generated from opensafely/research-template
/
project.yaml
142 lines (128 loc) · 4.96 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 10000
actions:
# Study populations
# Extract latests ethnicity record for cohort
generate_study_population_ethnicity:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_ethnicity
--output-dir=output/indicators
--output-format=feather
outputs:
highly_sensitive:
cohort: output/indicators/input_ethnicity.feather
# Extract cohort for indicator HYP001 by month
generate_study_population_hyp001:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_hyp001
--index-date-range "2020-03-01 to 2020-05-01 by month"
--output-dir=output/indicators
--output-format=feather
outputs:
highly_sensitive:
cohort: output/indicators/input_hyp001_*.feather
# Extract cohort for indicator HYP003 by month
generate_study_population_hyp003:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_hyp003
--index-date-range "2020-03-01 to 2020-05-01 by month"
--output-dir=output/indicators
--output-format=feather
outputs:
highly_sensitive:
cohort: output/indicators/input_hyp003_*.feather
# Extract cohort for indicator HYP007 by month
generate_study_population_hyp007:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_hyp007
--index-date-range "2020-03-01 to 2020-05-01 by month"
--output-dir=output/indicators
--output-format=feather
outputs:
highly_sensitive:
cohort: output/indicators/input_hyp007_*.feather
join_ethnicity:
run: >
cohort-joiner:v0.0.27
--lhs output/indicators/input_hyp*.feather
--rhs output/indicators/input_ethnicity.feather
--output-dir output/indicators/joined
needs: [generate_study_population_ethnicity, generate_study_population_hyp001, generate_study_population_hyp003, generate_study_population_hyp007]
outputs:
highly_sensitive:
cohort: output/indicators/joined/input_hyp*.feather
# Measures
# Generate measures for indicator HYP001 by month
generate_measures_hyp001:
run: >
cohortextractor:latest generate_measures
--study-definition study_definition_hyp001
--output-dir=output/indicators/joined
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure_csv: output/indicators/joined/measure_hyp001_*_rate.csv
# Generate measures for indicator HYP003 by month
generate_measures_hyp003:
run: >
cohortextractor:latest generate_measures
--study-definition study_definition_hyp003
--output-dir=output/indicators/joined
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure_csv: output/indicators/joined/measure_hyp003_*_rate.csv
# Generate measures for indicator HYP007 by month
generate_measures_hyp007:
run: >
cohortextractor:latest generate_measures
--study-definition study_definition_hyp007
--output-dir=output/indicators/joined
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure_csv: output/indicators/joined/measure_hyp007_*_rate.csv
generate_deciles:
run: >
deciles-charts:v0.0.21
--input-files output/indicators/joined/measure_*_*_rate.csv
--output-dir output/indicators/joined/
config:
show_outer_percentiles: false
tables:
output: true
charts:
output: true
needs: [generate_measures_hyp001, generate_measures_hyp003, generate_measures_hyp007]
outputs:
moderately_sensitive:
deciles_charts: output/indicators/joined/deciles_chart_*_*_practice_rate.png
deciles_tables: output/indicators/joined/deciles_table_*_*_practice_rate.csv
# check_data:
# run: r:latest analysis/check_bp_recording_values_dates.R
# needs: [join_ethnicity]
# outputs:
# moderately_sensitive:
# table_count_csv: output/indicators/joined/data_check/tab_hyp*_*_2020_03_01.csv
# skim_txt: output/indicators/joined/data_check/skim_df_hyp*_2020_03_01.txt
# table_date_diff_csv: output/indicators/joined/data_check/tab_hyp*_num_bp_date_diff_2020_03_01.csv
# plot_date_diff: output/indicators/joined/data_check/plot_hyp*_num_bp_date_diff_2020_03_01.png
# # Join all measure files for each indicator
# join_measures:
# run: r:latest analysis/join_measures.R
# needs: [generate_measures_hyp001, generate_measures_hyp003, generate_measures_hyp007]
# outputs:
# moderately_sensitive:
# measure_csv: output/indicators/joined/measures/measures_hyp*.csv
# # Join all deciles (by practice) files for each indicator
# join_deciles:
# run: r:latest analysis/join_deciles.R
# needs: [generate_deciles]
# outputs:
# moderately_sensitive:
# measure_csv: output/indicators/joined/deciles/deciles_hyp_practice.csv