generated from opensafely/research-template
/
project.yaml
145 lines (124 loc) · 3.86 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 100000
actions:
## # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml DIRECTLY
## This file is created by create_project.R
## Edit and run create_project.R to update the project.yaml
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Metadata for study design
## # # # # # # # # # # # # # # # # # # #
design:
run: r:latest analysis/00_design.R
outputs:
highly_sensitive:
dates_json: analysis/lib/dates.json
dates_rds: analysis/lib/dates.rds
## # # # # # # # # # # # # # # # # # # #
## Study definition
## # # # # # # # # # # # # # # # # # # #
study_definition:
run: cohortextractor:latest generate_cohort --study-definition study_definition
needs:
- design
outputs:
highly_sensitive:
cohort: output/input.csv
## # # # # # # # # # # # # # # # # # # #
## Process the data
## # # # # # # # # # # # # # # # # # # #
process_data:
run: r:latest analysis/01_data_process.R
needs:
- design
- study_definition
outputs:
highly_sensitive:
data: output/data/data_processed_*.rds
variables: analysis/lib/all_variables.rds
moderately_sensitive:
elig_dates: output/tables/elig_dates_tibble.csv
death_counts: output/tables/death_count_*.csv
## # # # # # # # # # # # # # # # # # # #
## Summary tables for each jcvi_group
## # # # # # # # # # # # # # # # # # # #
summary_table_02:
run: r:latest analysis/02_summary_tables.R 02
needs:
- process_data
outputs:
moderately_sensitive:
table: output/tables/summary_table_02.csv
summary_table_09:
run: r:latest analysis/02_summary_tables.R 09
needs:
- process_data
outputs:
moderately_sensitive:
table: output/tables/summary_table_09.csv
summary_table_11:
run: r:latest analysis/02_summary_tables.R 11
needs:
- process_data
outputs:
moderately_sensitive:
table: output/tables/summary_table_11.csv
## # # # # # # # # # # # # # # # # # # #
## Models for each jcvi_group and model_type
## # # # # # # # # # # # # # # # # # # #
model_02_unadj:
run: r:latest analysis/03_model.R 02 unadj
needs:
- process_data
outputs:
highly_sensitive:
model: output/models/model_02_unadj_*.rds
moderately_sensitive:
table: output/tables/table_02_unadj.csv
model_09_unadj:
run: r:latest analysis/03_model.R 09 unadj
needs:
- process_data
outputs:
highly_sensitive:
model: output/models/model_09_unadj_*.rds
moderately_sensitive:
table: output/tables/table_09_unadj.csv
model_11_unadj:
run: r:latest analysis/03_model.R 11 unadj
needs:
- process_data
outputs:
highly_sensitive:
model: output/models/model_11_unadj_*.rds
moderately_sensitive:
table: output/tables/table_11_unadj.csv
## # # # # # # # # # # # # # # # # # # #
## Cumulative incidence analysis
## # # # # # # # # # # # # # # # # # # #
cml_inc_model_jcvi_group:
run: r:latest analysis/04_cumulative_incidence.R jcvi_group
needs:
- design
- study_definition
- process_data
outputs:
highly_sensitive:
model: output/models/surv_model_jcvi_group.rds
moderately_sensitive:
cml_inc_plot: output/figures/cml_inc_plot_jcvi_group.png
survtable: output/tables/survtable_jcvi_group.csv
cml_inc_model_elig_date:
run: r:latest analysis/04_cumulative_incidence.R elig_date
needs:
- design
- study_definition
- process_data
outputs:
highly_sensitive:
model: output/models/surv_model_elig_date.rds
moderately_sensitive:
cml_inc_plot: output/figures/cml_inc_plot_elig_date.png
survtable: output/tables/survtable_elig_date.csv