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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 10000
actions:
generate_study_population_os_reports:
run: ehrql:v0 generate-dataset analysis/os_reports/dataset_definition_os_reports.py --output output/os_reports/input_os_reports.csv.gz
outputs:
highly_sensitive:
cohort: output/os_reports/input_os_reports.csv.gz
os_report_csvs:
run: r:latest analysis/os_reports/01_eol_service_Descriptives_csvs.R
needs: [generate_study_population_os_reports]
outputs:
moderately_sensitive:
monthly_deaths_Number: output/os_reports/eol_service/deaths_month*.csv
monthly_gp_CSV: output/os_reports/eol_service/gp_month*.csv
monthly_gp_Count: output/os_reports/eol_service/gp_count*.csv
monthly_med_CSV: output/os_reports/eol_service/eol_med*.csv
monthly_med_Count: output/os_reports/eol_service/eol_med_count*.csv
monthly_aevis_CSV: output/os_reports/eol_service/aevis_month*.csv
monthly_aevis_Count: output/os_reports/eol_service/aevis_count*.csv
monthly_op_CSV: output/os_reports/eol_service/opapp_month*.csv
monthly_op_Count: output/os_reports/eol_service/opapp_count*.csv
monthly_eladm_CSV: output/os_reports/eol_service/eladm_month*.csv
monthly_eladm_Count: output/os_reports/eol_service/eladm_count*.csv
quarterly_eladm_Count: output/os_reports/eol_service/eladm_quarter*.csv
monthly_emadm_CSV: output/os_reports/eol_service/emadm_month*.csv
monthly_emadm_Count: output/os_reports/eol_service/emadm_count*.csv
monthly_nursing_CSV: output/os_reports/eol_service/nursing_month*.csv
montly_nursing_Count: output/os_reports/eol_service/nursing_count*.csv
quarterly_nursing_Count: output/os_reports/eol_service/nursing_quarter*.csv
os_report_charts:
run: r:latest analysis/os_reports/02_eol_service_Descriptive_outputs.R
needs: [os_report_csvs]
outputs:
moderately_sensitive:
monthly_deaths_cod: output/os_reports/eol_service/charts/deaths_cod*.png
monthly_deaths_place: output/os_reports/eol_service/charts/deaths_place*.png
monthly_gp_cod: output/os_reports/eol_service/charts/gp_cod*.png
monthly_gp_place: output/os_reports/eol_service/charts/gp_place*.png
monthly_med_cod: output/os_reports/eol_service/charts/eol_med_cod*.png
monthly_med_place: output/os_reports/eol_service/charts/eol_med_place*.png
monthly_aevis_cod: output/os_reports/eol_service/charts/aevis_cod*.png
monthly_aevis_place: output/os_reports/eol_service/charts/aevis_place*.png
monthly_op_cod: output/os_reports/eol_service/charts/opapp_cod*.png
monthly_op_place: output/os_reports/eol_service/charts/opapp_place*.png
monthly_eladm_cod: output/os_reports/eol_service/charts/eladm_cod*.png
monthly_eladm_place: output/os_reports/eol_service/charts/eladm_place*.png
monthly_emadm_cod: output/os_reports/eol_service/charts/emadm_cod*.png
monthly_emadm_place: output/os_reports/eol_service/charts/emadm_place*.png
monthly_nursing_cod: output/os_reports/eol_service/charts/nursing_cod*.png
monthly_nursing_place: output/os_reports/eol_service/charts/nursing_place*.png
WP2_outputs:
run: r:latest analysis/os_reports/03_eol_WP2_quality_indicators.R
needs: [generate_study_population_os_reports]
outputs:
moderately_sensitive:
proportion_palcare_code: output/os_reports/WP2_quality_indicators/palcare*.csv
proportion_aeviv1: output/os_reports/WP2_quality_indicators/aevis1*.csv
proportion_aevis3: output/os_reports/WP2_quality_indicators/aevis3*.csv
proportion_eolmed: output/os_reports/WP2_quality_indicators/eolmed*.csv
proportion_specpal_code: output/os_reports/WP2_quality_indicators/specpal*.csv
proportion_cancer_palcare: output/os_reports/WP2_quality_indicators/cancer*.csv
WP2_outputs_advance_care_plan:
run: r:latest analysis/os_reports/05_eol_WP2_advance_care_plan_measures.R
needs: [generate_study_population_os_reports]
outputs:
moderately_sensitive:
acp_code: output/os_reports/WP2_quality_indicators/acp*.csv
acp3m_code: output/os_reports/WP2_quality_indicators/acp3m*.csv
acpdur_code: output/os_reports/WP2_quality_indicators/acpdur*.csv
WP3_descriptive_outputs:
run: r:latest analysis/os_reports/07_eol_WP3_MAIHDA.R
needs: [generate_study_population_os_reports]
outputs:
moderately_sensitive:
descriptive_stats: output/os_reports/WP3/count*.csv