Job request: 20410
- Organisation:
- University of Bristol
- Workspace:
- post-covid-neurodegenerative-extf
- ID:
- xbe7ryxc7mrsh3ga
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
-
- Job identifier:
-
plzqip3q6p644he5
-
- Job identifier:
-
v6o6zzgkke7dhftd
-
- Job identifier:
-
5eannsub4jdzxwia
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 350000
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.gz
vax_eligible_dates: output/vax_eligible_dates.csv.gz
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
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 - unvax
generate_study_population_unvax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax
--output-format csv.gz
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_unvax.csv.gz
## Generate study population - vax
generate_study_population_vax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vax
--output-format csv.gz
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_vax.csv.gz
## Preprocess data - prevax
preprocess_data_prevax:
run: r:latest analysis/preprocess/preprocess_data.R prevax
needs:
- generate_index_dates
- generate_study_population_prevax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_prevax_stage0.txt
describe_venn: output/not-for-review/describe_venn_prevax.txt
highly_sensitive:
cohort: output/input_prevax.rds
venn: output/venn_prevax.rds
## Preprocess data - unvax
preprocess_data_unvax:
run: r:latest analysis/preprocess/preprocess_data.R unvax
needs:
- generate_index_dates
- generate_study_population_unvax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_unvax_stage0.txt
describe_venn: output/not-for-review/describe_venn_unvax.txt
highly_sensitive:
cohort: output/input_unvax.rds
venn: output/venn_unvax.rds
## Preprocess data - vax
preprocess_data_vax:
run: r:latest analysis/preprocess/preprocess_data.R vax
needs:
- generate_index_dates
- generate_study_population_vax
outputs:
moderately_sensitive:
describe: output/not-for-review/describe_input_vax_stage0.txt
describe_venn: output/not-for-review/describe_venn_vax.txt
highly_sensitive:
cohort: output/input_vax.rds
venn: output/venn_vax.rds
count_study_def_variables:
run: r:latest analysis/descriptives/intitial_input_counts.R
needs:
- generate_study_population_prevax
- generate_study_population_unvax
- generate_study_population_vax
- preprocess_data_prevax
- preprocess_data_unvax
- preprocess_data_vax
outputs:
moderately_sensitive:
counts: output/study_counts_prepro.txt
vax_summary: output/describe_prepro_vax.txt
prevax_summary: output/describe_prepro_prevax.txt
unvax_summary: output/describe_prepro_unvax.txt
count_stage1_variables:
run: r:latest analysis/descriptives/second_input_counts.R
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_unvax
- stage1_data_cleaning_vax
outputs:
moderately_sensitive:
counts: output/study_counts_stage1clean.txt
vax_summary: output/describe_stage1clean_vax.txt
prevax_summary: output/describe_stage1clean_prevax.txt
unvax_summary: output/describe_stage1clean_unvax.txt
## Stage 1 - data cleaning - prevax
stage1_data_cleaning_prevax:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R prevax
needs:
- vax_eligibility_inputs
- preprocess_data_prevax
outputs:
moderately_sensitive:
consort: output/consort_prevax.csv
consort_rounded: output/consort_prevax_rounded.csv
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_stage1.rds
## Stage 1 - data cleaning - unvax
stage1_data_cleaning_unvax:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R unvax
needs:
- vax_eligibility_inputs
- preprocess_data_unvax
outputs:
moderately_sensitive:
consort: output/consort_unvax.csv
consort_rounded: output/consort_unvax_rounded.csv
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_stage1.rds
## Stage 1 - data cleaning - vax
stage1_data_cleaning_vax:
run: r:latest analysis/preprocess/Stage1_data_cleaning.R vax
needs:
- vax_eligibility_inputs
- preprocess_data_vax
outputs:
moderately_sensitive:
consort: output/consort_vax.csv
consort_rounded: output/consort_vax_rounded.csv
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_stage1.rds
make_consort_output:
run: r:latest analysis/model/make_other_output.R consort prevax;vax;unvax
needs:
- stage1_data_cleaning_prevax
- stage1_data_cleaning_vax
- stage1_data_cleaning_unvax
outputs:
moderately_sensitive:
consort_output_rounded: output/consort_output_rounded.csv
## Table 1 - prevax
table1_prevax:
run: r:latest analysis/descriptives/table1.R prevax
needs:
- stage1_data_cleaning_prevax
outputs:
moderately_sensitive:
table1: output/table1_prevax.csv
table1_rounded: output/table1_prevax_rounded.csv
## Table 1 - unvax
table1_unvax:
run: r:latest analysis/descriptives/table1.R unvax
needs:
- stage1_data_cleaning_unvax
outputs:
moderately_sensitive:
table1: output/table1_unvax.csv
table1_rounded: output/table1_unvax_rounded.csv
## Table 1 - vax
table1_vax:
run: r:latest analysis/descriptives/table1.R vax
needs:
- stage1_data_cleaning_vax
outputs:
moderately_sensitive:
table1: output/table1_vax.csv
table1_rounded: output/table1_vax_rounded.csv
## 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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=28;197;365;714 --controls_per_case=20 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-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/model/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:v0.0.27 --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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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
describe_model_input-cohort_unvax-sub_covid_nonhospitalised-any_dementia:
run: r:latest analysis/model/describe_file.R model_input-cohort_unvax-sub_covid_nonhospitalised-any_dementia
rds
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_nonhospitalised-any_dementia.txt
cox_ipw-cohort_unvax-sub_covid_nonhospitalised-any_dementia:
run: cox-ipw:v0.0.27 --df_input=model_input-cohort_unvax-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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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-any_dementia.csv
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-any_dementia.csv
make_model_input-cohort_unvax-sub_covid_nonhospitalised-cognitive_impairment:
run: r:latest analysis/model/make_model_input.R cohort_unvax-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_unvax-sub_covid_nonhospitalised-cognitive_impairment.rds
describe_model_input-cohort_unvax-sub_covid_nonhospitalised-cognitive_impairment:
run: r:latest analysis/model/describe_file.R model_input-cohort_unvax-sub_covid_nonhospitalised-cognitive_impairment
rds
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-cognitive_impairment
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_nonhospitalised-cognitive_impairment.txt
cox_ipw-cohort_unvax-sub_covid_nonhospitalised-cognitive_impairment:
run: cox-ipw:v0.0.27 --df_input=model_input-cohort_unvax-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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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-cognitive_impairment.csv
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-cognitive_impairment
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-cognitive_impairment.csv
make_model_input-cohort_unvax-sub_covid_nonhospitalised-migraine:
run: r:latest analysis/model/make_model_input.R cohort_unvax-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_unvax-sub_covid_nonhospitalised-migraine.rds
describe_model_input-cohort_unvax-sub_covid_nonhospitalised-migraine:
run: r:latest analysis/model/describe_file.R model_input-cohort_unvax-sub_covid_nonhospitalised-migraine
rds
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-migraine
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_nonhospitalised-migraine.txt
cox_ipw-cohort_unvax-sub_covid_nonhospitalised-migraine:
run: cox-ipw:v0.0.27 --df_input=model_input-cohort_unvax-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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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-migraine.csv
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-migraine
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-migraine.csv
make_model_input-cohort_unvax-sub_covid_nonhospitalised-motor_neurone_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-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_unvax-sub_covid_nonhospitalised-motor_neurone_disease.rds
describe_model_input-cohort_unvax-sub_covid_nonhospitalised-motor_neurone_disease:
run: r:latest analysis/model/describe_file.R model_input-cohort_unvax-sub_covid_nonhospitalised-motor_neurone_disease
rds
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-motor_neurone_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_nonhospitalised-motor_neurone_disease.txt
cox_ipw-cohort_unvax-sub_covid_nonhospitalised-motor_neurone_disease:
run: cox-ipw:v0.0.27 --df_input=model_input-cohort_unvax-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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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-motor_neurone_disease.csv
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-motor_neurone_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-motor_neurone_disease.csv
make_model_input-cohort_unvax-sub_covid_nonhospitalised-multiple_sclerosis:
run: r:latest analysis/model/make_model_input.R cohort_unvax-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_unvax-sub_covid_nonhospitalised-multiple_sclerosis.rds
describe_model_input-cohort_unvax-sub_covid_nonhospitalised-multiple_sclerosis:
run: r:latest analysis/model/describe_file.R model_input-cohort_unvax-sub_covid_nonhospitalised-multiple_sclerosis
rds
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-multiple_sclerosis
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_nonhospitalised-multiple_sclerosis.txt
cox_ipw-cohort_unvax-sub_covid_nonhospitalised-multiple_sclerosis:
run: cox-ipw:v0.0.27 --df_input=model_input-cohort_unvax-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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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-multiple_sclerosis.csv
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-multiple_sclerosis
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-multiple_sclerosis.csv
make_model_input-cohort_unvax-sub_covid_nonhospitalised-other_dementias:
run: r:latest analysis/model/make_model_input.R cohort_unvax-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_unvax-sub_covid_nonhospitalised-other_dementias.rds
describe_model_input-cohort_unvax-sub_covid_nonhospitalised-other_dementias:
run: r:latest analysis/model/describe_file.R model_input-cohort_unvax-sub_covid_nonhospitalised-other_dementias
rds
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-other_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_nonhospitalised-other_dementias.txt
cox_ipw-cohort_unvax-sub_covid_nonhospitalised-other_dementias:
run: cox-ipw:v0.0.27 --df_input=model_input-cohort_unvax-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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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-other_dementias.csv
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-other_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-other_dementias.csv
make_model_input-cohort_unvax-sub_covid_nonhospitalised-parkinson_disease:
run: r:latest analysis/model/make_model_input.R cohort_unvax-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_unvax-sub_covid_nonhospitalised-parkinson_disease.rds
describe_model_input-cohort_unvax-sub_covid_nonhospitalised-parkinson_disease:
run: r:latest analysis/model/describe_file.R model_input-cohort_unvax-sub_covid_nonhospitalised-parkinson_disease
rds
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-parkinson_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_nonhospitalised-parkinson_disease.txt
cox_ipw-cohort_unvax-sub_covid_nonhospitalised-parkinson_disease:
run: cox-ipw:v0.0.27 --df_input=model_input-cohort_unvax-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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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-parkinson_disease.csv
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-parkinson_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-parkinson_disease.csv
make_model_input-cohort_unvax-sub_covid_nonhospitalised-rem_sleep_disorder:
run: r:latest analysis/model/make_model_input.R cohort_unvax-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_unvax-sub_covid_nonhospitalised-rem_sleep_disorder.rds
describe_model_input-cohort_unvax-sub_covid_nonhospitalised-rem_sleep_disorder:
run: r:latest analysis/model/describe_file.R model_input-cohort_unvax-sub_covid_nonhospitalised-rem_sleep_disorder
rds
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-rem_sleep_disorder
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_nonhospitalised-rem_sleep_disorder.txt
cox_ipw-cohort_unvax-sub_covid_nonhospitalised-rem_sleep_disorder:
run: cox-ipw:v0.0.27 --df_input=model_input-cohort_unvax-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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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-rem_sleep_disorder.csv
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-rem_sleep_disorder
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-rem_sleep_disorder.csv
make_model_input-cohort_unvax-sub_covid_nonhospitalised-restless_leg_syndrome:
run: r:latest analysis/model/make_model_input.R cohort_unvax-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_unvax-sub_covid_nonhospitalised-restless_leg_syndrome.rds
describe_model_input-cohort_unvax-sub_covid_nonhospitalised-restless_leg_syndrome:
run: r:latest analysis/model/describe_file.R model_input-cohort_unvax-sub_covid_nonhospitalised-restless_leg_syndrome
rds
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-restless_leg_syndrome
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_nonhospitalised-restless_leg_syndrome.txt
cox_ipw-cohort_unvax-sub_covid_nonhospitalised-restless_leg_syndrome:
run: cox-ipw:v0.0.27 --df_input=model_input-cohort_unvax-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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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-restless_leg_syndrome.csv
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-restless_leg_syndrome
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-restless_leg_syndrome.csv
make_model_input-cohort_unvax-sub_covid_nonhospitalised-unspecified_dementias:
run: r:latest analysis/model/make_model_input.R cohort_unvax-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_unvax-sub_covid_nonhospitalised-unspecified_dementias.rds
describe_model_input-cohort_unvax-sub_covid_nonhospitalised-unspecified_dementias:
run: r:latest analysis/model/describe_file.R model_input-cohort_unvax-sub_covid_nonhospitalised-unspecified_dementias
rds
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-unspecified_dementias
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_nonhospitalised-unspecified_dementias.txt
cox_ipw-cohort_unvax-sub_covid_nonhospitalised-unspecified_dementias:
run: cox-ipw:v0.0.27 --df_input=model_input-cohort_unvax-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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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-unspecified_dementias.csv
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-unspecified_dementias
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-unspecified_dementias.csv
make_model_input-cohort_unvax-sub_covid_nonhospitalised-vascular_dementia:
run: r:latest analysis/model/make_model_input.R cohort_unvax-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_unvax-sub_covid_nonhospitalised-vascular_dementia.rds
describe_model_input-cohort_unvax-sub_covid_nonhospitalised-vascular_dementia:
run: r:latest analysis/model/describe_file.R model_input-cohort_unvax-sub_covid_nonhospitalised-vascular_dementia
rds
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-vascular_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_nonhospitalised-vascular_dementia.txt
cox_ipw-cohort_unvax-sub_covid_nonhospitalised-vascular_dementia:
run: cox-ipw:v0.0.27 --df_input=model_input-cohort_unvax-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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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-vascular_dementia.csv
needs:
- make_model_input-cohort_unvax-sub_covid_nonhospitalised-vascular_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-sub_covid_nonhospitalised-vascular_dementia.csv
make_model_input-cohort_vax-sub_covid_nonhospitalised-alzheimer_disease:
run: r:latest analysis/model/make_model_input.R cohort_vax-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_vax-sub_covid_nonhospitalised-alzheimer_disease.rds
describe_model_input-cohort_vax-sub_covid_nonhospitalised-alzheimer_disease:
run: r:latest analysis/model/describe_file.R model_input-cohort_vax-sub_covid_nonhospitalised-alzheimer_disease
rds
needs:
- make_model_input-cohort_vax-sub_covid_nonhospitalised-alzheimer_disease
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_nonhospitalised-alzheimer_disease.txt
cox_ipw-cohort_vax-sub_covid_nonhospitalised-alzheimer_disease:
run: cox-ipw:v0.0.27 --df_input=model_input-cohort_vax-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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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_nonhospitalised-alzheimer_disease.csv
needs:
- make_model_input-cohort_vax-sub_covid_nonhospitalised-alzheimer_disease
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-alzheimer_disease.csv
make_model_input-cohort_vax-sub_covid_nonhospitalised-any_dementia:
run: r:latest analysis/model/make_model_input.R cohort_vax-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_vax-sub_covid_nonhospitalised-any_dementia.rds
describe_model_input-cohort_vax-sub_covid_nonhospitalised-any_dementia:
run: r:latest analysis/model/describe_file.R model_input-cohort_vax-sub_covid_nonhospitalised-any_dementia
rds
needs:
- make_model_input-cohort_vax-sub_covid_nonhospitalised-any_dementia
outputs:
moderately_sensitive:
describe_model_input: output/describe-model_input-cohort_vax-sub_covid_nonhospitalised-any_dementia.txt
cox_ipw-cohort_vax-sub_covid_nonhospitalised-any_dementia:
run: cox-ipw:v0.0.27 --df_input=model_input-cohort_vax-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_num_tc_hdl_ratio
--cox_start=index_date --cox_stop=end_date_outcome --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_nonhospitalised-any_dementia.csv
needs:
- make_model_input-cohort_vax-sub_covid_nonhospitalised-any_dementia
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_covid_nonhospitalised-any_dementia.csv
make_model_input-cohort_vax-sub_covid_nonhospitalised-cognitive_impairment:
run: r:latest