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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 200000
actions:
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml DIRECTLY
## This file is created by create_project_actions.R
## Edit and run create_project_actions.R to update the project.yaml
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## Generate vaccination eligibility information
vax_eligibility_inputs:
run: r:latest analysis/metadates.R
outputs:
highly_sensitive:
study_dates_json: output/study_dates.json
vax_jcvi_groups: output/vax_jcvi_groups.csv.gz
vax_eligible_dates: output/vax_eligible_dates.csv.gz
## Generate prelim study_definition
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 dates for all study cohorts
generate_index_dates:
run: r:latest analysis/prelim.R
needs:
- vax_eligibility_inputs
- generate_study_population_prelim
outputs:
highly_sensitive:
index_dates: output/index_dates.csv.gz
## Generate study population - prevax_extf
generate_study_population_prevax_extf:
run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax_extf
--output-format csv.gz
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_prevax_extf.csv.gz
## Generate study population - unvax_extf
generate_study_population_unvax_extf:
run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax_extf
--output-format csv.gz
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_unvax_extf.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_extf
preprocess_data_prevax_extf:
run: r:latest analysis/preprocess_data.R prevax_extf
needs:
- generate_index_dates
- generate_study_population_prevax_extf
outputs:
moderately_sensitive:
describe: output/describe_input_prevax_extf_stage0.txt
describe_venn: output/describe_venn_prevax_extf.txt
highly_sensitive:
cohort: output/input_prevax_extf.rds
venn: output/venn_prevax_extf.rds
## Preprocess data - unvax_extf
preprocess_data_unvax_extf:
run: r:latest analysis/preprocess_data.R unvax_extf
needs:
- generate_index_dates
- generate_study_population_unvax_extf
outputs:
moderately_sensitive:
describe: output/describe_input_unvax_extf_stage0.txt
describe_venn: output/describe_venn_unvax_extf.txt
highly_sensitive:
cohort: output/input_unvax_extf.rds
venn: output/venn_unvax_extf.rds
## Preprocess data - vax
preprocess_data_vax:
run: r:latest analysis/preprocess_data.R vax
needs:
- generate_index_dates
- generate_study_population_vax
outputs:
moderately_sensitive:
describe: output/describe_input_vax_stage0.txt
describe_venn: output/describe_venn_vax.txt
highly_sensitive:
cohort: output/input_vax.rds
venn: output/venn_vax.rds
## Stage 1 - data cleaning - prevax_extf
stage1_data_cleaning_prevax_extf:
run: r:latest analysis/stage1_data_cleaning.R prevax_extf
needs:
- vax_eligibility_inputs
- preprocess_data_prevax_extf
outputs:
moderately_sensitive:
consort: output/consort_prevax_extf.csv
consort_rounded: output/consort_prevax_extf_rounded.csv
highly_sensitive:
cohort: output/input_prevax_extf_stage1.rds
## Stage 1 - data cleaning - unvax_extf
stage1_data_cleaning_unvax_extf:
run: r:latest analysis/stage1_data_cleaning.R unvax_extf
needs:
- vax_eligibility_inputs
- preprocess_data_unvax_extf
outputs:
moderately_sensitive:
consort: output/consort_unvax_extf.csv
consort_rounded: output/consort_unvax_extf_rounded.csv
highly_sensitive:
cohort: output/input_unvax_extf_stage1.rds
## Stage 1 - data cleaning - vax
stage1_data_cleaning_vax:
run: r:latest analysis/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
highly_sensitive:
cohort: output/input_vax_stage1.rds
## Table 1 - prevax_extf
table1_prevax_extf:
run: r:latest analysis/table1.R prevax_extf
needs:
- stage1_data_cleaning_prevax_extf
outputs:
moderately_sensitive:
table1: output/table1_prevax_extf.csv
table1_rounded: output/table1_prevax_extf_rounded.csv
## Table 1 - unvax_extf
table1_unvax_extf:
run: r:latest analysis/table1.R unvax_extf
needs:
- stage1_data_cleaning_unvax_extf
outputs:
moderately_sensitive:
table1: output/table1_unvax_extf.csv
table1_rounded: output/table1_unvax_extf_rounded.csv
## Table 1 - vax
table1_vax:
run: r:latest analysis/table1.R vax
needs:
- stage1_data_cleaning_vax
outputs:
moderately_sensitive:
table1: output/table1_vax.csv
table1_rounded: output/table1_vax_rounded.csv
## Run models
make_model_input-cohort_prevax_extf-main-addiction:
run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-addiction
needs:
- stage1_data_cleaning_prevax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax_extf-main-addiction.rds
cox_ipw-cohort_prevax_extf-main-addiction:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-main-addiction.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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_extf-main-addiction.csv
needs:
- make_model_input-cohort_prevax_extf-main-addiction
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax_extf-main-addiction.csv
make_model_input-cohort_prevax_extf-main-anxiety_general:
run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-anxiety_general
needs:
- stage1_data_cleaning_prevax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax_extf-main-anxiety_general.rds
cox_ipw-cohort_prevax_extf-main-anxiety_general:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-main-anxiety_general.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-anxiety_general.csv
needs:
- make_model_input-cohort_prevax_extf-main-anxiety_general
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax_extf-main-anxiety_general.csv
make_model_input-cohort_prevax_extf-main-anxiety_ptsd:
run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-anxiety_ptsd
needs:
- stage1_data_cleaning_prevax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax_extf-main-anxiety_ptsd.rds
cox_ipw-cohort_prevax_extf-main-anxiety_ptsd:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-main-anxiety_ptsd.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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_extf-main-anxiety_ptsd.csv
needs:
- make_model_input-cohort_prevax_extf-main-anxiety_ptsd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax_extf-main-anxiety_ptsd.csv
make_model_input-cohort_prevax_extf-main-depression:
run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-depression
needs:
- stage1_data_cleaning_prevax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax_extf-main-depression.rds
cox_ipw-cohort_prevax_extf-main-depression:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-main-depression.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-depression.csv
needs:
- make_model_input-cohort_prevax_extf-main-depression
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax_extf-main-depression.csv
make_model_input-cohort_prevax_extf-main-eating_disorders:
run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-eating_disorders
needs:
- stage1_data_cleaning_prevax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax_extf-main-eating_disorders.rds
cox_ipw-cohort_prevax_extf-main-eating_disorders:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-main-eating_disorders.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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_extf-main-eating_disorders.csv
needs:
- make_model_input-cohort_prevax_extf-main-eating_disorders
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax_extf-main-eating_disorders.csv
make_model_input-cohort_prevax_extf-main-self_harm:
run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-self_harm
needs:
- stage1_data_cleaning_prevax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax_extf-main-self_harm.rds
cox_ipw-cohort_prevax_extf-main-self_harm:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-main-self_harm.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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_extf-main-self_harm.csv
needs:
- make_model_input-cohort_prevax_extf-main-self_harm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax_extf-main-self_harm.csv
make_model_input-cohort_prevax_extf-main-serious_mental_illness:
run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-serious_mental_illness
needs:
- stage1_data_cleaning_prevax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax_extf-main-serious_mental_illness.rds
cox_ipw-cohort_prevax_extf-main-serious_mental_illness:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-main-serious_mental_illness.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax_extf-main-serious_mental_illness.csv
needs:
- make_model_input-cohort_prevax_extf-main-serious_mental_illness
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax_extf-main-serious_mental_illness.csv
make_model_input-cohort_prevax_extf-main-suicide:
run: r:latest analysis/make_model_input.R cohort_prevax_extf-main-suicide
needs:
- stage1_data_cleaning_prevax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax_extf-main-suicide.rds
cox_ipw-cohort_prevax_extf-main-suicide:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-main-suicide.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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_extf-main-suicide.csv
needs:
- make_model_input-cohort_prevax_extf-main-suicide
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax_extf-main-suicide.csv
make_model_input-cohort_unvax_extf-main-addiction:
run: r:latest analysis/make_model_input.R cohort_unvax_extf-main-addiction
needs:
- stage1_data_cleaning_unvax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax_extf-main-addiction.rds
cox_ipw-cohort_unvax_extf-main-addiction:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-main-addiction.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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_extf-main-addiction.csv
needs:
- make_model_input-cohort_unvax_extf-main-addiction
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax_extf-main-addiction.csv
make_model_input-cohort_unvax_extf-main-anxiety_general:
run: r:latest analysis/make_model_input.R cohort_unvax_extf-main-anxiety_general
needs:
- stage1_data_cleaning_unvax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax_extf-main-anxiety_general.rds
cox_ipw-cohort_unvax_extf-main-anxiety_general:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-main-anxiety_general.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax_extf-main-anxiety_general.csv
needs:
- make_model_input-cohort_unvax_extf-main-anxiety_general
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax_extf-main-anxiety_general.csv
make_model_input-cohort_unvax_extf-main-anxiety_ptsd:
run: r:latest analysis/make_model_input.R cohort_unvax_extf-main-anxiety_ptsd
needs:
- stage1_data_cleaning_unvax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax_extf-main-anxiety_ptsd.rds
cox_ipw-cohort_unvax_extf-main-anxiety_ptsd:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-main-anxiety_ptsd.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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_extf-main-anxiety_ptsd.csv
needs:
- make_model_input-cohort_unvax_extf-main-anxiety_ptsd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax_extf-main-anxiety_ptsd.csv
make_model_input-cohort_unvax_extf-main-depression:
run: r:latest analysis/make_model_input.R cohort_unvax_extf-main-depression
needs:
- stage1_data_cleaning_unvax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax_extf-main-depression.rds
cox_ipw-cohort_unvax_extf-main-depression:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-main-depression.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax_extf-main-depression.csv
needs:
- make_model_input-cohort_unvax_extf-main-depression
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax_extf-main-depression.csv
make_model_input-cohort_unvax_extf-main-eating_disorders:
run: r:latest analysis/make_model_input.R cohort_unvax_extf-main-eating_disorders
needs:
- stage1_data_cleaning_unvax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax_extf-main-eating_disorders.rds
cox_ipw-cohort_unvax_extf-main-eating_disorders:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-main-eating_disorders.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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_extf-main-eating_disorders.csv
needs:
- make_model_input-cohort_unvax_extf-main-eating_disorders
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax_extf-main-eating_disorders.csv
make_model_input-cohort_unvax_extf-main-self_harm:
run: r:latest analysis/make_model_input.R cohort_unvax_extf-main-self_harm
needs:
- stage1_data_cleaning_unvax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax_extf-main-self_harm.rds
cox_ipw-cohort_unvax_extf-main-self_harm:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-main-self_harm.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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_extf-main-self_harm.csv
needs:
- make_model_input-cohort_unvax_extf-main-self_harm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax_extf-main-self_harm.csv
make_model_input-cohort_unvax_extf-main-serious_mental_illness:
run: r:latest analysis/make_model_input.R cohort_unvax_extf-main-serious_mental_illness
needs:
- stage1_data_cleaning_unvax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax_extf-main-serious_mental_illness.rds
cox_ipw-cohort_unvax_extf-main-serious_mental_illness:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-main-serious_mental_illness.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax_extf-main-serious_mental_illness.csv
needs:
- make_model_input-cohort_unvax_extf-main-serious_mental_illness
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax_extf-main-serious_mental_illness.csv
make_model_input-cohort_unvax_extf-main-suicide:
run: r:latest analysis/make_model_input.R cohort_unvax_extf-main-suicide
needs:
- stage1_data_cleaning_unvax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax_extf-main-suicide.rds
cox_ipw-cohort_unvax_extf-main-suicide:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-main-suicide.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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_extf-main-suicide.csv
needs:
- make_model_input-cohort_unvax_extf-main-suicide
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax_extf-main-suicide.csv
make_model_input-cohort_vax-main-addiction:
run: r:latest analysis/make_model_input.R cohort_vax-main-addiction
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-addiction.rds
cox_ipw-cohort_vax-main-addiction:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-main-addiction.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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-addiction.csv
needs:
- make_model_input-cohort_vax-main-addiction
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-addiction.csv
make_model_input-cohort_vax-main-anxiety_general:
run: r:latest analysis/make_model_input.R cohort_vax-main-anxiety_general
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-anxiety_general.rds
cox_ipw-cohort_vax-main-anxiety_general:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-main-anxiety_general.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-anxiety_general.csv
needs:
- make_model_input-cohort_vax-main-anxiety_general
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-anxiety_general.csv
make_model_input-cohort_vax-main-anxiety_ptsd:
run: r:latest analysis/make_model_input.R cohort_vax-main-anxiety_ptsd
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-anxiety_ptsd.rds
cox_ipw-cohort_vax-main-anxiety_ptsd:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-main-anxiety_ptsd.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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-anxiety_ptsd.csv
needs:
- make_model_input-cohort_vax-main-anxiety_ptsd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-anxiety_ptsd.csv
make_model_input-cohort_vax-main-depression:
run: r:latest analysis/make_model_input.R cohort_vax-main-depression
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-depression.rds
cox_ipw-cohort_vax-main-depression:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-main-depression.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-depression.csv
needs:
- make_model_input-cohort_vax-main-depression
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-depression.csv
make_model_input-cohort_vax-main-eating_disorders:
run: r:latest analysis/make_model_input.R cohort_vax-main-eating_disorders
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-eating_disorders.rds
cox_ipw-cohort_vax-main-eating_disorders:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-main-eating_disorders.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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-eating_disorders.csv
needs:
- make_model_input-cohort_vax-main-eating_disorders
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-eating_disorders.csv
make_model_input-cohort_vax-main-self_harm:
run: r:latest analysis/make_model_input.R cohort_vax-main-self_harm
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-self_harm.rds
cox_ipw-cohort_vax-main-self_harm:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-main-self_harm.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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-self_harm.csv
needs:
- make_model_input-cohort_vax-main-self_harm
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-self_harm.csv
make_model_input-cohort_vax-main-serious_mental_illness:
run: r:latest analysis/make_model_input.R cohort_vax-main-serious_mental_illness
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-serious_mental_illness.rds
cox_ipw-cohort_vax-main-serious_mental_illness:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-main-serious_mental_illness.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-serious_mental_illness.csv
needs:
- make_model_input-cohort_vax-main-serious_mental_illness
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-serious_mental_illness.csv
make_model_input-cohort_vax-main-suicide:
run: r:latest analysis/make_model_input.R cohort_vax-main-suicide
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-suicide.rds
cox_ipw-cohort_vax-main-suicide:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-main-suicide.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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-suicide.csv
needs:
- make_model_input-cohort_vax-main-suicide
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-suicide.csv
make_model_input-cohort_prevax_extf-sub_age_18_39-anxiety_general:
run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_18_39-anxiety_general
needs:
- stage1_data_cleaning_prevax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax_extf-sub_age_18_39-anxiety_general.rds
cox_ipw-cohort_prevax_extf-sub_age_18_39-anxiety_general:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-sub_age_18_39-anxiety_general.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_18_39-anxiety_general.csv
needs:
- make_model_input-cohort_prevax_extf-sub_age_18_39-anxiety_general
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax_extf-sub_age_18_39-anxiety_general.csv
make_model_input-cohort_prevax_extf-sub_age_18_39-depression:
run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_18_39-depression
needs:
- stage1_data_cleaning_prevax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax_extf-sub_age_18_39-depression.rds
cox_ipw-cohort_prevax_extf-sub_age_18_39-depression:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-sub_age_18_39-depression.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_18_39-depression.csv
needs:
- make_model_input-cohort_prevax_extf-sub_age_18_39-depression
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax_extf-sub_age_18_39-depression.csv
make_model_input-cohort_prevax_extf-sub_age_18_39-serious_mental_illness:
run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_18_39-serious_mental_illness
needs:
- stage1_data_cleaning_prevax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax_extf-sub_age_18_39-serious_mental_illness.rds
cox_ipw-cohort_prevax_extf-sub_age_18_39-serious_mental_illness:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-sub_age_18_39-serious_mental_illness.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_18_39-serious_mental_illness.csv
needs:
- make_model_input-cohort_prevax_extf-sub_age_18_39-serious_mental_illness
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax_extf-sub_age_18_39-serious_mental_illness.csv
make_model_input-cohort_unvax_extf-sub_age_18_39-anxiety_general:
run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_age_18_39-anxiety_general
needs:
- stage1_data_cleaning_unvax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax_extf-sub_age_18_39-anxiety_general.rds
cox_ipw-cohort_unvax_extf-sub_age_18_39-anxiety_general:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-sub_age_18_39-anxiety_general.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax_extf-sub_age_18_39-anxiety_general.csv
needs:
- make_model_input-cohort_unvax_extf-sub_age_18_39-anxiety_general
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax_extf-sub_age_18_39-anxiety_general.csv
make_model_input-cohort_unvax_extf-sub_age_18_39-depression:
run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_age_18_39-depression
needs:
- stage1_data_cleaning_unvax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax_extf-sub_age_18_39-depression.rds
cox_ipw-cohort_unvax_extf-sub_age_18_39-depression:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-sub_age_18_39-depression.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax_extf-sub_age_18_39-depression.csv
needs:
- make_model_input-cohort_unvax_extf-sub_age_18_39-depression
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax_extf-sub_age_18_39-depression.csv
make_model_input-cohort_unvax_extf-sub_age_18_39-serious_mental_illness:
run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_age_18_39-serious_mental_illness
needs:
- stage1_data_cleaning_unvax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax_extf-sub_age_18_39-serious_mental_illness.rds
cox_ipw-cohort_unvax_extf-sub_age_18_39-serious_mental_illness:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-sub_age_18_39-serious_mental_illness.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax_extf-sub_age_18_39-serious_mental_illness.csv
needs:
- make_model_input-cohort_unvax_extf-sub_age_18_39-serious_mental_illness
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax_extf-sub_age_18_39-serious_mental_illness.csv
make_model_input-cohort_vax-sub_age_18_39-anxiety_general:
run: r:latest analysis/make_model_input.R cohort_vax-sub_age_18_39-anxiety_general
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-anxiety_general.rds
cox_ipw-cohort_vax-sub_age_18_39-anxiety_general:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-sub_age_18_39-anxiety_general.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-anxiety_general.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-anxiety_general
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-anxiety_general.csv
make_model_input-cohort_vax-sub_age_18_39-depression:
run: r:latest analysis/make_model_input.R cohort_vax-sub_age_18_39-depression
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-depression.rds
cox_ipw-cohort_vax-sub_age_18_39-depression:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-sub_age_18_39-depression.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-depression.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-depression
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-depression.csv
make_model_input-cohort_vax-sub_age_18_39-serious_mental_illness:
run: r:latest analysis/make_model_input.R cohort_vax-sub_age_18_39-serious_mental_illness
needs:
- stage1_data_cleaning_vax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-sub_age_18_39-serious_mental_illness.rds
cox_ipw-cohort_vax-sub_age_18_39-serious_mental_illness:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_vax-sub_age_18_39-serious_mental_illness.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-serious_mental_illness.csv
needs:
- make_model_input-cohort_vax-sub_age_18_39-serious_mental_illness
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-sub_age_18_39-serious_mental_illness.csv
make_model_input-cohort_prevax_extf-sub_age_40_59-anxiety_general:
run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_40_59-anxiety_general
needs:
- stage1_data_cleaning_prevax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax_extf-sub_age_40_59-anxiety_general.rds
cox_ipw-cohort_prevax_extf-sub_age_40_59-anxiety_general:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-sub_age_40_59-anxiety_general.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_40_59-anxiety_general.csv
needs:
- make_model_input-cohort_prevax_extf-sub_age_40_59-anxiety_general
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax_extf-sub_age_40_59-anxiety_general.csv
make_model_input-cohort_prevax_extf-sub_age_40_59-depression:
run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_40_59-depression
needs:
- stage1_data_cleaning_prevax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax_extf-sub_age_40_59-depression.rds
cox_ipw-cohort_prevax_extf-sub_age_40_59-depression:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-sub_age_40_59-depression.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_40_59-depression.csv
needs:
- make_model_input-cohort_prevax_extf-sub_age_40_59-depression
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax_extf-sub_age_40_59-depression.csv
make_model_input-cohort_prevax_extf-sub_age_40_59-serious_mental_illness:
run: r:latest analysis/make_model_input.R cohort_prevax_extf-sub_age_40_59-serious_mental_illness
needs:
- stage1_data_cleaning_prevax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax_extf-sub_age_40_59-serious_mental_illness.rds
cox_ipw-cohort_prevax_extf-sub_age_40_59-serious_mental_illness:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_prevax_extf-sub_age_40_59-serious_mental_illness.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax_extf-sub_age_40_59-serious_mental_illness.csv
needs:
- make_model_input-cohort_prevax_extf-sub_age_40_59-serious_mental_illness
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax_extf-sub_age_40_59-serious_mental_illness.csv
make_model_input-cohort_unvax_extf-sub_age_40_59-anxiety_general:
run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_age_40_59-anxiety_general
needs:
- stage1_data_cleaning_unvax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax_extf-sub_age_40_59-anxiety_general.rds
cox_ipw-cohort_unvax_extf-sub_age_40_59-anxiety_general:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-sub_age_40_59-anxiety_general.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax_extf-sub_age_40_59-anxiety_general.csv
needs:
- make_model_input-cohort_unvax_extf-sub_age_40_59-anxiety_general
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax_extf-sub_age_40_59-anxiety_general.csv
make_model_input-cohort_unvax_extf-sub_age_40_59-depression:
run: r:latest analysis/make_model_input.R cohort_unvax_extf-sub_age_40_59-depression
needs:
- stage1_data_cleaning_unvax_extf
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax_extf-sub_age_40_59-depression.rds
cox_ipw-cohort_unvax_extf-sub_age_40_59-depression:
run: cox-ipw:v0.0.25 --df_input=model_input-cohort_unvax_extf-sub_age_40_59-depression.rds
--ipw=FALSE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_chronic_obstructive_pulmonary_disease;cov_bin_ami;cov_bin_stroke_isch;cov_cat_history_depression;cov_cat_history_anxiety_general;cov_cat_history_eating_disorders;cov_cat_history_serious_mental_illness;cov_cat_history_self_harm
--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=10 --total_event_threshold=50
--episode_event_threshold=5 --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax_extf-sub_age_40_59-depression.csv
needs:
- make_model_input-cohort_unvax_extf-sub_age_40_59-depression
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax_extf-sub_age_40_59-depression.csv