generated from opensafely/research-template
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project.yaml
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/
project.yaml
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version: "3.0"
expectations:
population_size: 5000
actions:
monthly_practice_listsize_2018:
run: cohortextractor:latest generate_cohort --study-definition study_definition_listsize_monthly
--index-date-range '2018-06-01 to 2019-05-31 by month' --output-dir=output/listsize
--output-format=feather
outputs:
highly_sensitive:
extract: output/listsize/input_listsize_monthl*.feather
monthly_practice_listsize_2019:
run: cohortextractor:latest generate_cohort --study-definition study_definition_listsize_monthly
--index-date-range '2019-06-01 to 2020-05-31 by month' --output-dir=output/listsize
--output-format=feather
outputs:
highly_sensitive:
extract: output/listsize/input_listsize_month*.feather
monthly_practice_listsize_2020:
run: cohortextractor:latest generate_cohort --study-definition study_definition_listsize_monthly
--index-date-range '2020-06-01 to 2021-05-31 by month' --output-dir=output/listsize
--output-format=feather
outputs:
highly_sensitive:
extract: output/listsize/input_listsize_mont*.feather
monthly_practice_listsize_2021:
run: cohortextractor:latest generate_cohort --study-definition study_definition_listsize_monthly
--index-date-range '2021-06-01 to 2022-12-31 by month' --output-dir=output/listsize
--output-format=feather
outputs:
highly_sensitive:
extract: output/listsize/input_listsize_mon*.feather
monthly_practice_listsize_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition_listsize_monthly --output-dir=output/listsize
needs:
- monthly_practice_listsize_2018
- monthly_practice_listsize_2019
- monthly_practice_listsize_2020
- monthly_practice_listsize_2021
outputs:
moderately_sensitive:
measure_csv: output/listsize/measure_*.csv
# Other data
# ----------
# Add actions for other data to this section. Prefix them with a suitable name; place
# scripts in a similarly named sub-directory of the analysis directory; write outputs
# to a similarly named sub-directory of the output directory.
#
# For example, let's call our other data "metrics". We would prefix our actions
# "metrics_"; we would place our scripts in analysis/metrics; we would write outputs
# to output/metrics.
metrics_monthly_sro_data:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sro_monthly
--index-date-range '2018-06-01 to 2022-12-31 by month' --output-dir=output/metrics/monthly
--output-format=feather
outputs:
highly_sensitive:
extract: output/metrics/monthly/input_sro_monthly*.feather
metrics_monthly_sro_data_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition_sro_monthly --output-dir=output/metrics/monthly
needs:
- metrics_monthly_sro_data
outputs:
moderately_sensitive:
measure_csv: output/metrics/monthly/measure_*.csv
metrics_monthly_kids_data:
run: cohortextractor:latest generate_cohort --study-definition study_definition_kids_monthly
--index-date-range '2018-06-01 to 2022-12-31 by month' --output-dir=output/metrics/monthly
--output-format=feather
outputs:
highly_sensitive:
extract: output/metrics/monthly/input_kids_monthly*.feather
metrics_monthly_kids_data_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition_kids_monthly --output-dir=output/metrics/monthly
needs:
- metrics_monthly_kids_data
outputs:
moderately_sensitive:
measure_csv: output/metrics/monthly/measure*.csv
metrics_generate_deciles_charts:
run: >
deciles-charts:v0.0.33
--input-files output/metrics/monthly/measure_*.csv
--output-dir output/metrics
config:
show_outer_percentiles: true
needs:
- metrics_monthly_sro_data_measures
- metrics_monthly_kids_data_measures
outputs:
moderately_sensitive:
deciles_charts: output/metrics/deciles_chart_*.png
deciles_tables: output/metrics/deciles_table_*.csv
metrics_generate_deciles_charts_alternative:
run: >
python:latest
python
-m analysis.deciles_alternative
--input-files output/metrics/monthly/measure_*.csv
--output-dir output/metrics/shaded
config:
show_outer_percentiles: true
needs:
- metrics_monthly_sro_data_measures
- metrics_monthly_kids_data_measures
outputs:
moderately_sensitive:
deciles_charts: output/metrics/shaded/deciles_chart*.png
deciles_tables: output/metrics/shaded/deciles_table*.csv
# Metrics data extraction
# ------------
metrics_generate_sro_dataset_winter:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sro
--param start_date='2021-12-01' --param end_date='2022-03-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_sro_2021-12-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_sro_2021-12-01.feather
metrics_generate_sro_dataset_summer:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sro
--param start_date='2021-06-01' --param end_date='2021-09-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_sro_2021-06-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_sro_2021-06-01.feather
metrics_generate_kids_dataset_winter:
run: cohortextractor:latest generate_cohort --study-definition study_definition_kids
--param start_date='2021-12-01' --param end_date='2022-03-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_kids_2021-12-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_kids_2021-12-01.feather
metrics_generate_kids_dataset_summer:
run: cohortextractor:latest generate_cohort --study-definition study_definition_kids
--param start_date='2021-06-01' --param end_date='2021-09-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_kids_2021-06-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_kids_2021-06-01.feather
metrics_generate_endpopulation_dataset_winter:
run: cohortextractor:latest generate_cohort --study-definition study_definition_endpopulation
--param start_date='2021-12-01' --param end_date='2022-03-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_endpopulation_2021-12-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_endpopulation_2021-12-01.feather
metrics_generate_endpopulation_dataset_summer:
run: cohortextractor:latest generate_cohort --study-definition study_definition_endpopulation
--param start_date='2021-06-01' --param end_date='2021-09-30' --output-dir=output/metrics
--output-format=feather --output-file output/metrics/input_endpopulation_2021-06-01.feather
outputs:
highly_sensitive:
extract: output/metrics/input_endpopulation_2021-06-01.feather
metrics_generate_sro_measures:
run: cohortextractor:latest generate_measures --param start_date='2021-06-01'
--param end_date='2021-09-30' --study-definition study_definition_sro --output-dir=output/metrics
needs:
- metrics_generate_sro_dataset_summer
- metrics_generate_sro_dataset_winter
outputs:
moderately_sensitive:
measure_csv: output/metrics/mea*.csv
metrics_generate_kids_measures:
run: cohortextractor:latest generate_measures --param start_date='2021-06-01'
--param end_date='2021-09-30' --study-definition study_definition_kids --output-dir=output/metrics
needs:
- metrics_generate_kids_dataset_summer
- metrics_generate_kids_dataset_winter
outputs:
moderately_sensitive:
measure_csv: output/metrics/me*.csv
metrics_generate_endpopulation_measures:
run: cohortextractor:latest generate_measures --param start_date='2021-06-01'
--param end_date='2021-09-30' --study-definition study_definition_endpopulation
--output-dir=output/metrics
needs:
- metrics_generate_endpopulation_dataset_summer
- metrics_generate_endpopulation_dataset_winter
outputs:
moderately_sensitive:
measure_csv: output/metrics/m*.csv
identify_practices_to_remove:
run: r:latest analysis/metrics/identify_practices_to_remove.R
needs:
- metrics_generate_sro_measures
- metrics_generate_kids_measures
- metrics_generate_endpopulation_measures
outputs:
moderately_sensitive:
csv: output/metrics/practices_to_remove.csv
metrics_create_seasonal_data:
run: r:latest analysis/metrics/create_seasonal_data.R
needs:
- metrics_generate_sro_measures
- metrics_generate_kids_measures
outputs:
highly_sensitive:
csv: output/metrics/season_data_*.csv
metrics_create_seasonal_measures:
run: r:latest analysis/metrics/seasonal_measures.R
needs:
- metrics_create_seasonal_data
- appointments_generate_seasonal_summaries_by_booked_month
- appointments_generate_seasonal_summaries_by_start_month
- identify_practices_to_remove
outputs:
moderately_sensitive:
raw_csv: output/*/*/summer_winter_all_metrics.csv
plot_csv: output/*/*/summer_winter_*_histogram_data.csv
plot_png: output/*/*/summer_winter_*_histogram.png
plot_csv_redacted: output/*/*/redacted/summer_winter_*_histogram_data_redacted.csv
plot_png_redacted: output/*/*/redacted/summer_winter_*_histogram_redacted.png
# Epi
# -----------------
epi_generate_winter_outcomes:
run: cohortextractor:latest generate_cohort --study-definition study_definition_epi
--param start_date='2021-12-01' --param end_date='2022-03-30' --output-dir=output/epi/
--output-format=feather
outputs:
highly_sensitive:
extract: output/epi/*.feather
epi_model_irr:
run: r:latest analysis/epi/model_irr.R
needs:
- epi_generate_winter_outcomes
- classify_practices_by_decile
outputs:
moderately_sensitive:
data: output/epi/irr_data.csv
epi_irr_data_add_practice_count:
run: r:latest analysis/epi/practice_count.R
needs:
- epi_model_irr
- count_practices_by_decile
outputs:
moderately_sensitive:
data: output/epi/*_data.csv
epi_plot_irr:
run: r:latest analysis/epi/plot_irr.R
needs:
- epi_model_irr
outputs:
moderately_sensitive:
single_plots: output/epi/plots/*.png
combined_plots: output/epi/plots/combined/*.png
combined_plots_inc_rate: output/epi/plots/combined/inc_rate/*.png
# Appointments data
# -----------------
appointments_generate_dataset_sql:
run: >
sqlrunner:latest
analysis/appointments/dataset_query.sql
--output output/appointments/dataset_long.csv.gz
--dummy-data-file analysis/appointments/dummy_dataset_long.csv.gz
outputs:
highly_sensitive:
dataset: output/appointments/dataset_long.csv.gz
appointments_generate_monthly_measures_by_booked_month:
run: >
python:latest
python
-m analysis.appointments.generate_appointment_monthly_measures
--value-thresholds 0 2
--index-cols booked_month practice
needs: [appointments_generate_dataset_sql]
outputs:
highly_sensitive:
monthly_measure: output/appointments/measure_monthly_*_by_booked_month.csv
appointments_generate_monthly_measures_by_start_month:
run: >
python:latest
python
-m analysis.appointments.generate_appointment_monthly_measures
--value-thresholds 0 2
--index-cols start_month practice
needs: [appointments_generate_dataset_sql]
outputs:
highly_sensitive:
monthly_measure: output/appointments/measure_monthly_*_by_start_month.csv
calculate_total_num_appointments_monthly:
run: r:latest analysis/calculate_monthly_counts.R
needs:
- appointments_generate_monthly_measures_by_booked_month
- appointments_generate_monthly_measures_by_start_month
outputs:
moderately_sensitive:
overall_csvs: output/appointments/measure_monthly_overall_*.csv
appointments_generate_seasonal_summaries_by_start_month:
run: >
python:latest
python
-m analysis.appointments.generate_appointment_seasonal_summaries
--value-thresholds 0 2
--start-date 2021-06-01
--end-date 2022-03-31
--index-cols start_month practice
needs: [appointments_generate_dataset_sql]
outputs:
moderately_sensitive:
monthly_measure: output/appointments/measure_seasonal_*_by_start_month.csv
appointments_generate_seasonal_summaries_by_booked_month:
run: >
python:latest
python
-m analysis.appointments.generate_appointment_seasonal_summaries
--value-thresholds 0 2
--start-date 2021-06-01
--end-date 2022-03-31
--index-cols booked_month practice
needs: [appointments_generate_dataset_sql]
outputs:
moderately_sensitive:
monthly_measure: output/appointments/measure_seasonal_*_by_booked_month.csv
### Some of the measures need to be normalised by list size, specifically
### anything that starts with 'measure_monthly_num'
appointments_generate_normalised_counts:
run: r:latest analysis/normalise_counts.R
needs:
- appointments_generate_monthly_measures_by_booked_month
- appointments_generate_monthly_measures_by_start_month
- monthly_practice_listsize_measures
outputs:
moderately_sensitive:
normalised_csvs: output/appointments/measure_monthly_normalised_*.csv
check_csvs: output/check/*CHECK.csv
appointments_practice_checks:
run: r:latest analysis/appointments/appt_check.R
needs:
- appointments_generate_monthly_measures_by_booked_month
- appointments_generate_monthly_measures_by_start_month
- monthly_practice_listsize_measures
outputs:
moderately_sensitive:
check_practice_csvs: output/check/*dropped_*.csv
appointments_generate_deciles_charts:
run: >
deciles-charts:v0.0.33
--input-files output/appointments/measure_monthly_*.csv
--output-dir output/appointments
config:
show_outer_percentiles: true
needs:
- appointments_generate_monthly_measures_by_booked_month
- appointments_generate_monthly_measures_by_start_month
- appointments_generate_normalised_counts
outputs:
moderately_sensitive:
deciles_charts: output/appointments/deciles_chart_*.png
deciles_tables: output/appointments/deciles_table_*.csv
appointments_generate_deciles_charts_alternative:
run: >
python:latest
python
-m analysis.deciles_alternative
--input-files output/appointments/measure_monthly_*.csv
--output-dir output/appointments/shaded
config:
show_outer_percentiles: true
needs:
- appointments_generate_monthly_measures_by_booked_month
- appointments_generate_monthly_measures_by_start_month
- appointments_generate_normalised_counts
outputs:
moderately_sensitive:
deciles_charts: output/appointments/shaded/deciles_chart*.png
deciles_tables: output/appointments/shaded/deciles_table*.csv
# Combining data
# -----------------
combine_seasonal_data:
run: r:latest analysis/combine_seasonal_data.R
needs:
- metrics_create_seasonal_measures
- appointments_generate_seasonal_summaries_by_booked_month
- appointments_generate_seasonal_summaries_by_start_month
outputs:
moderately_sensitive:
csv: output/combined/combined_seasonal_data.csv
classify_practices_by_decile:
run: r:latest analysis/classify_practices_by_decile.R
needs:
- combine_seasonal_data
outputs:
moderately_sensitive:
csv: output/combined/combined_seasonal_data_with_deciles.csv
count_practices_by_decile:
run: r:latest analysis/count_practices_by_decile.R
needs:
- classify_practices_by_decile
outputs:
moderately_sensitive:
csv: output/combined/practice_counts_per_decile.csv
summarise_seasonal_comparisons:
run: r:latest analysis/summarise_seasonal_comparisons.R
needs:
- combine_seasonal_data
outputs:
moderately_sensitive:
csv: output/combined/seasonal_summaries.csv
redacted_csv: output/combined/seasonal_summaries_nondisclosive.csv
metrics_check_practice_counts:
run: r:latest analysis/check_practice_counts_for_metrics.R
needs:
- metrics_monthly_sro_data_measures
- metrics_monthly_kids_data_measures
outputs:
moderately_sensitive:
csv: output/practice-counts-check/*.csv
# Tests
# -----------------
run_python_tests:
run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
outputs:
moderately_sensitive:
log: output/pytest.xml
run_r_tests:
run: r:latest tests/testthat/run-all.R
outputs:
moderately_sensitive:
log: output/tests/run-all.log
# Presentations and documents
# ---------------------------
generate_preliminary_report:
run: r:latest -e 'rmarkdown::render("reports/preliminary_report.rmd", output_dir = "/workspace/output/docs", knit_root_dir = "/workspace",)'
needs:
- metrics_create_seasonal_measures
# - metrics_generate_deciles_charts
- metrics_generate_deciles_charts_alternative
# - appointments_generate_deciles_charts
- appointments_generate_deciles_charts_alternative
- appointments_generate_seasonal_summaries_by_booked_month
- appointments_generate_seasonal_summaries_by_start_month
- summarise_seasonal_comparisons
- identify_practices_to_remove
- epi_plot_irr
outputs:
moderately_sensitive:
report: output/docs/preliminary_report.html
generate_flowchart:
run: r:latest analysis/flowchart.R
needs:
- metrics_monthly_sro_data_measures
- metrics_monthly_kids_data_measures
- appointments_generate_monthly_measures_by_booked_month
- monthly_practice_listsize_measures
outputs:
moderately_sensitive:
csv: output/check/practice_counts.csv
png: output/check/*.png
create_release:
run: r:latest analysis/create_release.R
needs:
- generate_preliminary_report
# - appointments_generate_deciles_charts
- appointments_generate_deciles_charts_alternative
# - metrics_generate_deciles_charts
- metrics_generate_deciles_charts_alternative
- metrics_create_seasonal_measures
- summarise_seasonal_comparisons
- epi_irr_data_add_practice_count
- epi_plot_irr
outputs:
moderately_sensitive:
html: output/release/*.html
txt: output/meta-release/*.txt
plot_data: output/release/*/*.csv
plot_png: output/release/*/*.png