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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 100000
actions:
##### Dataset definitions #####
# Closed (completed) RTT pathways
generate_dataset_full:
run: ehrql:v1 generate-dataset analysis/dataset_definition_full.py
--output output/data/dataset_full.arrow
#--dummy-data-file dummy/dummy_ortho_clockstops.arrow
outputs:
highly_sensitive:
cohort: output/data/dataset_full.arrow
# Closed (completed) RTT pathways
generate_dataset_ortho:
run: ehrql:v1 generate-dataset analysis/dataset_definition_ortho.py
--output output/data/dataset_ortho.arrow
#--dummy-data-file dummy/dummy_ortho_clockstops.arrow
outputs:
highly_sensitive:
cohort: output/data/dataset_ortho.arrow
#### Check number of pathways over time ####
measures_checks:
run: ehrql:v1 generate-measures analysis/measures_checks.py
--output output/measures/measures_checks.csv
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_checks.csv
##### Opioid measures - closed pathways #####
measures_any_opioid:
run: ehrql:v1 generate-measures analysis/measures_opioid_all.py
--output output/measures/measures_any_opioid.csv
--
--codelist "opioid_codes"
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_any_opioid.csv
measures_long_opioid:
run: ehrql:v1 generate-measures analysis/measures_opioid_all.py
--output output/measures/measures_long_opioid.csv
--
--codelist "long_opioid_codes"
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_long_opioid.csv
measures_short_opioid:
run: ehrql:v1 generate-measures analysis/measures_opioid_all.py
--output output/measures/measures_short_opioid.csv
--
--codelist "short_opioid_codes"
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_short_opioid.csv
measures_weak_opioid:
run: ehrql:v1 generate-measures analysis/measures_opioid_all.py
--output output/measures/measures_weak_opioid.csv
--
--codelist "weak_opioid_codes"
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_weak_opioid.csv
measures_strong_opioid:
run: ehrql:v1 generate-measures analysis/measures_opioid_all.py
--output output/measures/measures_strong_opioid.csv
--
--codelist "strong_opioid_codes"
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_strong_opioid.csv
# Combine measures
opioids_by_week:
run: r:latest analysis/clockstops/opioids_by_week.R
needs: [measures_any_opioid, measures_weak_opioid, measures_strong_opioid, measures_long_opioid, measures_short_opioid]
outputs:
moderately_sensitive:
data: output/clockstops/opioid*.csv
##### Analysis - closed pathways #####
# checks_cohort_clockstops:
# run: r:latest analysis/clockstops/checks_cohort_clockstops.R
# needs: [generate_dataset_clockstops]
# outputs:
# moderately_sensitive:
# data: output/clockstops/check*.csv
final_cohort_exclusions:
run: r:latest analysis/clockstops/final_cohort_exclusions.R
needs: [generate_dataset_full, generate_dataset_ortho]
outputs:
highly_sensitive:
cohort: output/data/cohort*.csv.gz
moderately_sensitive:
#exclusions1: output/clockstops/cohort_full_exclusions.csv
exclusions2: output/clockstops/exclude*.csv
wait_time:
run: r:latest analysis/clockstops/wait_time.R
needs: [final_cohort_exclusions]
outputs:
moderately_sensitive:
data1: output/clockstops/rtt_dates.csv
data2: output/clockstops/wait_by_group.csv
frequency_tables_all:
run: r:latest analysis/clockstops/frequency_tables_all.R
needs: [final_cohort_exclusions]
outputs:
moderately_sensitive:
data1: output/clockstops/cat_var_dist_ortho.csv
frequency_tables_routine:
run: r:latest analysis/clockstops/frequency_tables_routine.R
needs: [final_cohort_exclusions]
outputs:
moderately_sensitive:
data1: output/clockstops/cat_var_dist_prior.csv
data2: output/clockstops/age_stats.csv
opioid_prescribing:
run: r:latest analysis/clockstops/opioid_prescribing.R
needs: [final_cohort_exclusions]
outputs:
moderately_sensitive:
data1: output/clockstops/med_by_period.csv
data2: output/clockstops/med_by_period_wait.csv
data3: output/clockstops/total_rx_wait.csv
######################################################################################