- University of Bristol
- Workspace:
- post-covid-neurodegenerative
- ID:
- fckoquysnok7lg5z
This page shows the technical details of what happened when authorised researcher Jose Ignacio Cuitun Coronado requested one or more actions to be run against real patient data in the project, within a secure environment.
By cross-referencing the indicated Requested Actions with the
Pipeline section below, you can infer what
security level
various outputs were written to. Outputs marked as
highly_sensitive
can never be viewed directly by a researcher; they can only
request that code runs against them. Outputs marked as
moderately_sensitive
can be viewed by an approved researcher by logging into a highly
secure environment. Only outputs marked as
moderately_sensitive
can be requested for release to the public, via a controlled
output review service.
Jobs
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- describe_model_input-cohort_prevax-sub_age_60_79-rem_sleep_disorder
- Status:
- Status: Succeeded
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- describe_model_input-cohort_prevax-sub_age_60_79-cognitive_impairment
- Status:
- Status: Succeeded
- Job identifier:
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- describe_model_input-cohort_unvax-sub_age_60_79-rem_sleep_disorder
- Status:
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- Action:
- describe_model_input-cohort_prevax-sub_age_60_79-alzheimer_disease
- Status:
- Status: Succeeded
- Job identifier:
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- Action:
- describe_model_input-cohort_unvax-sub_age_60_79-cognitive_impairment
- Status:
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- describe_model_input-cohort_prevax-sub_age_60_79-parkinson_disease
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- Status: Succeeded
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- Action:
- describe_model_input-cohort_vax-sub_age_60_79-cognitive_impairment
- Status:
- Status: Succeeded
- Job identifier:
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Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 200000
actions:
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml DIRECTLY
## This file is created by create_project_actions.R
## Edit and run create_project_actions.R to update the project.yaml
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
vax_eligibility_inputs:
run: r:latest analysis/metadates.R
outputs:
highly_sensitive:
study_dates_json: output/study_dates.json
vax_jcvi_groups: output/vax_jcvi_groups.csv
vax_eligible_dates: output/vax_eligible_dates.csv
generate_study_population_prelim:
run: cohortextractor:latest generate_cohort --study-definition study_definition_prelim
--output-format 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:
describe_model_input: output/describe-model_input-cohort_vax-main-any_dementia.txt
cox_ipw-cohort_vax-main-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-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_vax-main-any_dementia.csv
needs:
- make_model_input-cohort_vax-main-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-any_dementia.csv
make_model_input-cohort_vax-main-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_vax-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_vax-main-cognitive_impairment.rds
describe_model_input-cohort_vax-main-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_vax-main-cognitive_impairment
rds
needs:
- make_model_input-cohort_vax-main-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-main-cognitive_impairment.txt
cox_ipw-cohort_vax-main-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-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_vax-main-cognitive_impairment.csv
needs:
- make_model_input-cohort_vax-main-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-cognitive_impairment.csv
make_model_input-cohort_vax-main-migraine:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-migraine.rds
describe_model_input-cohort_vax-main-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_vax-main-migraine rds
needs:
- make_model_input-cohort_vax-main-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-main-migraine.txt
cox_ipw-cohort_vax-main-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-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_vax-main-migraine.csv
needs:
- make_model_input-cohort_vax-main-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-migraine.csv
make_model_input-cohort_vax-main-motor_neurone_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-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_vax-main-motor_neurone_disease.rds
describe_model_input-cohort_vax-main-motor_neurone_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-main-motor_neurone_disease
rds
needs:
- make_model_input-cohort_vax-main-motor_neurone_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-main-motor_neurone_disease.txt
cox_ipw-cohort_vax-main-motor_neurone_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-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_vax-main-motor_neurone_disease.csv
needs:
- make_model_input-cohort_vax-main-motor_neurone_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-motor_neurone_disease.csv
make_model_input-cohort_vax-main-multiple_sclerosis:
run: r:latest analysis/model/make_model_input.R cohort_vax-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_vax-main-multiple_sclerosis.rds
describe_model_input-cohort_vax-main-multiple_sclerosis:
run: r:latest analysis/describe_file.R model_input-cohort_vax-main-multiple_sclerosis
rds
needs:
- make_model_input-cohort_vax-main-multiple_sclerosis
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-main-multiple_sclerosis.txt
cox_ipw-cohort_vax-main-multiple_sclerosis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-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_vax-main-multiple_sclerosis.csv
needs:
- make_model_input-cohort_vax-main-multiple_sclerosis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-multiple_sclerosis.csv
make_model_input-cohort_vax-main-other_dementias:
run: r:latest analysis/model/make_model_input.R cohort_vax-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_vax-main-other_dementias.rds
describe_model_input-cohort_vax-main-other_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_vax-main-other_dementias
rds
needs:
- make_model_input-cohort_vax-main-other_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-main-other_dementias.txt
cox_ipw-cohort_vax-main-other_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-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_vax-main-other_dementias.csv
needs:
- make_model_input-cohort_vax-main-other_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-other_dementias.csv
make_model_input-cohort_vax-main-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-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_vax-main-parkinson_disease.rds
describe_model_input-cohort_vax-main-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-main-parkinson_disease
rds
needs:
- make_model_input-cohort_vax-main-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-main-parkinson_disease.txt
cox_ipw-cohort_vax-main-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-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_vax-main-parkinson_disease.csv
needs:
- make_model_input-cohort_vax-main-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-parkinson_disease.csv
make_model_input-cohort_vax-main-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_vax-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_vax-main-rem_sleep_disorder.rds
describe_model_input-cohort_vax-main-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_vax-main-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_vax-main-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-main-rem_sleep_disorder.txt
cox_ipw-cohort_vax-main-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-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_vax-main-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_vax-main-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-rem_sleep_disorder.csv
make_model_input-cohort_vax-main-restless_leg_syndrome:
run: r:latest analysis/model/make_model_input.R cohort_vax-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_vax-main-restless_leg_syndrome.rds
describe_model_input-cohort_vax-main-restless_leg_syndrome:
run: r:latest analysis/describe_file.R model_input-cohort_vax-main-restless_leg_syndrome
rds
needs:
- make_model_input-cohort_vax-main-restless_leg_syndrome
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-main-restless_leg_syndrome.txt
cox_ipw-cohort_vax-main-restless_leg_syndrome:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-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_vax-main-restless_leg_syndrome.csv
needs:
- make_model_input-cohort_vax-main-restless_leg_syndrome
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-restless_leg_syndrome.csv
make_model_input-cohort_vax-main-unspecified_dementias:
run: r:latest analysis/model/make_model_input.R cohort_vax-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_vax-main-unspecified_dementias.rds
describe_model_input-cohort_vax-main-unspecified_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_vax-main-unspecified_dementias
rds
needs:
- make_model_input-cohort_vax-main-unspecified_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-main-unspecified_dementias.txt
cox_ipw-cohort_vax-main-unspecified_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-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_vax-main-unspecified_dementias.csv
needs:
- make_model_input-cohort_vax-main-unspecified_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-unspecified_dementias.csv
make_model_input-cohort_vax-main-vascular_dementia:
run: r:latest analysis/model/make_model_input.R cohort_vax-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_vax-main-vascular_dementia.rds
describe_model_input-cohort_vax-main-vascular_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_vax-main-vascular_dementia
rds
needs:
- make_model_input-cohort_vax-main-vascular_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-main-vascular_dementia.txt
cox_ipw-cohort_vax-main-vascular_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-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_vax-main-vascular_dementia.csv
needs:
- make_model_input-cohort_vax-main-vascular_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-vascular_dementia.csv
make_model_input-cohort_prevax-sub_age_18_39-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-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-sub_age_18_39-alzheimer_disease.rds
describe_model_input-cohort_prevax-sub_age_18_39-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_18_39-alzheimer_disease
rds
needs:
- make_model_input-cohort_prevax-sub_age_18_39-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_18_39-alzheimer_disease.txt
cox_ipw-cohort_prevax-sub_age_18_39-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-alzheimer_disease.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-alzheimer_disease.csv
make_model_input-cohort_prevax-sub_age_18_39-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-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-sub_age_18_39-any_dementia.rds
describe_model_input-cohort_prevax-sub_age_18_39-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_18_39-any_dementia
rds
needs:
- make_model_input-cohort_prevax-sub_age_18_39-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_18_39-any_dementia.txt
cox_ipw-cohort_prevax-sub_age_18_39-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-any_dementia.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-any_dementia.csv
make_model_input-cohort_prevax-sub_age_18_39-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-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-sub_age_18_39-cognitive_impairment.rds
describe_model_input-cohort_prevax-sub_age_18_39-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_18_39-cognitive_impairment
rds
needs:
- make_model_input-cohort_prevax-sub_age_18_39-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_18_39-cognitive_impairment.txt
cox_ipw-cohort_prevax-sub_age_18_39-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-cognitive_impairment.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-cognitive_impairment.csv
make_model_input-cohort_prevax-sub_age_18_39-migraine:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_18_39-migraine.rds
describe_model_input-cohort_prevax-sub_age_18_39-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_18_39-migraine
rds
needs:
- make_model_input-cohort_prevax-sub_age_18_39-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_18_39-migraine.txt
cox_ipw-cohort_prevax-sub_age_18_39-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-migraine.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-migraine.csv
make_model_input-cohort_prevax-sub_age_18_39-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-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-sub_age_18_39-parkinson_disease.rds
describe_model_input-cohort_prevax-sub_age_18_39-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_18_39-parkinson_disease
rds
needs:
- make_model_input-cohort_prevax-sub_age_18_39-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_18_39-parkinson_disease.txt
cox_ipw-cohort_prevax-sub_age_18_39-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-parkinson_disease.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-parkinson_disease.csv
make_model_input-cohort_prevax-sub_age_18_39-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-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-sub_age_18_39-rem_sleep_disorder.rds
describe_model_input-cohort_prevax-sub_age_18_39-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_18_39-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_prevax-sub_age_18_39-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_18_39-rem_sleep_disorder.txt
cox_ipw-cohort_prevax-sub_age_18_39-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_prevax-sub_age_18_39-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_18_39-rem_sleep_disorder.csv
make_model_input-cohort_unvax-sub_age_18_39-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-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-sub_age_18_39-alzheimer_disease.rds
describe_model_input-cohort_unvax-sub_age_18_39-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_18_39-alzheimer_disease
rds
needs:
- make_model_input-cohort_unvax-sub_age_18_39-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_18_39-alzheimer_disease.txt
cox_ipw-cohort_unvax-sub_age_18_39-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-alzheimer_disease.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-alzheimer_disease.csv
make_model_input-cohort_unvax-sub_age_18_39-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-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-sub_age_18_39-any_dementia.rds
describe_model_input-cohort_unvax-sub_age_18_39-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_18_39-any_dementia
rds
needs:
- make_model_input-cohort_unvax-sub_age_18_39-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_18_39-any_dementia.txt
cox_ipw-cohort_unvax-sub_age_18_39-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-any_dementia.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-any_dementia.csv
make_model_input-cohort_unvax-sub_age_18_39-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-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-sub_age_18_39-cognitive_impairment.rds
describe_model_input-cohort_unvax-sub_age_18_39-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_18_39-cognitive_impairment
rds
needs:
- make_model_input-cohort_unvax-sub_age_18_39-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_18_39-cognitive_impairment.txt
cox_ipw-cohort_unvax-sub_age_18_39-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-cognitive_impairment.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-cognitive_impairment.csv
make_model_input-cohort_unvax-sub_age_18_39-migraine:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_18_39-migraine.rds
describe_model_input-cohort_unvax-sub_age_18_39-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_18_39-migraine
rds
needs:
- make_model_input-cohort_unvax-sub_age_18_39-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_18_39-migraine.txt
cox_ipw-cohort_unvax-sub_age_18_39-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-migraine.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-migraine.csv
make_model_input-cohort_unvax-sub_age_18_39-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-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-sub_age_18_39-parkinson_disease.rds
describe_model_input-cohort_unvax-sub_age_18_39-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_18_39-parkinson_disease
rds
needs:
- make_model_input-cohort_unvax-sub_age_18_39-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_18_39-parkinson_disease.txt
cox_ipw-cohort_unvax-sub_age_18_39-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-parkinson_disease.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-parkinson_disease.csv
make_model_input-cohort_unvax-sub_age_18_39-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-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-sub_age_18_39-rem_sleep_disorder.rds
describe_model_input-cohort_unvax-sub_age_18_39-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_18_39-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_unvax-sub_age_18_39-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_18_39-rem_sleep_disorder.txt
cox_ipw-cohort_unvax-sub_age_18_39-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_unvax-sub_age_18_39-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_18_39-rem_sleep_disorder.csv
make_model_input-cohort_vax-sub_age_18_39-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-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-sub_age_18_39-alzheimer_disease.rds
describe_model_input-cohort_vax-sub_age_18_39-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_18_39-alzheimer_disease
rds
needs:
- make_model_input-cohort_vax-sub_age_18_39-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_18_39-alzheimer_disease.txt
cox_ipw-cohort_vax-sub_age_18_39-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-alzheimer_disease.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-alzheimer_disease.csv
make_model_input-cohort_vax-sub_age_18_39-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-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-sub_age_18_39-any_dementia.rds
describe_model_input-cohort_vax-sub_age_18_39-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_18_39-any_dementia
rds
needs:
- make_model_input-cohort_vax-sub_age_18_39-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_18_39-any_dementia.txt
cox_ipw-cohort_vax-sub_age_18_39-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-any_dementia.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-any_dementia.csv
make_model_input-cohort_vax-sub_age_18_39-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-cognitive_impairment
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-cognitive_impairment.rds
describe_model_input-cohort_vax-sub_age_18_39-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_18_39-cognitive_impairment
rds
needs:
- make_model_input-cohort_vax-sub_age_18_39-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_18_39-cognitive_impairment.txt
cox_ipw-cohort_vax-sub_age_18_39-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-cognitive_impairment.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-cognitive_impairment.csv
make_model_input-cohort_vax-sub_age_18_39-migraine:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-migraine.rds
describe_model_input-cohort_vax-sub_age_18_39-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_18_39-migraine
rds
needs:
- make_model_input-cohort_vax-sub_age_18_39-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_18_39-migraine.txt
cox_ipw-cohort_vax-sub_age_18_39-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-migraine.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-migraine.csv
make_model_input-cohort_vax-sub_age_18_39-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-parkinson_disease
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-parkinson_disease.rds
describe_model_input-cohort_vax-sub_age_18_39-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_18_39-parkinson_disease
rds
needs:
- make_model_input-cohort_vax-sub_age_18_39-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_18_39-parkinson_disease.txt
cox_ipw-cohort_vax-sub_age_18_39-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-parkinson_disease.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-parkinson_disease.csv
make_model_input-cohort_vax-sub_age_18_39-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-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_vax-sub_age_18_39-rem_sleep_disorder.rds
describe_model_input-cohort_vax-sub_age_18_39-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_18_39-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_vax-sub_age_18_39-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_18_39-rem_sleep_disorder.txt
cox_ipw-cohort_vax-sub_age_18_39-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-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=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-rem_sleep_disorder.csv
make_model_input-cohort_prevax-sub_age_40_59-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-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-sub_age_40_59-alzheimer_disease.rds
describe_model_input-cohort_prevax-sub_age_40_59-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_40_59-alzheimer_disease
rds
needs:
- make_model_input-cohort_prevax-sub_age_40_59-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_40_59-alzheimer_disease.txt
cox_ipw-cohort_prevax-sub_age_40_59-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-alzheimer_disease.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-alzheimer_disease.csv
make_model_input-cohort_prevax-sub_age_40_59-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-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-sub_age_40_59-any_dementia.rds
describe_model_input-cohort_prevax-sub_age_40_59-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_40_59-any_dementia
rds
needs:
- make_model_input-cohort_prevax-sub_age_40_59-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_40_59-any_dementia.txt
cox_ipw-cohort_prevax-sub_age_40_59-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-any_dementia.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-any_dementia.csv
make_model_input-cohort_prevax-sub_age_40_59-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-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-sub_age_40_59-cognitive_impairment.rds
describe_model_input-cohort_prevax-sub_age_40_59-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_40_59-cognitive_impairment
rds
needs:
- make_model_input-cohort_prevax-sub_age_40_59-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_40_59-cognitive_impairment.txt
cox_ipw-cohort_prevax-sub_age_40_59-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-cognitive_impairment.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-cognitive_impairment.csv
make_model_input-cohort_prevax-sub_age_40_59-migraine:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_40_59-migraine.rds
describe_model_input-cohort_prevax-sub_age_40_59-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_40_59-migraine
rds
needs:
- make_model_input-cohort_prevax-sub_age_40_59-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_40_59-migraine.txt
cox_ipw-cohort_prevax-sub_age_40_59-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-migraine.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-migraine.csv
make_model_input-cohort_prevax-sub_age_40_59-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-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-sub_age_40_59-parkinson_disease.rds
describe_model_input-cohort_prevax-sub_age_40_59-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_40_59-parkinson_disease
rds
needs:
- make_model_input-cohort_prevax-sub_age_40_59-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_40_59-parkinson_disease.txt
cox_ipw-cohort_prevax-sub_age_40_59-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-parkinson_disease.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-parkinson_disease.csv
make_model_input-cohort_prevax-sub_age_40_59-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-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-sub_age_40_59-rem_sleep_disorder.rds
describe_model_input-cohort_prevax-sub_age_40_59-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_40_59-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_prevax-sub_age_40_59-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_40_59-rem_sleep_disorder.txt
cox_ipw-cohort_prevax-sub_age_40_59-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_prevax-sub_age_40_59-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_40_59-rem_sleep_disorder.csv
make_model_input-cohort_unvax-sub_age_40_59-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-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-sub_age_40_59-alzheimer_disease.rds
describe_model_input-cohort_unvax-sub_age_40_59-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_40_59-alzheimer_disease
rds
needs:
- make_model_input-cohort_unvax-sub_age_40_59-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_40_59-alzheimer_disease.txt
cox_ipw-cohort_unvax-sub_age_40_59-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-alzheimer_disease.csv
needs:
- make_model_input-cohort_unvax-sub_age_40_59-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_40_59-alzheimer_disease.csv
make_model_input-cohort_unvax-sub_age_40_59-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-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-sub_age_40_59-any_dementia.rds
describe_model_input-cohort_unvax-sub_age_40_59-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_40_59-any_dementia
rds
needs:
- make_model_input-cohort_unvax-sub_age_40_59-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_40_59-any_dementia.txt
cox_ipw-cohort_unvax-sub_age_40_59-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-any_dementia.csv
needs:
- make_model_input-cohort_unvax-sub_age_40_59-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_40_59-any_dementia.csv
make_model_input-cohort_unvax-sub_age_40_59-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-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-sub_age_40_59-cognitive_impairment.rds
describe_model_input-cohort_unvax-sub_age_40_59-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_40_59-cognitive_impairment
rds
needs:
- make_model_input-cohort_unvax-sub_age_40_59-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_40_59-cognitive_impairment.txt
cox_ipw-cohort_unvax-sub_age_40_59-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-cognitive_impairment.csv
needs:
- make_model_input-cohort_unvax-sub_age_40_59-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_40_59-cognitive_impairment.csv
make_model_input-cohort_unvax-sub_age_40_59-migraine:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_40_59-migraine.rds
describe_model_input-cohort_unvax-sub_age_40_59-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_40_59-migraine
rds
needs:
- make_model_input-cohort_unvax-sub_age_40_59-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_40_59-migraine.txt
cox_ipw-cohort_unvax-sub_age_40_59-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-migraine.csv
needs:
- make_model_input-cohort_unvax-sub_age_40_59-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_40_59-migraine.csv
make_model_input-cohort_unvax-sub_age_40_59-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-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-sub_age_40_59-parkinson_disease.rds
describe_model_input-cohort_unvax-sub_age_40_59-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_40_59-parkinson_disease
rds
needs:
- make_model_input-cohort_unvax-sub_age_40_59-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_40_59-parkinson_disease.txt
cox_ipw-cohort_unvax-sub_age_40_59-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-parkinson_disease.csv
needs:
- make_model_input-cohort_unvax-sub_age_40_59-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_40_59-parkinson_disease.csv
make_model_input-cohort_unvax-sub_age_40_59-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-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-sub_age_40_59-rem_sleep_disorder.rds
describe_model_input-cohort_unvax-sub_age_40_59-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_40_59-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_unvax-sub_age_40_59-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_40_59-rem_sleep_disorder.txt
cox_ipw-cohort_unvax-sub_age_40_59-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_unvax-sub_age_40_59-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_40_59-rem_sleep_disorder.csv
make_model_input-cohort_vax-sub_age_40_59-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-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-sub_age_40_59-alzheimer_disease.rds
describe_model_input-cohort_vax-sub_age_40_59-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_40_59-alzheimer_disease
rds
needs:
- make_model_input-cohort_vax-sub_age_40_59-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_40_59-alzheimer_disease.txt
cox_ipw-cohort_vax-sub_age_40_59-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-alzheimer_disease.csv
needs:
- make_model_input-cohort_vax-sub_age_40_59-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_40_59-alzheimer_disease.csv
make_model_input-cohort_vax-sub_age_40_59-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-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-sub_age_40_59-any_dementia.rds
describe_model_input-cohort_vax-sub_age_40_59-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_40_59-any_dementia
rds
needs:
- make_model_input-cohort_vax-sub_age_40_59-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_40_59-any_dementia.txt
cox_ipw-cohort_vax-sub_age_40_59-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-any_dementia.csv
needs:
- make_model_input-cohort_vax-sub_age_40_59-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_40_59-any_dementia.csv
make_model_input-cohort_vax-sub_age_40_59-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-cognitive_impairment
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_40_59-cognitive_impairment.rds
describe_model_input-cohort_vax-sub_age_40_59-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_40_59-cognitive_impairment
rds
needs:
- make_model_input-cohort_vax-sub_age_40_59-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_40_59-cognitive_impairment.txt
cox_ipw-cohort_vax-sub_age_40_59-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-cognitive_impairment.csv
needs:
- make_model_input-cohort_vax-sub_age_40_59-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_40_59-cognitive_impairment.csv
make_model_input-cohort_vax-sub_age_40_59-migraine:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_40_59-migraine.rds
describe_model_input-cohort_vax-sub_age_40_59-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_40_59-migraine
rds
needs:
- make_model_input-cohort_vax-sub_age_40_59-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_40_59-migraine.txt
cox_ipw-cohort_vax-sub_age_40_59-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-migraine.csv
needs:
- make_model_input-cohort_vax-sub_age_40_59-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_40_59-migraine.csv
make_model_input-cohort_vax-sub_age_40_59-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-parkinson_disease
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_40_59-parkinson_disease.rds
describe_model_input-cohort_vax-sub_age_40_59-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_40_59-parkinson_disease
rds
needs:
- make_model_input-cohort_vax-sub_age_40_59-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_40_59-parkinson_disease.txt
cox_ipw-cohort_vax-sub_age_40_59-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-parkinson_disease.csv
needs:
- make_model_input-cohort_vax-sub_age_40_59-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_40_59-parkinson_disease.csv
make_model_input-cohort_vax-sub_age_40_59-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-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_vax-sub_age_40_59-rem_sleep_disorder.rds
describe_model_input-cohort_vax-sub_age_40_59-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_40_59-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_vax-sub_age_40_59-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_40_59-rem_sleep_disorder.txt
cox_ipw-cohort_vax-sub_age_40_59-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_40_59-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=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_vax-sub_age_40_59-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_40_59-rem_sleep_disorder.csv
make_model_input-cohort_prevax-sub_age_60_79-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-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-sub_age_60_79-alzheimer_disease.rds
describe_model_input-cohort_prevax-sub_age_60_79-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_60_79-alzheimer_disease
rds
needs:
- make_model_input-cohort_prevax-sub_age_60_79-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_60_79-alzheimer_disease.txt
cox_ipw-cohort_prevax-sub_age_60_79-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-alzheimer_disease.csv
needs:
- make_model_input-cohort_prevax-sub_age_60_79-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_60_79-alzheimer_disease.csv
make_model_input-cohort_prevax-sub_age_60_79-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-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-sub_age_60_79-any_dementia.rds
describe_model_input-cohort_prevax-sub_age_60_79-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_60_79-any_dementia
rds
needs:
- make_model_input-cohort_prevax-sub_age_60_79-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_60_79-any_dementia.txt
cox_ipw-cohort_prevax-sub_age_60_79-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-any_dementia.csv
needs:
- make_model_input-cohort_prevax-sub_age_60_79-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_60_79-any_dementia.csv
make_model_input-cohort_prevax-sub_age_60_79-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-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-sub_age_60_79-cognitive_impairment.rds
describe_model_input-cohort_prevax-sub_age_60_79-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_60_79-cognitive_impairment
rds
needs:
- make_model_input-cohort_prevax-sub_age_60_79-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_60_79-cognitive_impairment.txt
cox_ipw-cohort_prevax-sub_age_60_79-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-cognitive_impairment.csv
needs:
- make_model_input-cohort_prevax-sub_age_60_79-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_60_79-cognitive_impairment.csv
make_model_input-cohort_prevax-sub_age_60_79-migraine:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_60_79-migraine.rds
describe_model_input-cohort_prevax-sub_age_60_79-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_60_79-migraine
rds
needs:
- make_model_input-cohort_prevax-sub_age_60_79-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_60_79-migraine.txt
cox_ipw-cohort_prevax-sub_age_60_79-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-migraine.csv
needs:
- make_model_input-cohort_prevax-sub_age_60_79-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_60_79-migraine.csv
make_model_input-cohort_prevax-sub_age_60_79-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-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-sub_age_60_79-parkinson_disease.rds
describe_model_input-cohort_prevax-sub_age_60_79-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_60_79-parkinson_disease
rds
needs:
- make_model_input-cohort_prevax-sub_age_60_79-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_60_79-parkinson_disease.txt
cox_ipw-cohort_prevax-sub_age_60_79-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-parkinson_disease.csv
needs:
- make_model_input-cohort_prevax-sub_age_60_79-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_60_79-parkinson_disease.csv
make_model_input-cohort_prevax-sub_age_60_79-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-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-sub_age_60_79-rem_sleep_disorder.rds
describe_model_input-cohort_prevax-sub_age_60_79-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_60_79-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_prevax-sub_age_60_79-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_60_79-rem_sleep_disorder.txt
cox_ipw-cohort_prevax-sub_age_60_79-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_prevax-sub_age_60_79-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_60_79-rem_sleep_disorder.csv
make_model_input-cohort_unvax-sub_age_60_79-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-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-sub_age_60_79-alzheimer_disease.rds
describe_model_input-cohort_unvax-sub_age_60_79-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_60_79-alzheimer_disease
rds
needs:
- make_model_input-cohort_unvax-sub_age_60_79-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_60_79-alzheimer_disease.txt
cox_ipw-cohort_unvax-sub_age_60_79-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-alzheimer_disease.csv
needs:
- make_model_input-cohort_unvax-sub_age_60_79-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_60_79-alzheimer_disease.csv
make_model_input-cohort_unvax-sub_age_60_79-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-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-sub_age_60_79-any_dementia.rds
describe_model_input-cohort_unvax-sub_age_60_79-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_60_79-any_dementia
rds
needs:
- make_model_input-cohort_unvax-sub_age_60_79-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_60_79-any_dementia.txt
cox_ipw-cohort_unvax-sub_age_60_79-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-any_dementia.csv
needs:
- make_model_input-cohort_unvax-sub_age_60_79-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_60_79-any_dementia.csv
make_model_input-cohort_unvax-sub_age_60_79-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-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-sub_age_60_79-cognitive_impairment.rds
describe_model_input-cohort_unvax-sub_age_60_79-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_60_79-cognitive_impairment
rds
needs:
- make_model_input-cohort_unvax-sub_age_60_79-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_60_79-cognitive_impairment.txt
cox_ipw-cohort_unvax-sub_age_60_79-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-cognitive_impairment.csv
needs:
- make_model_input-cohort_unvax-sub_age_60_79-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_60_79-cognitive_impairment.csv
make_model_input-cohort_unvax-sub_age_60_79-migraine:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_60_79-migraine.rds
describe_model_input-cohort_unvax-sub_age_60_79-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_60_79-migraine
rds
needs:
- make_model_input-cohort_unvax-sub_age_60_79-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_60_79-migraine.txt
cox_ipw-cohort_unvax-sub_age_60_79-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-migraine.csv
needs:
- make_model_input-cohort_unvax-sub_age_60_79-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_60_79-migraine.csv
make_model_input-cohort_unvax-sub_age_60_79-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-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-sub_age_60_79-parkinson_disease.rds
describe_model_input-cohort_unvax-sub_age_60_79-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_60_79-parkinson_disease
rds
needs:
- make_model_input-cohort_unvax-sub_age_60_79-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_60_79-parkinson_disease.txt
cox_ipw-cohort_unvax-sub_age_60_79-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-parkinson_disease.csv
needs:
- make_model_input-cohort_unvax-sub_age_60_79-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_60_79-parkinson_disease.csv
make_model_input-cohort_unvax-sub_age_60_79-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-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-sub_age_60_79-rem_sleep_disorder.rds
describe_model_input-cohort_unvax-sub_age_60_79-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_60_79-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_unvax-sub_age_60_79-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_60_79-rem_sleep_disorder.txt
cox_ipw-cohort_unvax-sub_age_60_79-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_unvax-sub_age_60_79-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_60_79-rem_sleep_disorder.csv
make_model_input-cohort_vax-sub_age_60_79-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-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-sub_age_60_79-alzheimer_disease.rds
describe_model_input-cohort_vax-sub_age_60_79-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_60_79-alzheimer_disease
rds
needs:
- make_model_input-cohort_vax-sub_age_60_79-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_60_79-alzheimer_disease.txt
cox_ipw-cohort_vax-sub_age_60_79-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-alzheimer_disease.csv
needs:
- make_model_input-cohort_vax-sub_age_60_79-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_60_79-alzheimer_disease.csv
make_model_input-cohort_vax-sub_age_60_79-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-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-sub_age_60_79-any_dementia.rds
describe_model_input-cohort_vax-sub_age_60_79-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_60_79-any_dementia
rds
needs:
- make_model_input-cohort_vax-sub_age_60_79-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_60_79-any_dementia.txt
cox_ipw-cohort_vax-sub_age_60_79-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-any_dementia.csv
needs:
- make_model_input-cohort_vax-sub_age_60_79-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_60_79-any_dementia.csv
make_model_input-cohort_vax-sub_age_60_79-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-cognitive_impairment
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_60_79-cognitive_impairment.rds
describe_model_input-cohort_vax-sub_age_60_79-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_60_79-cognitive_impairment
rds
needs:
- make_model_input-cohort_vax-sub_age_60_79-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_60_79-cognitive_impairment.txt
cox_ipw-cohort_vax-sub_age_60_79-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-cognitive_impairment.csv
needs:
- make_model_input-cohort_vax-sub_age_60_79-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_60_79-cognitive_impairment.csv
make_model_input-cohort_vax-sub_age_60_79-migraine:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_60_79-migraine.rds
describe_model_input-cohort_vax-sub_age_60_79-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_60_79-migraine
rds
needs:
- make_model_input-cohort_vax-sub_age_60_79-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_60_79-migraine.txt
cox_ipw-cohort_vax-sub_age_60_79-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-migraine.csv
needs:
- make_model_input-cohort_vax-sub_age_60_79-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_60_79-migraine.csv
make_model_input-cohort_vax-sub_age_60_79-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-parkinson_disease
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_60_79-parkinson_disease.rds
describe_model_input-cohort_vax-sub_age_60_79-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_60_79-parkinson_disease
rds
needs:
- make_model_input-cohort_vax-sub_age_60_79-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_60_79-parkinson_disease.txt
cox_ipw-cohort_vax-sub_age_60_79-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-parkinson_disease.csv
needs:
- make_model_input-cohort_vax-sub_age_60_79-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_60_79-parkinson_disease.csv
make_model_input-cohort_vax-sub_age_60_79-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-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_vax-sub_age_60_79-rem_sleep_disorder.rds
describe_model_input-cohort_vax-sub_age_60_79-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_60_79-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_vax-sub_age_60_79-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_60_79-rem_sleep_disorder.txt
cox_ipw-cohort_vax-sub_age_60_79-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_60_79-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=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_vax-sub_age_60_79-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_60_79-rem_sleep_disorder.csv
make_model_input-cohort_prevax-sub_age_80_110-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-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-sub_age_80_110-alzheimer_disease.rds
describe_model_input-cohort_prevax-sub_age_80_110-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_80_110-alzheimer_disease
rds
needs:
- make_model_input-cohort_prevax-sub_age_80_110-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_80_110-alzheimer_disease.txt
cox_ipw-cohort_prevax-sub_age_80_110-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-alzheimer_disease.csv
needs:
- make_model_input-cohort_prevax-sub_age_80_110-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_80_110-alzheimer_disease.csv
make_model_input-cohort_prevax-sub_age_80_110-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-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-sub_age_80_110-any_dementia.rds
describe_model_input-cohort_prevax-sub_age_80_110-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_80_110-any_dementia
rds
needs:
- make_model_input-cohort_prevax-sub_age_80_110-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_80_110-any_dementia.txt
cox_ipw-cohort_prevax-sub_age_80_110-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-any_dementia.csv
needs:
- make_model_input-cohort_prevax-sub_age_80_110-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_80_110-any_dementia.csv
make_model_input-cohort_prevax-sub_age_80_110-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-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-sub_age_80_110-cognitive_impairment.rds
describe_model_input-cohort_prevax-sub_age_80_110-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_80_110-cognitive_impairment
rds
needs:
- make_model_input-cohort_prevax-sub_age_80_110-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_80_110-cognitive_impairment.txt
cox_ipw-cohort_prevax-sub_age_80_110-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-cognitive_impairment.csv
needs:
- make_model_input-cohort_prevax-sub_age_80_110-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_80_110-cognitive_impairment.csv
make_model_input-cohort_prevax-sub_age_80_110-migraine:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_age_80_110-migraine.rds
describe_model_input-cohort_prevax-sub_age_80_110-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_80_110-migraine
rds
needs:
- make_model_input-cohort_prevax-sub_age_80_110-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_80_110-migraine.txt
cox_ipw-cohort_prevax-sub_age_80_110-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-migraine.csv
needs:
- make_model_input-cohort_prevax-sub_age_80_110-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_80_110-migraine.csv
make_model_input-cohort_prevax-sub_age_80_110-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-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-sub_age_80_110-parkinson_disease.rds
describe_model_input-cohort_prevax-sub_age_80_110-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_80_110-parkinson_disease
rds
needs:
- make_model_input-cohort_prevax-sub_age_80_110-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_80_110-parkinson_disease.txt
cox_ipw-cohort_prevax-sub_age_80_110-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-parkinson_disease.csv
needs:
- make_model_input-cohort_prevax-sub_age_80_110-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_80_110-parkinson_disease.csv
make_model_input-cohort_prevax-sub_age_80_110-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-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-sub_age_80_110-rem_sleep_disorder.rds
describe_model_input-cohort_prevax-sub_age_80_110-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_80_110-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_prevax-sub_age_80_110-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_age_80_110-rem_sleep_disorder.txt
cox_ipw-cohort_prevax-sub_age_80_110-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_prevax-sub_age_80_110-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_age_80_110-rem_sleep_disorder.csv
make_model_input-cohort_unvax-sub_age_80_110-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-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-sub_age_80_110-alzheimer_disease.rds
describe_model_input-cohort_unvax-sub_age_80_110-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_80_110-alzheimer_disease
rds
needs:
- make_model_input-cohort_unvax-sub_age_80_110-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_80_110-alzheimer_disease.txt
cox_ipw-cohort_unvax-sub_age_80_110-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-alzheimer_disease.csv
needs:
- make_model_input-cohort_unvax-sub_age_80_110-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_80_110-alzheimer_disease.csv
make_model_input-cohort_unvax-sub_age_80_110-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-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-sub_age_80_110-any_dementia.rds
describe_model_input-cohort_unvax-sub_age_80_110-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_80_110-any_dementia
rds
needs:
- make_model_input-cohort_unvax-sub_age_80_110-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_80_110-any_dementia.txt
cox_ipw-cohort_unvax-sub_age_80_110-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-any_dementia.csv
needs:
- make_model_input-cohort_unvax-sub_age_80_110-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_80_110-any_dementia.csv
make_model_input-cohort_unvax-sub_age_80_110-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-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-sub_age_80_110-cognitive_impairment.rds
describe_model_input-cohort_unvax-sub_age_80_110-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_80_110-cognitive_impairment
rds
needs:
- make_model_input-cohort_unvax-sub_age_80_110-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_80_110-cognitive_impairment.txt
cox_ipw-cohort_unvax-sub_age_80_110-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-cognitive_impairment.csv
needs:
- make_model_input-cohort_unvax-sub_age_80_110-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_80_110-cognitive_impairment.csv
make_model_input-cohort_unvax-sub_age_80_110-migraine:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_age_80_110-migraine.rds
describe_model_input-cohort_unvax-sub_age_80_110-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_80_110-migraine
rds
needs:
- make_model_input-cohort_unvax-sub_age_80_110-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_80_110-migraine.txt
cox_ipw-cohort_unvax-sub_age_80_110-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-migraine.csv
needs:
- make_model_input-cohort_unvax-sub_age_80_110-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_80_110-migraine.csv
make_model_input-cohort_unvax-sub_age_80_110-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-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-sub_age_80_110-parkinson_disease.rds
describe_model_input-cohort_unvax-sub_age_80_110-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_80_110-parkinson_disease
rds
needs:
- make_model_input-cohort_unvax-sub_age_80_110-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_80_110-parkinson_disease.txt
cox_ipw-cohort_unvax-sub_age_80_110-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-parkinson_disease.csv
needs:
- make_model_input-cohort_unvax-sub_age_80_110-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_80_110-parkinson_disease.csv
make_model_input-cohort_unvax-sub_age_80_110-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-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-sub_age_80_110-rem_sleep_disorder.rds
describe_model_input-cohort_unvax-sub_age_80_110-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_80_110-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_unvax-sub_age_80_110-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_age_80_110-rem_sleep_disorder.txt
cox_ipw-cohort_unvax-sub_age_80_110-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_unvax-sub_age_80_110-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_age_80_110-rem_sleep_disorder.csv
make_model_input-cohort_vax-sub_age_80_110-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-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-sub_age_80_110-alzheimer_disease.rds
describe_model_input-cohort_vax-sub_age_80_110-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_80_110-alzheimer_disease
rds
needs:
- make_model_input-cohort_vax-sub_age_80_110-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_80_110-alzheimer_disease.txt
cox_ipw-cohort_vax-sub_age_80_110-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-alzheimer_disease.csv
needs:
- make_model_input-cohort_vax-sub_age_80_110-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_80_110-alzheimer_disease.csv
make_model_input-cohort_vax-sub_age_80_110-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-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-sub_age_80_110-any_dementia.rds
describe_model_input-cohort_vax-sub_age_80_110-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_80_110-any_dementia
rds
needs:
- make_model_input-cohort_vax-sub_age_80_110-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_80_110-any_dementia.txt
cox_ipw-cohort_vax-sub_age_80_110-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-any_dementia.csv
needs:
- make_model_input-cohort_vax-sub_age_80_110-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_80_110-any_dementia.csv
make_model_input-cohort_vax-sub_age_80_110-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-cognitive_impairment
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_80_110-cognitive_impairment.rds
describe_model_input-cohort_vax-sub_age_80_110-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_80_110-cognitive_impairment
rds
needs:
- make_model_input-cohort_vax-sub_age_80_110-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_80_110-cognitive_impairment.txt
cox_ipw-cohort_vax-sub_age_80_110-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-cognitive_impairment.csv
needs:
- make_model_input-cohort_vax-sub_age_80_110-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_80_110-cognitive_impairment.csv
make_model_input-cohort_vax-sub_age_80_110-migraine:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_80_110-migraine.rds
describe_model_input-cohort_vax-sub_age_80_110-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_80_110-migraine
rds
needs:
- make_model_input-cohort_vax-sub_age_80_110-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_80_110-migraine.txt
cox_ipw-cohort_vax-sub_age_80_110-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-migraine.csv
needs:
- make_model_input-cohort_vax-sub_age_80_110-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_80_110-migraine.csv
make_model_input-cohort_vax-sub_age_80_110-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-parkinson_disease
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_80_110-parkinson_disease.rds
describe_model_input-cohort_vax-sub_age_80_110-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_80_110-parkinson_disease
rds
needs:
- make_model_input-cohort_vax-sub_age_80_110-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_80_110-parkinson_disease.txt
cox_ipw-cohort_vax-sub_age_80_110-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-parkinson_disease.csv
needs:
- make_model_input-cohort_vax-sub_age_80_110-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_80_110-parkinson_disease.csv
make_model_input-cohort_vax-sub_age_80_110-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-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_vax-sub_age_80_110-rem_sleep_disorder.rds
describe_model_input-cohort_vax-sub_age_80_110-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_80_110-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_vax-sub_age_80_110-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_age_80_110-rem_sleep_disorder.txt
cox_ipw-cohort_vax-sub_age_80_110-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_80_110-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=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_vax-sub_age_80_110-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_80_110-rem_sleep_disorder.csv
make_model_input-cohort_unvax-sub_covid_history-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-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-sub_covid_history-alzheimer_disease.rds
describe_model_input-cohort_unvax-sub_covid_history-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-alzheimer_disease
rds
needs:
- make_model_input-cohort_unvax-sub_covid_history-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-alzheimer_disease.txt
cox_ipw-cohort_unvax-sub_covid_history-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-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-sub_covid_history-alzheimer_disease.csv
needs:
- make_model_input-cohort_unvax-sub_covid_history-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_history-alzheimer_disease.csv
make_model_input-cohort_unvax-sub_covid_history-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-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-sub_covid_history-any_dementia.rds
describe_model_input-cohort_unvax-sub_covid_history-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-any_dementia
rds
needs:
- make_model_input-cohort_unvax-sub_covid_history-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-any_dementia.txt
cox_ipw-cohort_unvax-sub_covid_history-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-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-sub_covid_history-any_dementia.csv
needs:
- make_model_input-cohort_unvax-sub_covid_history-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_history-any_dementia.csv
make_model_input-cohort_unvax-sub_covid_history-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-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-sub_covid_history-cognitive_impairment.rds
describe_model_input-cohort_unvax-sub_covid_history-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-cognitive_impairment
rds
needs:
- make_model_input-cohort_unvax-sub_covid_history-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-cognitive_impairment.txt
cox_ipw-cohort_unvax-sub_covid_history-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-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-sub_covid_history-cognitive_impairment.csv
needs:
- make_model_input-cohort_unvax-sub_covid_history-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_history-cognitive_impairment.csv
make_model_input-cohort_unvax-sub_covid_history-migraine:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_covid_history-migraine.rds
describe_model_input-cohort_unvax-sub_covid_history-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-migraine
rds
needs:
- make_model_input-cohort_unvax-sub_covid_history-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-migraine.txt
cox_ipw-cohort_unvax-sub_covid_history-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-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-sub_covid_history-migraine.csv
needs:
- make_model_input-cohort_unvax-sub_covid_history-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_history-migraine.csv
make_model_input-cohort_unvax-sub_covid_history-motor_neurone_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-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-sub_covid_history-motor_neurone_disease.rds
describe_model_input-cohort_unvax-sub_covid_history-motor_neurone_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-motor_neurone_disease
rds
needs:
- make_model_input-cohort_unvax-sub_covid_history-motor_neurone_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-motor_neurone_disease.txt
cox_ipw-cohort_unvax-sub_covid_history-motor_neurone_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-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-sub_covid_history-motor_neurone_disease.csv
needs:
- make_model_input-cohort_unvax-sub_covid_history-motor_neurone_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_history-motor_neurone_disease.csv
make_model_input-cohort_unvax-sub_covid_history-multiple_sclerosis:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-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-sub_covid_history-multiple_sclerosis.rds
describe_model_input-cohort_unvax-sub_covid_history-multiple_sclerosis:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-multiple_sclerosis
rds
needs:
- make_model_input-cohort_unvax-sub_covid_history-multiple_sclerosis
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-multiple_sclerosis.txt
cox_ipw-cohort_unvax-sub_covid_history-multiple_sclerosis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-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-sub_covid_history-multiple_sclerosis.csv
needs:
- make_model_input-cohort_unvax-sub_covid_history-multiple_sclerosis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_history-multiple_sclerosis.csv
make_model_input-cohort_unvax-sub_covid_history-other_dementias:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-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-sub_covid_history-other_dementias.rds
describe_model_input-cohort_unvax-sub_covid_history-other_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-other_dementias
rds
needs:
- make_model_input-cohort_unvax-sub_covid_history-other_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-other_dementias.txt
cox_ipw-cohort_unvax-sub_covid_history-other_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-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-sub_covid_history-other_dementias.csv
needs:
- make_model_input-cohort_unvax-sub_covid_history-other_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_history-other_dementias.csv
make_model_input-cohort_unvax-sub_covid_history-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-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-sub_covid_history-parkinson_disease.rds
describe_model_input-cohort_unvax-sub_covid_history-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-parkinson_disease
rds
needs:
- make_model_input-cohort_unvax-sub_covid_history-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-parkinson_disease.txt
cox_ipw-cohort_unvax-sub_covid_history-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-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-sub_covid_history-parkinson_disease.csv
needs:
- make_model_input-cohort_unvax-sub_covid_history-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_history-parkinson_disease.csv
make_model_input-cohort_unvax-sub_covid_history-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-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-sub_covid_history-rem_sleep_disorder.rds
describe_model_input-cohort_unvax-sub_covid_history-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_unvax-sub_covid_history-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-rem_sleep_disorder.txt
cox_ipw-cohort_unvax-sub_covid_history-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-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-sub_covid_history-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_unvax-sub_covid_history-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_history-rem_sleep_disorder.csv
make_model_input-cohort_unvax-sub_covid_history-restless_leg_syndrome:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-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-sub_covid_history-restless_leg_syndrome.rds
describe_model_input-cohort_unvax-sub_covid_history-restless_leg_syndrome:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-restless_leg_syndrome
rds
needs:
- make_model_input-cohort_unvax-sub_covid_history-restless_leg_syndrome
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-restless_leg_syndrome.txt
cox_ipw-cohort_unvax-sub_covid_history-restless_leg_syndrome:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-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-sub_covid_history-restless_leg_syndrome.csv
needs:
- make_model_input-cohort_unvax-sub_covid_history-restless_leg_syndrome
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_history-restless_leg_syndrome.csv
make_model_input-cohort_unvax-sub_covid_history-unspecified_dementias:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-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-sub_covid_history-unspecified_dementias.rds
describe_model_input-cohort_unvax-sub_covid_history-unspecified_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-unspecified_dementias
rds
needs:
- make_model_input-cohort_unvax-sub_covid_history-unspecified_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-unspecified_dementias.txt
cox_ipw-cohort_unvax-sub_covid_history-unspecified_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-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-sub_covid_history-unspecified_dementias.csv
needs:
- make_model_input-cohort_unvax-sub_covid_history-unspecified_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_history-unspecified_dementias.csv
make_model_input-cohort_unvax-sub_covid_history-vascular_dementia:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-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-sub_covid_history-vascular_dementia.rds
describe_model_input-cohort_unvax-sub_covid_history-vascular_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-vascular_dementia
rds
needs:
- make_model_input-cohort_unvax-sub_covid_history-vascular_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-vascular_dementia.txt
cox_ipw-cohort_unvax-sub_covid_history-vascular_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-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-sub_covid_history-vascular_dementia.csv
needs:
- make_model_input-cohort_unvax-sub_covid_history-vascular_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_history-vascular_dementia.csv
make_model_input-cohort_vax-sub_covid_history-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-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-sub_covid_history-alzheimer_disease.rds
describe_model_input-cohort_vax-sub_covid_history-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-alzheimer_disease
rds
needs:
- make_model_input-cohort_vax-sub_covid_history-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-alzheimer_disease.txt
cox_ipw-cohort_vax-sub_covid_history-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-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-sub_covid_history-alzheimer_disease.csv
needs:
- make_model_input-cohort_vax-sub_covid_history-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_history-alzheimer_disease.csv
make_model_input-cohort_vax-sub_covid_history-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-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-sub_covid_history-any_dementia.rds
describe_model_input-cohort_vax-sub_covid_history-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-any_dementia
rds
needs:
- make_model_input-cohort_vax-sub_covid_history-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-any_dementia.txt
cox_ipw-cohort_vax-sub_covid_history-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-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_vax-sub_covid_history-any_dementia.csv
needs:
- make_model_input-cohort_vax-sub_covid_history-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_history-any_dementia.csv
make_model_input-cohort_vax-sub_covid_history-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-cognitive_impairment
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_history-cognitive_impairment.rds
describe_model_input-cohort_vax-sub_covid_history-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-cognitive_impairment
rds
needs:
- make_model_input-cohort_vax-sub_covid_history-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-cognitive_impairment.txt
cox_ipw-cohort_vax-sub_covid_history-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-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_vax-sub_covid_history-cognitive_impairment.csv
needs:
- make_model_input-cohort_vax-sub_covid_history-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_history-cognitive_impairment.csv
make_model_input-cohort_vax-sub_covid_history-migraine:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_history-migraine.rds
describe_model_input-cohort_vax-sub_covid_history-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-migraine
rds
needs:
- make_model_input-cohort_vax-sub_covid_history-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-migraine.txt
cox_ipw-cohort_vax-sub_covid_history-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-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_vax-sub_covid_history-migraine.csv
needs:
- make_model_input-cohort_vax-sub_covid_history-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_history-migraine.csv
make_model_input-cohort_vax-sub_covid_history-motor_neurone_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-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_vax-sub_covid_history-motor_neurone_disease.rds
describe_model_input-cohort_vax-sub_covid_history-motor_neurone_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-motor_neurone_disease
rds
needs:
- make_model_input-cohort_vax-sub_covid_history-motor_neurone_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-motor_neurone_disease.txt
cox_ipw-cohort_vax-sub_covid_history-motor_neurone_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-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_vax-sub_covid_history-motor_neurone_disease.csv
needs:
- make_model_input-cohort_vax-sub_covid_history-motor_neurone_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_history-motor_neurone_disease.csv
make_model_input-cohort_vax-sub_covid_history-multiple_sclerosis:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-multiple_sclerosis
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_history-multiple_sclerosis.rds
describe_model_input-cohort_vax-sub_covid_history-multiple_sclerosis:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-multiple_sclerosis
rds
needs:
- make_model_input-cohort_vax-sub_covid_history-multiple_sclerosis
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-multiple_sclerosis.txt
cox_ipw-cohort_vax-sub_covid_history-multiple_sclerosis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-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_vax-sub_covid_history-multiple_sclerosis.csv
needs:
- make_model_input-cohort_vax-sub_covid_history-multiple_sclerosis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_history-multiple_sclerosis.csv
make_model_input-cohort_vax-sub_covid_history-other_dementias:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-other_dementias
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_history-other_dementias.rds
describe_model_input-cohort_vax-sub_covid_history-other_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-other_dementias
rds
needs:
- make_model_input-cohort_vax-sub_covid_history-other_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-other_dementias.txt
cox_ipw-cohort_vax-sub_covid_history-other_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-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_vax-sub_covid_history-other_dementias.csv
needs:
- make_model_input-cohort_vax-sub_covid_history-other_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_history-other_dementias.csv
make_model_input-cohort_vax-sub_covid_history-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-parkinson_disease
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_history-parkinson_disease.rds
describe_model_input-cohort_vax-sub_covid_history-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-parkinson_disease
rds
needs:
- make_model_input-cohort_vax-sub_covid_history-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-parkinson_disease.txt
cox_ipw-cohort_vax-sub_covid_history-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-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_vax-sub_covid_history-parkinson_disease.csv
needs:
- make_model_input-cohort_vax-sub_covid_history-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_history-parkinson_disease.csv
make_model_input-cohort_vax-sub_covid_history-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-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_vax-sub_covid_history-rem_sleep_disorder.rds
describe_model_input-cohort_vax-sub_covid_history-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_vax-sub_covid_history-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-rem_sleep_disorder.txt
cox_ipw-cohort_vax-sub_covid_history-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-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_vax-sub_covid_history-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_vax-sub_covid_history-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_history-rem_sleep_disorder.csv
make_model_input-cohort_vax-sub_covid_history-restless_leg_syndrome:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-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_vax-sub_covid_history-restless_leg_syndrome.rds
describe_model_input-cohort_vax-sub_covid_history-restless_leg_syndrome:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-restless_leg_syndrome
rds
needs:
- make_model_input-cohort_vax-sub_covid_history-restless_leg_syndrome
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-restless_leg_syndrome.txt
cox_ipw-cohort_vax-sub_covid_history-restless_leg_syndrome:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-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_vax-sub_covid_history-restless_leg_syndrome.csv
needs:
- make_model_input-cohort_vax-sub_covid_history-restless_leg_syndrome
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_history-restless_leg_syndrome.csv
make_model_input-cohort_vax-sub_covid_history-unspecified_dementias:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-unspecified_dementias
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_history-unspecified_dementias.rds
describe_model_input-cohort_vax-sub_covid_history-unspecified_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-unspecified_dementias
rds
needs:
- make_model_input-cohort_vax-sub_covid_history-unspecified_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-unspecified_dementias.txt
cox_ipw-cohort_vax-sub_covid_history-unspecified_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-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_vax-sub_covid_history-unspecified_dementias.csv
needs:
- make_model_input-cohort_vax-sub_covid_history-unspecified_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_history-unspecified_dementias.csv
make_model_input-cohort_vax-sub_covid_history-vascular_dementia:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-vascular_dementia
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_history-vascular_dementia.rds
describe_model_input-cohort_vax-sub_covid_history-vascular_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-vascular_dementia
rds
needs:
- make_model_input-cohort_vax-sub_covid_history-vascular_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-vascular_dementia.txt
cox_ipw-cohort_vax-sub_covid_history-vascular_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-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_vax-sub_covid_history-vascular_dementia.csv
needs:
- make_model_input-cohort_vax-sub_covid_history-vascular_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_history-vascular_dementia.csv
make_model_input-cohort_prevax-sub_covid_hospitalised-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-alzheimer_disease.rds
describe_model_input-cohort_prevax-sub_covid_hospitalised-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-alzheimer_disease
rds
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-alzheimer_disease.txt
cox_ipw-cohort_prevax-sub_covid_hospitalised-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-alzheimer_disease.csv
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-alzheimer_disease.csv
make_model_input-cohort_prevax-sub_covid_hospitalised-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-any_dementia.rds
describe_model_input-cohort_prevax-sub_covid_hospitalised-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-any_dementia
rds
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-any_dementia.txt
cox_ipw-cohort_prevax-sub_covid_hospitalised-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-any_dementia.csv
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-any_dementia.csv
make_model_input-cohort_prevax-sub_covid_hospitalised-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-cognitive_impairment.rds
describe_model_input-cohort_prevax-sub_covid_hospitalised-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-cognitive_impairment
rds
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-cognitive_impairment.txt
cox_ipw-cohort_prevax-sub_covid_hospitalised-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-cognitive_impairment.csv
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-cognitive_impairment.csv
make_model_input-cohort_prevax-sub_covid_hospitalised-migraine:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-migraine.rds
describe_model_input-cohort_prevax-sub_covid_hospitalised-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-migraine
rds
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-migraine.txt
cox_ipw-cohort_prevax-sub_covid_hospitalised-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-migraine.csv
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-migraine.csv
make_model_input-cohort_prevax-sub_covid_hospitalised-motor_neurone_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-motor_neurone_disease.rds
describe_model_input-cohort_prevax-sub_covid_hospitalised-motor_neurone_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-motor_neurone_disease
rds
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-motor_neurone_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-motor_neurone_disease.txt
cox_ipw-cohort_prevax-sub_covid_hospitalised-motor_neurone_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-motor_neurone_disease.csv
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-motor_neurone_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-motor_neurone_disease.csv
make_model_input-cohort_prevax-sub_covid_hospitalised-multiple_sclerosis:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-multiple_sclerosis.rds
describe_model_input-cohort_prevax-sub_covid_hospitalised-multiple_sclerosis:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-multiple_sclerosis
rds
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-multiple_sclerosis
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-multiple_sclerosis.txt
cox_ipw-cohort_prevax-sub_covid_hospitalised-multiple_sclerosis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-multiple_sclerosis.csv
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-multiple_sclerosis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-multiple_sclerosis.csv
make_model_input-cohort_prevax-sub_covid_hospitalised-other_dementias:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-other_dementias.rds
describe_model_input-cohort_prevax-sub_covid_hospitalised-other_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-other_dementias
rds
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-other_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-other_dementias.txt
cox_ipw-cohort_prevax-sub_covid_hospitalised-other_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-other_dementias.csv
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-other_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-other_dementias.csv
make_model_input-cohort_prevax-sub_covid_hospitalised-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-parkinson_disease.rds
describe_model_input-cohort_prevax-sub_covid_hospitalised-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-parkinson_disease
rds
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-parkinson_disease.txt
cox_ipw-cohort_prevax-sub_covid_hospitalised-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-parkinson_disease.csv
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-parkinson_disease.csv
make_model_input-cohort_prevax-sub_covid_hospitalised-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-rem_sleep_disorder.rds
describe_model_input-cohort_prevax-sub_covid_hospitalised-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-rem_sleep_disorder.txt
cox_ipw-cohort_prevax-sub_covid_hospitalised-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-rem_sleep_disorder.csv
make_model_input-cohort_prevax-sub_covid_hospitalised-restless_leg_syndrome:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-restless_leg_syndrome.rds
describe_model_input-cohort_prevax-sub_covid_hospitalised-restless_leg_syndrome:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-restless_leg_syndrome
rds
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-restless_leg_syndrome
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-restless_leg_syndrome.txt
cox_ipw-cohort_prevax-sub_covid_hospitalised-restless_leg_syndrome:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-restless_leg_syndrome.csv
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-restless_leg_syndrome
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-restless_leg_syndrome.csv
make_model_input-cohort_prevax-sub_covid_hospitalised-unspecified_dementias:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-unspecified_dementias.rds
describe_model_input-cohort_prevax-sub_covid_hospitalised-unspecified_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-unspecified_dementias
rds
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-unspecified_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-unspecified_dementias.txt
cox_ipw-cohort_prevax-sub_covid_hospitalised-unspecified_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-unspecified_dementias.csv
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-unspecified_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-unspecified_dementias.csv
make_model_input-cohort_prevax-sub_covid_hospitalised-vascular_dementia:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-vascular_dementia.rds
describe_model_input-cohort_prevax-sub_covid_hospitalised-vascular_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-vascular_dementia
rds
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-vascular_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-vascular_dementia.txt
cox_ipw-cohort_prevax-sub_covid_hospitalised-vascular_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-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-sub_covid_hospitalised-vascular_dementia.csv
needs:
- make_model_input-cohort_prevax-sub_covid_hospitalised-vascular_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-vascular_dementia.csv
make_model_input-cohort_unvax-sub_covid_hospitalised-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-alzheimer_disease.rds
describe_model_input-cohort_unvax-sub_covid_hospitalised-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-alzheimer_disease
rds
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-alzheimer_disease.txt
cox_ipw-cohort_unvax-sub_covid_hospitalised-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-alzheimer_disease.csv
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-alzheimer_disease.csv
make_model_input-cohort_unvax-sub_covid_hospitalised-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-any_dementia.rds
describe_model_input-cohort_unvax-sub_covid_hospitalised-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-any_dementia
rds
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-any_dementia.txt
cox_ipw-cohort_unvax-sub_covid_hospitalised-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-any_dementia.csv
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-any_dementia.csv
make_model_input-cohort_unvax-sub_covid_hospitalised-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-cognitive_impairment.rds
describe_model_input-cohort_unvax-sub_covid_hospitalised-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-cognitive_impairment
rds
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-cognitive_impairment.txt
cox_ipw-cohort_unvax-sub_covid_hospitalised-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-cognitive_impairment.csv
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-cognitive_impairment.csv
make_model_input-cohort_unvax-sub_covid_hospitalised-migraine:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-migraine.rds
describe_model_input-cohort_unvax-sub_covid_hospitalised-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-migraine
rds
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-migraine.txt
cox_ipw-cohort_unvax-sub_covid_hospitalised-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-migraine.csv
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-migraine.csv
make_model_input-cohort_unvax-sub_covid_hospitalised-motor_neurone_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-motor_neurone_disease.rds
describe_model_input-cohort_unvax-sub_covid_hospitalised-motor_neurone_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-motor_neurone_disease
rds
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-motor_neurone_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-motor_neurone_disease.txt
cox_ipw-cohort_unvax-sub_covid_hospitalised-motor_neurone_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-motor_neurone_disease.csv
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-motor_neurone_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-motor_neurone_disease.csv
make_model_input-cohort_unvax-sub_covid_hospitalised-multiple_sclerosis:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-multiple_sclerosis.rds
describe_model_input-cohort_unvax-sub_covid_hospitalised-multiple_sclerosis:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-multiple_sclerosis
rds
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-multiple_sclerosis
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-multiple_sclerosis.txt
cox_ipw-cohort_unvax-sub_covid_hospitalised-multiple_sclerosis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-multiple_sclerosis.csv
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-multiple_sclerosis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-multiple_sclerosis.csv
make_model_input-cohort_unvax-sub_covid_hospitalised-other_dementias:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-other_dementias.rds
describe_model_input-cohort_unvax-sub_covid_hospitalised-other_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-other_dementias
rds
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-other_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-other_dementias.txt
cox_ipw-cohort_unvax-sub_covid_hospitalised-other_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-other_dementias.csv
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-other_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-other_dementias.csv
make_model_input-cohort_unvax-sub_covid_hospitalised-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-parkinson_disease.rds
describe_model_input-cohort_unvax-sub_covid_hospitalised-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-parkinson_disease
rds
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-parkinson_disease.txt
cox_ipw-cohort_unvax-sub_covid_hospitalised-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-parkinson_disease.csv
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-parkinson_disease.csv
make_model_input-cohort_unvax-sub_covid_hospitalised-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-rem_sleep_disorder.rds
describe_model_input-cohort_unvax-sub_covid_hospitalised-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-rem_sleep_disorder.txt
cox_ipw-cohort_unvax-sub_covid_hospitalised-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-rem_sleep_disorder.csv
make_model_input-cohort_unvax-sub_covid_hospitalised-restless_leg_syndrome:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-restless_leg_syndrome.rds
describe_model_input-cohort_unvax-sub_covid_hospitalised-restless_leg_syndrome:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-restless_leg_syndrome
rds
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-restless_leg_syndrome
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-restless_leg_syndrome.txt
cox_ipw-cohort_unvax-sub_covid_hospitalised-restless_leg_syndrome:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-restless_leg_syndrome.csv
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-restless_leg_syndrome
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-restless_leg_syndrome.csv
make_model_input-cohort_unvax-sub_covid_hospitalised-unspecified_dementias:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-unspecified_dementias.rds
describe_model_input-cohort_unvax-sub_covid_hospitalised-unspecified_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-unspecified_dementias
rds
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-unspecified_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-unspecified_dementias.txt
cox_ipw-cohort_unvax-sub_covid_hospitalised-unspecified_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-unspecified_dementias.csv
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-unspecified_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-unspecified_dementias.csv
make_model_input-cohort_unvax-sub_covid_hospitalised-vascular_dementia:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-vascular_dementia.rds
describe_model_input-cohort_unvax-sub_covid_hospitalised-vascular_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-vascular_dementia
rds
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-vascular_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-vascular_dementia.txt
cox_ipw-cohort_unvax-sub_covid_hospitalised-vascular_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-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-sub_covid_hospitalised-vascular_dementia.csv
needs:
- make_model_input-cohort_unvax-sub_covid_hospitalised-vascular_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-vascular_dementia.csv
make_model_input-cohort_vax-sub_covid_hospitalised-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-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-sub_covid_hospitalised-alzheimer_disease.rds
describe_model_input-cohort_vax-sub_covid_hospitalised-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-alzheimer_disease
rds
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-alzheimer_disease.txt
cox_ipw-cohort_vax-sub_covid_hospitalised-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-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-sub_covid_hospitalised-alzheimer_disease.csv
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_hospitalised-alzheimer_disease.csv
make_model_input-cohort_vax-sub_covid_hospitalised-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-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-sub_covid_hospitalised-any_dementia.rds
describe_model_input-cohort_vax-sub_covid_hospitalised-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-any_dementia
rds
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-any_dementia.txt
cox_ipw-cohort_vax-sub_covid_hospitalised-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-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_vax-sub_covid_hospitalised-any_dementia.csv
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_hospitalised-any_dementia.csv
make_model_input-cohort_vax-sub_covid_hospitalised-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-cognitive_impairment
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_hospitalised-cognitive_impairment.rds
describe_model_input-cohort_vax-sub_covid_hospitalised-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-cognitive_impairment
rds
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-cognitive_impairment.txt
cox_ipw-cohort_vax-sub_covid_hospitalised-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-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_vax-sub_covid_hospitalised-cognitive_impairment.csv
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_hospitalised-cognitive_impairment.csv
make_model_input-cohort_vax-sub_covid_hospitalised-migraine:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_hospitalised-migraine.rds
describe_model_input-cohort_vax-sub_covid_hospitalised-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-migraine
rds
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-migraine.txt
cox_ipw-cohort_vax-sub_covid_hospitalised-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-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_vax-sub_covid_hospitalised-migraine.csv
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_hospitalised-migraine.csv
make_model_input-cohort_vax-sub_covid_hospitalised-motor_neurone_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-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_vax-sub_covid_hospitalised-motor_neurone_disease.rds
describe_model_input-cohort_vax-sub_covid_hospitalised-motor_neurone_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-motor_neurone_disease
rds
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-motor_neurone_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-motor_neurone_disease.txt
cox_ipw-cohort_vax-sub_covid_hospitalised-motor_neurone_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-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_vax-sub_covid_hospitalised-motor_neurone_disease.csv
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-motor_neurone_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_hospitalised-motor_neurone_disease.csv
make_model_input-cohort_vax-sub_covid_hospitalised-multiple_sclerosis:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-multiple_sclerosis
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_hospitalised-multiple_sclerosis.rds
describe_model_input-cohort_vax-sub_covid_hospitalised-multiple_sclerosis:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-multiple_sclerosis
rds
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-multiple_sclerosis
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-multiple_sclerosis.txt
cox_ipw-cohort_vax-sub_covid_hospitalised-multiple_sclerosis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-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_vax-sub_covid_hospitalised-multiple_sclerosis.csv
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-multiple_sclerosis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_hospitalised-multiple_sclerosis.csv
make_model_input-cohort_vax-sub_covid_hospitalised-other_dementias:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-other_dementias
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_hospitalised-other_dementias.rds
describe_model_input-cohort_vax-sub_covid_hospitalised-other_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-other_dementias
rds
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-other_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-other_dementias.txt
cox_ipw-cohort_vax-sub_covid_hospitalised-other_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-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_vax-sub_covid_hospitalised-other_dementias.csv
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-other_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_hospitalised-other_dementias.csv
make_model_input-cohort_vax-sub_covid_hospitalised-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-parkinson_disease
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_hospitalised-parkinson_disease.rds
describe_model_input-cohort_vax-sub_covid_hospitalised-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-parkinson_disease
rds
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-parkinson_disease.txt
cox_ipw-cohort_vax-sub_covid_hospitalised-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-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_vax-sub_covid_hospitalised-parkinson_disease.csv
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_hospitalised-parkinson_disease.csv
make_model_input-cohort_vax-sub_covid_hospitalised-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-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_vax-sub_covid_hospitalised-rem_sleep_disorder.rds
describe_model_input-cohort_vax-sub_covid_hospitalised-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-rem_sleep_disorder.txt
cox_ipw-cohort_vax-sub_covid_hospitalised-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-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_vax-sub_covid_hospitalised-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_hospitalised-rem_sleep_disorder.csv
make_model_input-cohort_vax-sub_covid_hospitalised-restless_leg_syndrome:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-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_vax-sub_covid_hospitalised-restless_leg_syndrome.rds
describe_model_input-cohort_vax-sub_covid_hospitalised-restless_leg_syndrome:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-restless_leg_syndrome
rds
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-restless_leg_syndrome
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-restless_leg_syndrome.txt
cox_ipw-cohort_vax-sub_covid_hospitalised-restless_leg_syndrome:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-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_vax-sub_covid_hospitalised-restless_leg_syndrome.csv
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-restless_leg_syndrome
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_hospitalised-restless_leg_syndrome.csv
make_model_input-cohort_vax-sub_covid_hospitalised-unspecified_dementias:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-unspecified_dementias
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_hospitalised-unspecified_dementias.rds
describe_model_input-cohort_vax-sub_covid_hospitalised-unspecified_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-unspecified_dementias
rds
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-unspecified_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-unspecified_dementias.txt
cox_ipw-cohort_vax-sub_covid_hospitalised-unspecified_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-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_vax-sub_covid_hospitalised-unspecified_dementias.csv
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-unspecified_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_hospitalised-unspecified_dementias.csv
make_model_input-cohort_vax-sub_covid_hospitalised-vascular_dementia:
run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-vascular_dementia
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_covid_hospitalised-vascular_dementia.rds
describe_model_input-cohort_vax-sub_covid_hospitalised-vascular_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-vascular_dementia
rds
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-vascular_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-vascular_dementia.txt
cox_ipw-cohort_vax-sub_covid_hospitalised-vascular_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-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_vax-sub_covid_hospitalised-vascular_dementia.csv
needs:
- make_model_input-cohort_vax-sub_covid_hospitalised-vascular_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_hospitalised-vascular_dementia.csv
make_model_input-cohort_prevax-sub_covid_nonhospitalised-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-alzheimer_disease.rds
describe_model_input-cohort_prevax-sub_covid_nonhospitalised-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-alzheimer_disease
rds
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-alzheimer_disease.txt
cox_ipw-cohort_prevax-sub_covid_nonhospitalised-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-alzheimer_disease.csv
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-alzheimer_disease.csv
make_model_input-cohort_prevax-sub_covid_nonhospitalised-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-any_dementia.rds
describe_model_input-cohort_prevax-sub_covid_nonhospitalised-any_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-any_dementia
rds
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-any_dementia.txt
cox_ipw-cohort_prevax-sub_covid_nonhospitalised-any_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-any_dementia.csv
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-any_dementia.csv
make_model_input-cohort_prevax-sub_covid_nonhospitalised-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-cognitive_impairment.rds
describe_model_input-cohort_prevax-sub_covid_nonhospitalised-cognitive_impairment:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-cognitive_impairment
rds
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-cognitive_impairment.txt
cox_ipw-cohort_prevax-sub_covid_nonhospitalised-cognitive_impairment:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-cognitive_impairment.csv
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-cognitive_impairment.csv
make_model_input-cohort_prevax-sub_covid_nonhospitalised-migraine:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-migraine
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-migraine.rds
describe_model_input-cohort_prevax-sub_covid_nonhospitalised-migraine:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-migraine
rds
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-migraine.txt
cox_ipw-cohort_prevax-sub_covid_nonhospitalised-migraine:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-migraine.csv
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-migraine.csv
make_model_input-cohort_prevax-sub_covid_nonhospitalised-motor_neurone_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-motor_neurone_disease.rds
describe_model_input-cohort_prevax-sub_covid_nonhospitalised-motor_neurone_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-motor_neurone_disease
rds
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-motor_neurone_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-motor_neurone_disease.txt
cox_ipw-cohort_prevax-sub_covid_nonhospitalised-motor_neurone_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-motor_neurone_disease.csv
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-motor_neurone_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-motor_neurone_disease.csv
make_model_input-cohort_prevax-sub_covid_nonhospitalised-multiple_sclerosis:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-multiple_sclerosis.rds
describe_model_input-cohort_prevax-sub_covid_nonhospitalised-multiple_sclerosis:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-multiple_sclerosis
rds
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-multiple_sclerosis
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-multiple_sclerosis.txt
cox_ipw-cohort_prevax-sub_covid_nonhospitalised-multiple_sclerosis:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-multiple_sclerosis.csv
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-multiple_sclerosis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-multiple_sclerosis.csv
make_model_input-cohort_prevax-sub_covid_nonhospitalised-other_dementias:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-other_dementias.rds
describe_model_input-cohort_prevax-sub_covid_nonhospitalised-other_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-other_dementias
rds
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-other_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-other_dementias.txt
cox_ipw-cohort_prevax-sub_covid_nonhospitalised-other_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-other_dementias.csv
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-other_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-other_dementias.csv
make_model_input-cohort_prevax-sub_covid_nonhospitalised-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-parkinson_disease.rds
describe_model_input-cohort_prevax-sub_covid_nonhospitalised-parkinson_disease:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-parkinson_disease
rds
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-parkinson_disease.txt
cox_ipw-cohort_prevax-sub_covid_nonhospitalised-parkinson_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-parkinson_disease.csv
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-parkinson_disease.csv
make_model_input-cohort_prevax-sub_covid_nonhospitalised-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-rem_sleep_disorder.rds
describe_model_input-cohort_prevax-sub_covid_nonhospitalised-rem_sleep_disorder:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-rem_sleep_disorder.txt
cox_ipw-cohort_prevax-sub_covid_nonhospitalised-rem_sleep_disorder:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-rem_sleep_disorder.csv
make_model_input-cohort_prevax-sub_covid_nonhospitalised-restless_leg_syndrome:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-restless_leg_syndrome.rds
describe_model_input-cohort_prevax-sub_covid_nonhospitalised-restless_leg_syndrome:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-restless_leg_syndrome
rds
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-restless_leg_syndrome
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-restless_leg_syndrome.txt
cox_ipw-cohort_prevax-sub_covid_nonhospitalised-restless_leg_syndrome:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-restless_leg_syndrome.csv
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-restless_leg_syndrome
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-restless_leg_syndrome.csv
make_model_input-cohort_prevax-sub_covid_nonhospitalised-unspecified_dementias:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-unspecified_dementias.rds
describe_model_input-cohort_prevax-sub_covid_nonhospitalised-unspecified_dementias:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-unspecified_dementias
rds
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-unspecified_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-unspecified_dementias.txt
cox_ipw-cohort_prevax-sub_covid_nonhospitalised-unspecified_dementias:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-unspecified_dementias.csv
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-unspecified_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-unspecified_dementias.csv
make_model_input-cohort_prevax-sub_covid_nonhospitalised-vascular_dementia:
run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-vascular_dementia.rds
describe_model_input-cohort_prevax-sub_covid_nonhospitalised-vascular_dementia:
run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-vascular_dementia
rds
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-vascular_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-vascular_dementia.txt
cox_ipw-cohort_prevax-sub_covid_nonhospitalised-vascular_dementia:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-vascular_dementia.csv
needs:
- make_model_input-cohort_prevax-sub_covid_nonhospitalised-vascular_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-vascular_dementia.csv
make_model_input-cohort_unvax-sub_covid_nonhospitalised-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-alzheimer_disease.rds
describe_model_input-cohort_unvax-sub_covid_nonhospitalised-alzheimer_disease:
run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_nonhospitalised-alzheimer_disease
rds
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_nonhospitalised-alzheimer_disease.txt
cox_ipw-cohort_unvax-sub_covid_nonhospitalised-alzheimer_disease:
run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-alzheimer_disease.csv
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-alzheimer_disease.csv
make_model_input-cohort_unvax-sub_covid_nonhospitalised-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-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-sub_covid_nonhospitalised-any_dementia.rds