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: 400000
actions:
generate_study_population_allpts:
run: cohortextractor:latest generate_cohort --study-definition study_definition_allpts
outputs:
highly_sensitive:
cohort: output/input_allpts.csv
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
create_cohorts_allpts:
run: stata-mp:latest analysis/001_define_covariates_allpts.do
needs: [generate_study_population_allpts]
outputs:
highly_sensitive:
log1: logs/cleaning_dataset_allpts.log
data1: output/data/file_eia_allpts.dta
create_cohorts:
run: stata-mp:latest analysis/000_define_covariates.do
needs: [generate_study_population]
outputs:
highly_sensitive:
log1: logs/cleaning_dataset.log
data1: output/data/file_eia_all.dta
run_baseline_tables_allpts:
run: stata-mp:latest analysis/101_baseline_characteristics_allpts.do
needs: [create_cohorts_allpts]
outputs:
moderately_sensitive:
log1: logs/descriptive_tables_allpts.log
doc1: output/tables/baseline_allpts.csv
run_baseline_tables:
run: stata-mp:latest analysis/100_baseline_characteristics.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/descriptive_tables.log
doc1: output/tables/baseline_bydiagnosis.csv
doc2: output/tables/baseline_byyear.csv
doc3: output/tables/referral_bydiag_nomiss.csv
doc4: output/tables/referral_byyear_nomiss.csv
doc5: output/tables/referral_byregion_nomiss.csv
doc6: output/tables/drug_bydiag_miss.csv
doc7: output/tables/drug_byyear_miss.csv
doc8: output/tables/drug_byyear_ra_miss.csv
doc9: output/tables/drug_byyear_psa_miss.csv
doc10: output/tables/drug_byyear_undiff_miss.csv
doc11: output/tables/drug_byyearanddisease.csv
doc12: output/tables/drug_byyearandregion.csv
doc13: output/tables/diag_count_bymonth.csv
doc14: output/tables/diag_count_byyear.csv
doc15: output/tables/appt_count_bymonth.csv
doc16: output/tables/diag_count_byyear_ethn.csv
doc17: output/tables/diag_count_byyear_imd.csv
doc18: output/tables/diag_count_bymonth_female.csv
doc19: output/tables/diag_count_bymonth_male.csv
doc20: output/tables/diag_count_byyear_female.csv
doc21: output/tables/diag_count_byyear_male.csv
figure1: output/figures/incidence_twoway_rounded.svg
figure2: output/figures/incidence_twoway_appt.svg
figure3: output/figures/incidence_twoway_rounded_female.svg
figure4: output/figures/incidence_twoway_rounded_male.svg
run_itsa_models:
run: stata-mp:latest analysis/200_itsa_models.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/itsa_models.log
figure1: output/figures/ITSA_diagnostic_delay_newey.svg
figure2: output/figures/ITSA_diagnostic_delay_prais.svg
figure3: output/figures/ITSA_diagnostic_delay_GP_newey.svg
figure4: output/figures/ITSA_diagnostic_delay_GP_prais.svg
doc1: output/tables/gp_to_appt_ITSA_table.csv
run_itsa_models_drugs:
run: stata-mp:latest analysis/201_itsa_models_drugs.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/itsa_models_drugs.log
figure1: output/figures/ITSA_csDMARD_delay_newey.svg
figure2: output/figures/ITSA_csDMARD_delay_prais.svg
figure3: output/figures/ITSA_csDMARD_delay_newey_sensitivity.svg
figure4: output/figures/ITSA_csDMARD_delay_prais_sensitivity.svg
doc1: output/tables/appt_to_csdmard_ITSA_table.csv
run_box_plots:
run: stata-mp:latest analysis/300_box_plots.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/box_plots.log
figure 1: output/figures/regional_qs1_bar_overall.svg
figure 2: output/figures/regional_qs1_bar_2019.svg
figure 3: output/figures/regional_qs1_bar_2020.svg
figure 4: output/figures/regional_qs2_bar_overall.svg
figure 5: output/figures/regional_qs2_bar_2019.svg
figure 6: output/figures/regional_qs2_bar_2020.svg
figure 7: output/figures/regional_qs2_bar_GP_overall.svg
figure 8: output/figures/regional_qs2_bar_GP_2019.svg
figure 9: output/figures/regional_qs2_bar_GP_2020.svg
figure 10: output/figures/regional_qs2_bar_GP_merged.svg
figure 11: output/figures/regional_qs2_bar_GP_ethnicity.svg
figure 12: output/figures/regional_qs2_bar_GP_imd.svg
figure 13: output/figures/regional_csdmard_bar_overall.svg
figure 14: output/figures/regional_csdmard_bar_2019.svg
figure 15: output/figures/regional_csdmard_bar_2020.svg
figure 16: output/figures/regional_csdmard_bar_merged.svg
figure 17: output/figures/regional_csdmard_bar_ethnicity.svg
figure 18: output/figures/regional_csdmard_bar_imd.svg
run_redacted_tables:
run: stata-mp:latest analysis/400_redacted_tables.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/redacted_tables.log
doc1: output/tables/table_1_rounded_bydiag.csv
doc2: output/tables/table_mean_bydiag_rounded.csv
doc3: output/tables/table_median_bydiag_rounded.csv
doc4: output/tables/table_median_bydiag_rounded_to21.csv
doc5: output/tables/ITSA_tables_appt_delay_rounded.csv
doc6: output/tables/ITSA_tables_csdmard_delay_rounded.csv
doc7: output/tables/drug_byyearanddisease_rounded.csv
doc8: output/tables/first_csdmard_rounded.csv
doc9: output/tables/drug_byyearandregion_rounded.csv
doc10: output/tables/referral_byregion_rounded.csv
doc11: output/tables/consultation_medium_rounded.csv
doc12: output/tables/table_median_bydiag_rounded_to21_report.csv
doc13: output/tables/first_csdmard_rounded_report.csv
run_redacted_tables_allpts:
run: stata-mp:latest analysis/401_redacted_tables_allpts.do
needs: [create_cohorts_allpts]
outputs:
moderately_sensitive:
log1: logs/redacted_tables_allpts.log
doc1: output/tables/table_1_rounded_allpts.csv
convert_image_formats:
run: python:latest python analysis/convert_images.py --input_dir output/figures --output_dir output/figures
needs: [run_baseline_tables, run_itsa_models, run_itsa_models_drugs, run_box_plots, run_redacted_tables]
outputs:
moderately_sensitive:
figures: output/figures/*.png
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/analysis/report.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [convert_image_formats,run_baseline_tables, run_itsa_models, run_itsa_models_drugs, run_box_plots, run_redacted_tables]
outputs:
moderately_sensitive:
notebook: output/report.html