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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 150000
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
## Generate study population history - prevax
generate_study_population_history_prevax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax_history
--output-format csv.gz
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_prevax_history.csv.gz
## Generate study population history - unvax
generate_study_population_history_unvax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax_history
--output-format csv.gz
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_unvax_history.csv.gz
## Generate study population history - vax
generate_study_population_history_vax:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vax_history
--output-format csv.gz
needs:
- vax_eligibility_inputs
- generate_index_dates
outputs:
highly_sensitive:
cohort: output/input_vax_history.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:
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:
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:
highly_sensitive:
cohort: output/input_vax.rds
venn: output/venn_vax.rds
## 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_midpoint6: output/consort_prevax_midpoint6.csv
highly_sensitive:
cohort: output/input_prevax_stage1.rds
describe_stage1_data_cleaning_prevax:
run: r:latest analysis/model/describe_file.R input_prevax_stage1 rds
needs:
- stage1_data_cleaning_prevax
outputs:
moderately_sensitive:
describe_model_input: output/describe-input_prevax_stage1.txt
## 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_midpoint6: output/consort_unvax_midpoint6.csv
highly_sensitive:
cohort: output/input_unvax_stage1.rds
describe_stage1_data_cleaning_unvax:
run: r:latest analysis/model/describe_file.R input_unvax_stage1 rds
needs:
- stage1_data_cleaning_unvax
outputs:
moderately_sensitive:
describe_model_input: output/describe-input_unvax_stage1.txt
## Stage 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_midpoint6: output/consort_vax_midpoint6.csv
highly_sensitive:
cohort: output/input_vax_stage1.rds
describe_stage1_data_cleaning_vax:
run: r:latest analysis/model/describe_file.R input_vax_stage1 rds
needs:
- stage1_data_cleaning_vax
outputs:
moderately_sensitive:
describe_model_input: output/describe-input_vax_stage1.txt
## Join stage1 and history data - prevax
preprocess_stage1_history_data_cleaning_prevax:
run: r:latest analysis/preprocess/preprocess_stage1_history_data_cleaning.R prevax
needs:
- stage1_data_cleaning_prevax
- generate_study_population_history_prevax
outputs:
highly_sensitive:
cohort_final: output/input_prevax_new_stage1.rds
## Join stage1 and history data - unvax
preprocess_stage1_history_data_cleaning_unvax:
run: r:latest analysis/preprocess/preprocess_stage1_history_data_cleaning.R unvax
needs:
- stage1_data_cleaning_unvax
- generate_study_population_history_unvax
outputs:
highly_sensitive:
cohort_final: output/input_unvax_new_stage1.rds
## Join stage1 and history data - vax
preprocess_stage1_history_data_cleaning_vax:
run: r:latest analysis/preprocess/preprocess_stage1_history_data_cleaning.R vax
needs:
- stage1_data_cleaning_vax
- generate_study_population_history_vax
outputs:
highly_sensitive:
cohort_final: output/input_vax_new_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_midpoint6: output/consort_output_midpoint6.csv
make_table1_output:
run: r:latest analysis/model/make_other_output.R table1 prevax;vax;unvax
needs:
- table1_prevax
- table1_vax
- table1_unvax
outputs:
moderately_sensitive:
table1_output_midpoint6: output/table1_output_midpoint6.csv
make_extendedtable1_part1_output:
run: r:latest analysis/model/make_other_output.R extendedtable1_part1 prevax;vax;unvax
needs:
- extendedtable1_part1_prevax
- extendedtable1_part1_vax
- extendedtable1_part1_unvax
outputs:
moderately_sensitive:
table1_output_midpoint6: output/extendedtable1_part1_output_midpoint6.csv
make_extendedtable1_part2_output:
run: r:latest analysis/model/make_other_output.R extendedtable1_part2 prevax;vax;unvax
needs:
- extendedtable1_part2_prevax
- extendedtable1_part2_vax
- extendedtable1_part2_unvax
outputs:
moderately_sensitive:
table1_output_midpoint6: output/extendedtable1_part2_output_midpoint6.csv
make_table2_output:
run: r:latest analysis/model/make_other_output.R table2 prevax;vax;unvax
needs:
- table2_prevax
- table2_vax
- table2_unvax
outputs:
moderately_sensitive:
table2_output_midpoint6: output/table2_output_midpoint6.csv
## Table 1 - prevax
table1_prevax:
run: r:latest analysis/descriptives/table1.R prevax
needs:
- preprocess_stage1_history_data_cleaning_prevax
outputs:
moderately_sensitive:
table1: output/table1_prevax.csv
table1_midpoint6: output/table1_prevax_midpoint6.csv
extendedtable1_part1_prevax:
run: r:latest analysis/descriptives/extendedtable1_part1.R prevax
needs:
- preprocess_stage1_history_data_cleaning_prevax
outputs:
moderately_sensitive:
extendedtable1_part1: output/extendedtable1_part1_prevax.csv
extendedtable1_part1_midpoint6: output/extendedtable1_part1_prevax_midpoint6.csv
extendedtable1_part2_prevax:
run: r:latest analysis/descriptives/extendedtable1_part2.R prevax
needs:
- preprocess_stage1_history_data_cleaning_prevax
outputs:
moderately_sensitive:
extendedtable1_part2: output/extendedtable1_part2_prevax.csv
extendedtable1_part2_midpoint6: output/extendedtable1_part2_prevax_midpoint6.csv
## Table 1 - unvax
table1_unvax:
run: r:latest analysis/descriptives/table1.R unvax
needs:
- preprocess_stage1_history_data_cleaning_unvax
outputs:
moderately_sensitive:
table1: output/table1_unvax.csv
table1_midpoint6: output/table1_unvax_midpoint6.csv
extendedtable1_part1_unvax:
run: r:latest analysis/descriptives/extendedtable1_part1.R unvax
needs:
- preprocess_stage1_history_data_cleaning_unvax
outputs:
moderately_sensitive:
extendedtable1_part1: output/extendedtable1_part1_unvax.csv
extendedtable1_part1_midpoint6: output/extendedtable1_part1_unvax_midpoint6.csv
extendedtable1_part2_unvax:
run: r:latest analysis/descriptives/extendedtable1_part2.R unvax
needs:
- preprocess_stage1_history_data_cleaning_unvax
outputs:
moderately_sensitive:
extendedtable1_part2: output/extendedtable1_part2_unvax.csv
extendedtable1_part2_midpoint6: output/extendedtable1_part2_unvax_midpoint6.csv
## Table 1 - vax
table1_vax:
run: r:latest analysis/descriptives/table1.R vax
needs:
- preprocess_stage1_history_data_cleaning_vax
outputs:
moderately_sensitive:
table1: output/table1_vax.csv
table1_midpoint6: output/table1_vax_midpoint6.csv
extendedtable1_part1_vax:
run: r:latest analysis/descriptives/extendedtable1_part1.R vax
needs:
- preprocess_stage1_history_data_cleaning_vax
outputs:
moderately_sensitive:
extendedtable1_part1: output/extendedtable1_part1_vax.csv
extendedtable1_part1_midpoint6: output/extendedtable1_part1_vax_midpoint6.csv
extendedtable1_part2_vax:
run: r:latest analysis/descriptives/extendedtable1_part2.R vax
needs:
- preprocess_stage1_history_data_cleaning_vax
outputs:
moderately_sensitive:
extendedtable1_part2: output/extendedtable1_part2_vax.csv
extendedtable1_part2_midpoint6: output/extendedtable1_part2_vax_midpoint6.csv
## Stage 5 - Run models
make_model_input-cohort_prevax-main-composite_ai:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-composite_ai
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-composite_ai.rds
cox_ipw-cohort_prevax-main-composite_ai:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-main-composite_ai.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;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-composite_ai.csv
needs:
- make_model_input-cohort_prevax-main-composite_ai
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-composite_ai.csv
make_model_input-cohort_prevax-main-grp1_ifa:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-grp1_ifa
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-grp1_ifa.rds
cox_ipw-cohort_prevax-main-grp1_ifa:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-main-grp1_ifa.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;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-grp1_ifa.csv
needs:
- make_model_input-cohort_prevax-main-grp1_ifa
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-grp1_ifa.csv
make_model_input-cohort_prevax-main-grp2_ctd:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-grp2_ctd
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-grp2_ctd.rds
cox_ipw-cohort_prevax-main-grp2_ctd:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-main-grp2_ctd.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;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-grp2_ctd.csv
needs:
- make_model_input-cohort_prevax-main-grp2_ctd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-grp2_ctd.csv
make_model_input-cohort_prevax-main-grp3_isd:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-grp3_isd
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-grp3_isd.rds
cox_ipw-cohort_prevax-main-grp3_isd:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-main-grp3_isd.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;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-grp3_isd.csv
needs:
- make_model_input-cohort_prevax-main-grp3_isd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-grp3_isd.csv
make_model_input-cohort_prevax-main-grp4_agi_ibd:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-grp4_agi_ibd
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-grp4_agi_ibd.rds
cox_ipw-cohort_prevax-main-grp4_agi_ibd:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-main-grp4_agi_ibd.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;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-grp4_agi_ibd.csv
needs:
- make_model_input-cohort_prevax-main-grp4_agi_ibd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-grp4_agi_ibd.csv
make_model_input-cohort_prevax-main-grp5_atv:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-grp5_atv
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-grp5_atv.rds
cox_ipw-cohort_prevax-main-grp5_atv:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-main-grp5_atv.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;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-grp5_atv.csv
needs:
- make_model_input-cohort_prevax-main-grp5_atv
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-grp5_atv.csv
make_model_input-cohort_prevax-main-grp6_trd:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-grp6_trd
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-grp6_trd.rds
cox_ipw-cohort_prevax-main-grp6_trd:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-main-grp6_trd.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;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-grp6_trd.csv
needs:
- make_model_input-cohort_prevax-main-grp6_trd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-grp6_trd.csv
make_model_input-cohort_prevax-main-grp7_htd:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-grp7_htd
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-grp7_htd.rds
cox_ipw-cohort_prevax-main-grp7_htd:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-main-grp7_htd.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;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-grp7_htd.csv
needs:
- make_model_input-cohort_prevax-main-grp7_htd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-grp7_htd.csv
make_model_input-cohort_prevax-main-grp8_ind:
run: r:latest analysis/model/make_model_input.R cohort_prevax-main-grp8_ind
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_prevax-main-grp8_ind.rds
cox_ipw-cohort_prevax-main-grp8_ind:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_prevax-main-grp8_ind.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2020-01-01
--study_stop=2021-12-14 --cut_points=1;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-grp8_ind.csv
needs:
- make_model_input-cohort_prevax-main-grp8_ind
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_prevax-main-grp8_ind.csv
make_model_input-cohort_unvax-main-composite_ai:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-composite_ai
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-composite_ai.rds
cox_ipw-cohort_unvax-main-composite_ai:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-main-composite_ai.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-composite_ai.csv
needs:
- make_model_input-cohort_unvax-main-composite_ai
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-composite_ai.csv
make_model_input-cohort_unvax-main-grp1_ifa:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-grp1_ifa
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-grp1_ifa.rds
cox_ipw-cohort_unvax-main-grp1_ifa:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-main-grp1_ifa.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-grp1_ifa.csv
needs:
- make_model_input-cohort_unvax-main-grp1_ifa
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-grp1_ifa.csv
make_model_input-cohort_unvax-main-grp2_ctd:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-grp2_ctd
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-grp2_ctd.rds
cox_ipw-cohort_unvax-main-grp2_ctd:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-main-grp2_ctd.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-grp2_ctd.csv
needs:
- make_model_input-cohort_unvax-main-grp2_ctd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-grp2_ctd.csv
make_model_input-cohort_unvax-main-grp3_isd:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-grp3_isd
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-grp3_isd.rds
cox_ipw-cohort_unvax-main-grp3_isd:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-main-grp3_isd.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-grp3_isd.csv
needs:
- make_model_input-cohort_unvax-main-grp3_isd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-grp3_isd.csv
make_model_input-cohort_unvax-main-grp4_agi_ibd:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-grp4_agi_ibd
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-grp4_agi_ibd.rds
cox_ipw-cohort_unvax-main-grp4_agi_ibd:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-main-grp4_agi_ibd.rds
--ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-grp4_agi_ibd.csv
needs:
- make_model_input-cohort_unvax-main-grp4_agi_ibd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-grp4_agi_ibd.csv
make_model_input-cohort_unvax-main-grp5_atv:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-grp5_atv
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-grp5_atv.rds
cox_ipw-cohort_unvax-main-grp5_atv:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-main-grp5_atv.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-grp5_atv.csv
needs:
- make_model_input-cohort_unvax-main-grp5_atv
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-grp5_atv.csv
make_model_input-cohort_unvax-main-grp6_trd:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-grp6_trd
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-grp6_trd.rds
cox_ipw-cohort_unvax-main-grp6_trd:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-main-grp6_trd.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-grp6_trd.csv
needs:
- make_model_input-cohort_unvax-main-grp6_trd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-grp6_trd.csv
make_model_input-cohort_unvax-main-grp7_htd:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-grp7_htd
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-grp7_htd.rds
cox_ipw-cohort_unvax-main-grp7_htd:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-main-grp7_htd.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-grp7_htd.csv
needs:
- make_model_input-cohort_unvax-main-grp7_htd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-grp7_htd.csv
make_model_input-cohort_unvax-main-grp8_ind:
run: r:latest analysis/model/make_model_input.R cohort_unvax-main-grp8_ind
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_unvax-main-grp8_ind.rds
cox_ipw-cohort_unvax-main-grp8_ind:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_unvax-main-grp8_ind.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-grp8_ind.csv
needs:
- make_model_input-cohort_unvax-main-grp8_ind
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_unvax-main-grp8_ind.csv
make_model_input-cohort_vax-main-composite_ai:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-composite_ai
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-composite_ai.rds
cox_ipw-cohort_vax-main-composite_ai:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-main-composite_ai.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-composite_ai.csv
needs:
- make_model_input-cohort_vax-main-composite_ai
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-composite_ai.csv
make_model_input-cohort_vax-main-grp1_ifa:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-grp1_ifa
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-grp1_ifa.rds
cox_ipw-cohort_vax-main-grp1_ifa:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-main-grp1_ifa.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-grp1_ifa.csv
needs:
- make_model_input-cohort_vax-main-grp1_ifa
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-grp1_ifa.csv
make_model_input-cohort_vax-main-grp2_ctd:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-grp2_ctd
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-grp2_ctd.rds
cox_ipw-cohort_vax-main-grp2_ctd:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-main-grp2_ctd.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-grp2_ctd.csv
needs:
- make_model_input-cohort_vax-main-grp2_ctd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-grp2_ctd.csv
make_model_input-cohort_vax-main-grp3_isd:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-grp3_isd
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-grp3_isd.rds
cox_ipw-cohort_vax-main-grp3_isd:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-main-grp3_isd.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-grp3_isd.csv
needs:
- make_model_input-cohort_vax-main-grp3_isd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-grp3_isd.csv
make_model_input-cohort_vax-main-grp4_agi_ibd:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-grp4_agi_ibd
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-grp4_agi_ibd.rds
cox_ipw-cohort_vax-main-grp4_agi_ibd:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-main-grp4_agi_ibd.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-grp4_agi_ibd.csv
needs:
- make_model_input-cohort_vax-main-grp4_agi_ibd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-grp4_agi_ibd.csv
make_model_input-cohort_vax-main-grp5_atv:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-grp5_atv
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-grp5_atv.rds
cox_ipw-cohort_vax-main-grp5_atv:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-main-grp5_atv.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-grp5_atv.csv
needs:
- make_model_input-cohort_vax-main-grp5_atv
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-grp5_atv.csv
make_model_input-cohort_vax-main-grp6_trd:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-grp6_trd
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-grp6_trd.rds
cox_ipw-cohort_vax-main-grp6_trd:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-main-grp6_trd.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-grp6_trd.csv
needs:
- make_model_input-cohort_vax-main-grp6_trd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-grp6_trd.csv
make_model_input-cohort_vax-main-grp7_htd:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-grp7_htd
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-grp7_htd.rds
cox_ipw-cohort_vax-main-grp7_htd:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-main-grp7_htd.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;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-grp7_htd.csv
needs:
- make_model_input-cohort_vax-main-grp7_htd
outputs:
moderately_sensitive:
model_output: output/model_output-cohort_vax-main-grp7_htd.csv
make_model_input-cohort_vax-main-grp8_ind:
run: r:latest analysis/model/make_model_input.R cohort_vax-main-grp8_ind
needs:
- preprocess_stage1_history_data_cleaning_prevax
- preprocess_stage1_history_data_cleaning_vax
- preprocess_stage1_history_data_cleaning_unvax
outputs:
highly_sensitive:
model_input: output/model_input-cohort_vax-main-grp8_ind.rds
cox_ipw-cohort_vax-main-grp8_ind:
run: cox-ipw:v0.0.31 --df_input=model_input-cohort_vax-main-grp8_ind.rds --ipw=TRUE
--exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
--covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_num_consulation_rate;cov_num_outpatient_rate;cov_cat_smoking_status;cov_bin_healthcare_worker;cov_bin_carehome_status;cov_bin_dementia;cov_bin_liver_disease;cov_bin_ckd;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_copd;cov_bin_ami;cov_bin_isch_stroke
--cox_start=index_date --cox_stop=end_date_outcome --study_start=2021-06-01
--study_stop=2021-12-14 --cut_points=1;197 --controls_per_case=20 --total_event_threshold=50