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project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to today by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_*.csv.gz
generate_study_population_broad_comparison:
run: cohortextractor:latest generate_cohort --study-definition study_definition_broad_comparison --index-date-range "2019-01-01 to today by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_broad_*.csv.gz
generate_study_population_covidcheck:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covidcheck_2
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_covidcheck_2.csv.gz
generate_study_population_samedayab:
run: cohortextractor:latest generate_cohort --study-definition study_definition_sameday_ab
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_sameday_ab.csv.gz
generate_study_population_withab:
run: cohortextractor:latest generate_cohort --study-definition study_definition_withab_cohort
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_withab_cohort.csv.gz
generate_study_population_infection:
run: cohortextractor:latest generate_cohort --study-definition study_definition_infection --index-date-range "2019-01-01 to today by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_infection_*.csv.gz
generate_study_population_indication:
run: cohortextractor:latest generate_cohort --study-definition study_definition_indication --index-date-range "2019-01-01 to today by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_indication_*.csv.gz
generate_study_population_elderly:
run: cohortextractor:latest generate_cohort --study-definition study_definition_elderly
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_elderly.csv.gz
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
needs: [generate_study_population]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_*.csv
generate_measures_infection:
run: cohortextractor:latest generate_measures --study-definition study_definition_infection --skip-existing --output-dir=output/measures
needs: [generate_study_population_infection]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_infection_*.csv
generate_measures_indication:
run: cohortextractor:latest generate_measures --study-definition study_definition_indication --skip-existing --output-dir=output/measures
needs: [generate_study_population_indication]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_indication_*.csv
generate_measures_broad:
run: cohortextractor:latest generate_measures --study-definition study_definition_broad_comparison --skip-existing --output-dir=output/measures
needs: [generate_study_population_broad_comparison]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_broad_*.csv
## for appropriateness of antibiotic prescribing
# generate_study_population_repeat_antibiotics:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_ab_repeat --index-date-range "2019-01-01 to today by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
# outputs:
# highly_sensitive:
# cohort: output/measures/input_ab_repeat_*.csv.gz
# describe_repeat_ab_process:
# run: r:latest analysis/process/ab_repeat_transform.R
# needs: [generate_study_population_repeat_antibiotics]
# outputs:
# moderately_sensitive:
# rds1: output/measures/repeatab_uti.rds
# rds2: output/measures/repeatab_lrti.rds
# rds3: output/measures/repeatab_urti.rds
# describe_elderly_agedis:
# run: r:latest analysis/tables/gen_csv_age_check.R
# needs: [generate_study_population_elderly]
# outputs:
# moderately_sensitive:
# agetable: output/age_quant.csv
# describe:
# run: r:latest analysis/plot/overall_ab_prescribing.R
# needs: [generate_measures]
# outputs:
# moderately_sensitive:
# cohort: output/overall.png
# boxplot: output/overallbox.png
describe_percentile:
run: r:latest analysis/plot/overall_ab_prescribing_2575percentile.R
needs: [generate_measures]
outputs:
moderately_sensitive:
percentile: output/overall_25th_75th_percentile.jpeg
table_total: output/total_number_antibacterial_prescriptions.csv
describe_percentile_starpu:
run: r:latest analysis/plot/starpu_ab_percentile.R
needs: [generate_measures]
outputs:
moderately_sensitive:
percentile_STARPU: output/overall_25th_75th_percentile_STARPU.jpeg
percentile_csv_STARPU: output/monthly_quantile_ab_STARPU.csv
# generate_notebook_starpu:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/starpu.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
# needs: [generate_measures]
# outputs:
# moderately_sensitive:
# notebook: output/starpu.html
# figures: output/*
# #tables: output/tables/*
# #csvs: output/*/* # two possible subfolders
# #text: output/text/*
describe_service_eval_baseline_table:
run: r:latest analysis/tables/baseline_table.R
needs: [generate_study_population]
outputs:
moderately_sensitive:
baseline_overall: output/overall_counts_blt.csv
baseline_table: output/blt_one_random_obs_perpat.csv
describe_baseline_table_split_2019:
run: r:latest analysis/tables/baseline_table_2019.R
needs: [describe_basic_record_process]
outputs:
moderately_sensitive:
baseline_overall_2019: output/overall_counts_blt_2019.csv
baseline_table_2019: output/blt_one_random_obs_perpat_2019.csv
describe_baseline_table_split_2020:
run: r:latest analysis/tables/baseline_table_2020.R
needs: [describe_basic_record_process]
outputs:
moderately_sensitive:
baseline_overall_2020: output/overall_counts_blt_2020.csv
baseline_table_2020: output/blt_one_random_obs_perpat_2020.csv
describe_baseline_table_split_2021:
run: r:latest analysis/tables/baseline_table_2021.R
needs: [describe_basic_record_process]
outputs:
moderately_sensitive:
baseline_overall_2021: output/overall_counts_blt_2021.csv
baseline_table_2021: output/blt_one_random_obs_perpat_2021.csv
describe_baseline_table_split_2022:
run: r:latest analysis/tables/baseline_table_2022.R
needs: [describe_basic_record_process]
outputs:
moderately_sensitive:
baseline_overall_2022: output/overall_counts_blt_2022.csv
baseline_table_2022: output/blt_one_random_obs_perpat_2022.csv
describe_service_eval_covid_check:
run: r:latest analysis/tables/baseline_table_covid_check.R
needs: [generate_study_population_covidcheck]
outputs:
moderately_sensitive:
baseline_covidcheck: output/overall_covid.csv
blt_covidcheck: output/blt_covid_check.csv
# describe_consultation_rate:
# run: r:latest analysis/plot/incident_consultation_age_stacked_barchart.R
# needs: [generate_measures]
# outputs:
# moderately_sensitive:
# bar1: output/consult_age_UTI.png
# bar2: output/consult_age_LRTI.png
# bar3: output/consult_age_URTI.png
# bar4: output/consult_age_sinusitis.png
# bar5: output/consult_age_ot_externa.png
# bar6: output/consult_age_otmedia.png
# bar7: output/consult_age_repeatedUTI.png
# describe_consultation_prescribed:
# run: r:latest analysis/plot/consultation_prescibed_percentage.R
# needs: [generate_study_population]
# outputs:
# moderately_sensitive:
# bar1: output/prescribed_percentage_UTI.png
# csvs: output/uti_prescrib_check.csv
#generate_notebook_starpu:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/starpu.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_risk --ExecutePreprocessor.timeout=86400
# needs: [generate_measures]
# outputs:
# moderately_sensitive:
# notebook: output/hospitalisation_risk/starpu.html
# figures: output/hospitalisation_risk/*
#tables: output/tables/*
#csvs: output/*/* # two possible subfolders
#text: output/text/*
# generate_notebook_hospitalisation_analysis:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_analysis.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_risk --ExecutePreprocessor.timeout=86400
# needs: [generate_study_population]
# outputs:
# moderately_sensitive:
# notebook: output/hospitalisation_risk/hospitalisation_analysis.html
# figures: output/hospitalisation_risk/*
# generate_notebook_hospitalisation_analysis:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/hospitalisation_analysis.ipynb --execute --to html --output-dir=/workspace/output/hospitalisation_risk --ExecutePreprocessor.timeout=86400
# needs: [generate_study_population]
# outputs:
# moderately_sensitive:
# notebook: output/hospitalisation_risk/hospitalisation_analysis.html
# figures: output/hospitalisation_risk/*
describe_prior_ab_12mb4:
run: r:latest analysis/plot/ab_1yb4_stackedbar_2.R
needs: [generate_study_population]
outputs:
moderately_sensitive:
plot: output/AB_1yb4_line.jpeg
plot_sex: output/AB_1yb4_SEX.jpeg
#count_table: output/prior_ab_by_month.csv
describe_consultation_rate_all_incident:
run: r:latest analysis/plot/consultation_by_age_infection_incident.R
needs: [generate_measures_infection]
outputs:
moderately_sensitive:
plot1.1: output/consult_age_incident_UTI.jpeg
plot1.2: output/consult_age_incident_URTI.jpeg
plot1.3: output/consult_age_incident_LRTI.jpeg
plot1.4: output/consult_age_incident_sinusitis.jpeg
plot1.5: output/consult_age_incident_otmedia.jpeg
plot1.6: output/consult_age_incident_ot_externa.jpeg
plot2: output/consult_all_incident.jpeg
csv1: output/consultation_rate_incident.csv
csv2: output/consultation_GP_rate_incident.csv
describe_consultation_rate_all_prevalent:
run: r:latest analysis/plot/consultation_by_age_infection_prevalent.R
needs: [generate_measures_infection]
outputs:
moderately_sensitive:
plot1.1: output/consult_age_prevalent_UTI.jpeg
plot1.2: output/consult_age_prevalent_URTI.jpeg
plot1.3: output/consult_age_prevalent_LRTI.jpeg
plot1.4: output/consult_age_prevalent_sinusitis.jpeg
plot1.5: output/consult_age_prevalent_otmedia.jpeg
plot1.6: output/consult_age_prevalent_ot_externa.jpeg
plot2: output/consult_all_prevalent.jpeg
csv1: output/consultation_rate_prevalent.csv
csv2: output/consultation_GP_rate_prevalent.csv
describe_consultation_rate_all_incident_redacted:
run: r:latest analysis/redaction/consultation_by_age_infection_incident.R
needs: [generate_measures_infection,generate_measures_indication]
outputs:
moderately_sensitive:
plot1.1: output/redacted/consult_age_incident_UTI.jpeg
plot1.2: output/redacted/consult_age_incident_URTI.jpeg
plot1.3: output/redacted/consult_age_incident_LRTI.jpeg
plot1.4: output/redacted/consult_age_incident_sinusitis.jpeg
plot1.5: output/redacted/consult_age_incident_otmedia.jpeg
plot1.6: output/redacted/consult_age_incident_ot_externa.jpeg
plot1.7: output/redacted/consult_age_incident_all.jpeg
csv1: output/redacted/consultation_rate_incident_check.csv
csv2: output/redacted/consultation_rate_incident.csv
csv3: output/redacted/consultation_rate_incident_year.csv
describe_consultation_rate_all_prevalent_redacted:
run: r:latest analysis/redaction/consultation_by_age_infection_prevalent.R
needs: [generate_measures_infection,generate_measures_indication]
outputs:
moderately_sensitive:
plot1.1: output/redacted/consult_age_prevalent_UTI.jpeg
plot1.2: output/redacted/consult_age_prevalent_URTI.jpeg
plot1.3: output/redacted/consult_age_prevalent_LRTI.jpeg
plot1.4: output/redacted/consult_age_prevalent_sinusitis.jpeg
plot1.5: output/redacted/consult_age_prevalent_otmedia.jpeg
plot1.6: output/redacted/consult_age_prevalent_ot_externa.jpeg
plot1.7: output/redacted/consult_age_prevalent_all.jpeg
csv1: output/redacted/consultation_rate_prevalent_check.csv
csv2: output/redacted/consultation_rate_prevalent.csv
csv3: output/redacted/consultation_rate_prevalent_year.csv
describe_consultation_rate_all_GP_redacted:
run: r:latest analysis/redaction/consultation_by_age_infection_GP.R
needs: [generate_measures_infection]
outputs:
moderately_sensitive:
plot1: output/redacted/consult_all_prevalent.jpeg
plot2: output/redacted/consult_all_incident.jpeg
plot3: output/redacted/consult_all.jpeg
csv1: output/redacted/consultation_rate_GP_check.csv
csv1.2: output/redacted/consultation_all_GP_check.csv
csv2: output/redacted/consultation_GP_rate_prevalent.csv
csv3: output/redacted/consultation_GP_rate_incident.csv
csv4: output/redacted/consultation_GP_rate_all.csv
table: output/redacted/consultation_GP_rate_yr.csv
describe_consultation_model_process_1:
run: r:latest analysis/process/consultation_variables_1.R
needs: [generate_measures_indication,generate_measures_infection, describe_basic_record_process]
outputs:
moderately_sensitive:
rds1: output/measures/consult_UTI.rds
rds2: output/measures/consult_LRTI.rds
rds3: output/measures/consult_URTI.rds
rds4: output/measures/consult_sinusitis.rds
rds5: output/measures/consult_otmedia.rds
rds6: output/measures/consult_ot_externa.rds
rds7: output/measures/consult_indications.rds
describe_consultation_model_process_2:
run: r:latest analysis/process/consultation_variables_2.R
needs: [describe_consultation_model_process_1]
outputs:
moderately_sensitive:
rds1: output/measures/monthly_consult_UTI.rds
rds2: output/measures/monthly_consult_LRTI.rds
rds3: output/measures/monthly_consult_URTI.rds
rds4: output/measures/monthly_consult_sinusitis.rds
rds5: output/measures/monthly_consult_otmedia.rds
rds6: output/measures/monthly_consult_ot_externa.rds
# # # # describe_consultation_model_1:
# # # # run: r:latest analysis/model/consult_model_1.R
# # # # needs: [describe_consultation_model_process_2]
# # # # outputs:
# # # # moderately_sensitive:
# # # # jpeg: output/consult_model1.jpeg
# # # # rds: output/consult_model1.rds
# # # # describe_consultation_model_2:
# # # # run: r:latest analysis/model/consult_model_2.R
# # # # needs: [describe_consultation_model_process_2]
# # # # outputs:
# # # # moderately_sensitive:
# # # # jpeg: output/consult_model2.jpeg
# # # # rds: output/consult_model2.rds
# describe_consultation_model_3:
# run: r:latest analysis/model/consult_model_3.R
# needs: [describe_consultation_model_process_2]
# outputs:
# moderately_sensitive:
# jpeg: output/consult_model3.jpeg
# rds: output/consult_model3.rds
# # # # check_consultation_model: #Poisson vs. NBR
# # # # run: r:latest -e 'rmarkdown::render("analysis/process/report/check_consultation_model.Rmd", output_dir = "output/report")'
# # # # needs: [describe_consultation_model_process_2]
# # # # outputs:
# # # # moderately_sensitive:
# # # # html: output/report/check_consultation_model.html
# # # # consultation_model: # compare modeling1 &2
# # # # run: r:latest -e 'rmarkdown::render("analysis/model/consultation_model.rmd", output_dir = "output/report")'
# # # # needs: [describe_consultation_model_process_1]
# # # # outputs:
# # # # moderately_sensitive:
# # # # html: output/report/consultation_model.html
consultation_model_ITS2: # compare modeling1 &2
run: r:latest -e 'rmarkdown::render("analysis/model/consultation_model_ITS2.rmd", output_dir = "output/report")'
needs: [describe_consultation_model_process_1]
outputs:
moderately_sensitive:
html: output/report/consultation_model_ITS2.html
consultation_model_ITS2_incident:
run: r:latest -e 'rmarkdown::render("analysis/model/consultation_model_ITS2_incident.Rmd", output_dir = "output/report")'
needs: [describe_consultation_rate_all_incident_redacted]
outputs:
moderately_sensitive:
html: output/report/consultation_model_ITS2_incident.html
consultation_model_ITS2_prevalent:
run: r:latest -e 'rmarkdown::render("analysis/model/consultation_model_ITS2_prevalent.Rmd", output_dir = "output/report")'
needs: [describe_consultation_rate_all_prevalent_redacted]
outputs:
moderately_sensitive:
html: output/report/consultation_model_ITS2_prevalent.html
consultation_model_ITS2_combined: # overall, incident, prevalent
run: r:latest -e 'rmarkdown::render("analysis/model/consultation_model_ITS2_combined.rmd", output_dir = "output/report")'
needs: [describe_consultation_model_process_1,describe_consultation_rate_all_incident_redacted,describe_consultation_rate_all_prevalent_redacted]
outputs:
moderately_sensitive:
html: output/report/consultation_model_ITS2_combined.html
consultation_model_ITS2_combined_plot: # overall, incident, prevalent
run: r:latest -e 'rmarkdown::render("analysis/model/consultation_model_ITS2_combined_plot.rmd", output_dir = "output/report")'
needs: [describe_consultation_model_process_1,describe_consultation_rate_all_incident_redacted,describe_consultation_rate_all_prevalent_redacted]
outputs:
moderately_sensitive:
html: output/report/consultation_model_ITS2_combined_plot.html
csv: output/report/consultation_ITS_plot_indicetnt.csv
consultation_model_ITS2_combined_recovery: # overall, incident, prevalent
run: r:latest -e 'rmarkdown::render("analysis/model/consultation_model_ITS2_combined_recovery.rmd", output_dir = "output/report")'
needs: [describe_consultation_model_process_1,describe_consultation_rate_all_incident_redacted,describe_consultation_rate_all_prevalent_redacted]
outputs:
moderately_sensitive:
html: output/report/consultation_model_ITS2_combined_recovery.html
# # # # consultation_model_ITS2_harmonic_month: #sine,cosine harmonic month
# # # # run: r:latest -e 'rmarkdown::render("analysis/model/consultation_model_ITS2_harmonic_month.Rmd", output_dir = "output/report")'
# # # # needs: [describe_consultation_model_process_1]
# # # # outputs:
# # # # moderately_sensitive:
# # # # html: output/report/consultation_model_ITS2_harmonic_month.html
# # # # consultation_model_ITS2_harmonic_month_incident:
# # # # run: r:latest -e 'rmarkdown::render("analysis/model/consultation_model_ITS2_harmonic_month_incident.Rmd", output_dir = "output/report")'
# # # # needs: [describe_consultation_rate_all_incident_redacted]
# # # # outputs:
# # # # moderately_sensitive:
# # # # html: output/report/consultation_model_ITS2_harmonic_month_incident.html
# # # # consultation_model_ITS2_harmonic_month_prevalent:
# # # # run: r:latest -e 'rmarkdown::render("analysis/model/consultation_model_ITS2_harmonic_month_prevalent.Rmd", output_dir = "output/report")'
# # # # needs: [describe_consultation_rate_all_prevalent_redacted]
# # # # outputs:
# # # # moderately_sensitive:
# # # # html: output/report/consultation_model_ITS2_harmonic_month_prevalent.html
# consultation_model_zero_truncated: # zero-truncated negative binomial
# run: r:latest -e 'rmarkdown::render("analysis/model/consultation_model_zero_truncated.rmd", output_dir = "output/report")'
# needs: [describe_consultation_model_process_1]
# outputs:
# moderately_sensitive:
# html: output/report/consultation_model_zero_truncated.html
# consultation_model_3: # model 3 for adjusting autocorrelation
# run: r:latest -e 'rmarkdown::render("analysis/model/consultation_model_3.rmd", output_dir = "output/report")'
# needs: [describe_consultation_model_process_1]
# outputs:
# moderately_sensitive:
# html: output/report/consultation_model_3.html
# check_consultation_model_urti: #
# run: r:latest -e 'rmarkdown::render("analysis/process/report/check_consultation_model_urti.Rmd", output_dir = "output/report")'
# needs: [generate_measures_infection, describe_basic_record_process]
# outputs:
# moderately_sensitive:
# html: output/report/check_consultation_model_urti.html
# check_consultation_model_lrti: #
# run: r:latest -e 'rmarkdown::render("analysis/process/report/check_consultation_model_lrti.Rmd", output_dir = "output/report")'
# needs: [generate_measures_infection, describe_basic_record_process]
# outputs:
# moderately_sensitive:
# html: output/report/check_consultation_model_lrti.html
# check_consultation_model_sinusitis: #
# run: r:latest -e 'rmarkdown::render("analysis/process/report/check_consultation_model_sinusitis.Rmd", output_dir = "output/report")'
# needs: [generate_measures_infection, describe_basic_record_process]
# outputs:
# moderately_sensitive:
# html: output/report/check_consultation_model_sinusitis.html
# check_consultation_model_ot_externa: #
# run: r:latest -e 'rmarkdown::render("analysis/process/report/check_consultation_model_ot_externa.Rmd", output_dir = "output/report")'
# needs: [generate_measures_infection, describe_basic_record_process]
# outputs:
# moderately_sensitive:
# html: output/report/check_consultation_model_ot_externa.html
# check_consultation_model_otmedia: #
# run: r:latest -e 'rmarkdown::render("analysis/process/report/check_consultation_model_otmedia.Rmd", output_dir = "output/report")'
# needs: [generate_measures_infection, describe_basic_record_process]
# outputs:
# moderately_sensitive:
# html: output/report/check_consultation_model_otmedia.html
# # describe_infection_prescribed_percent:
# # run: r:latest analysis/plot/infection_prescibed_percent.R
# # needs: [generate_measures_infection]
# # outputs:
# # moderately_sensitive:
# # plot1: output/infection_ab_precent_p1.jpeg
# # plot2: output/infection_ab_precent_p2.jpeg
# # plot3: output/infection_ab_precent_i1.jpeg
# # plot4: output/infection_ab_precent_i2.jpeg
# # plot5: output/infection_ab_precent_all.jpeg
# # csv1: output/prescribed_infection_prevalent.csv
# # csv2: output/prescribed_infection_incident.csv
# # describe_top10ABtypes_byInfection:
# # run: r:latest analysis/plot/abtypes_top10.R
# # needs: [generate_measures_infection]
# # outputs:
# # moderately_sensitive:
# # plot1: output/abtype_UTI.jpeg
# # plot2: output/abtype_URTI.jpeg
# # plot3: output/abtype_LRTI.jpeg
# # plot4: output/abtype_sinusitis.jpeg
# # plot5: output/abtype_ot_externa.jpeg
# # plot6: output/abtype_otmedia.jpeg
# # plot7: output/abtype_percent_UTI.jpeg
# # plot8: output/abtype_percent_URTI.jpeg
# # plot9: output/abtype_percent_LRTI.jpeg
# # plot10: output/abtype_percent_sinusitis.jpeg
# # plot11: output/abtype_percent_ot_externa.jpeg
# # plot12: output/abtype_percent_otmedia.jpeg
# # csv: output/abtype_top10_by_infection.csv
# # describe_top10ABtypes_byInfection_line:
# # run: r:latest analysis/plot/abtypes_top10_line.R
# # needs: [generate_measures_infection]
# # outputs:
# # moderately_sensitive:
# # plot13: output/abtype_UTI_line.jpeg
# # plot14: output/abtype_URTI_line.jpeg
# # plot15: output/abtype_LRTI_line.jpeg
# # plot16: output/abtype_sinusitis_line.jpeg
# # plot17: output/abtype_ot_externa_line.jpeg
# # plot18: output/abtype_otmedia_line.jpeg
# # plot19: output/abtype_percent_UTI_line.jpeg
# # plot20: output/abtype_percent_URTI_line.jpeg
# # plot21: output/abtype_percent_LRTI_line.jpeg
# # plot22: output/abtype_percent_sinusitis_line.jpeg
# # plot23: output/abtype_percent_ot_externa_line.jpeg
# # plot24: output/abtype_percent_otmedia_line.jpeg
# # csv: output/abtype_top10_by_infection_line.csv
# describe_top10ABtypes_total:
# run: r:latest analysis/plot/types_ab_prescriptions.R
# needs: [generate_study_population]
# outputs:
# moderately_sensitive:
# plot1: output/abtype_all_Rx.jpeg
# plot2: output/abtype_all_Rx_percent.jpeg
describe_same_day_ab:
run: r:latest analysis/plot/same_day_covid_ab.R
needs: [generate_study_population_samedayab]
outputs:
moderately_sensitive:
table1: output/sameday_positive_1_sgss.csv
table2: output/sameday_positive_2_sgss.csv
table3: output/sameday_ab_1_sgss.csv
table4: output/sameday_ab_2_sgss.csv
table5: output/sameday_positive_1_gp.csv
table6: output/sameday_positive_2_gp.csv
table7: output/sameday_ab_1_gp.csv
table8: output/sameday_ab_2_gp.csv
table9: output/same_day_ab_prop_line_sgss_table.csv
table10: output/same_day_ab_prop_line_gp_table.csv
plot1: output/same_day_ab_prop_line_sgss.jpeg
plot2: output/same_day_ab_prop_line_gp.jpeg
describe_broad_by_region:
run: r:latest analysis/plot/broad_percentage_by_region.R
needs: [generate_study_population_withab,describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3,describe_ab_type_process_pre]
outputs:
moderately_sensitive:
plot1: output/broad_prescriptions_by_region.jpeg
plot2: output/broad_proportion_by_region.jpeg
describe_broad_by_age:
run: r:latest analysis/plot/broad_percentage_by_age.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3,describe_ab_type_process_pre]
outputs:
moderately_sensitive:
plot1: output/broad_prescriptions_by_age.jpeg
plot2: output/broad_proportion_by_age.jpeg
describe_broad_by_region_noA:
run: r:latest analysis/plot/broad_percentage_by_region_noA.R
needs: [generate_study_population_withab,describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3,describe_ab_type_process_pre]
outputs:
moderately_sensitive:
plot1: output/broad_prescriptions_by_region_noA.jpeg
plot2: output/broad_proportion_by_region_noA.jpeg
describe_broad_by_age_noA:
run: r:latest analysis/plot/broad_percentage_by_age_noA.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3,describe_ab_type_process_pre]
outputs:
moderately_sensitive:
plot1: output/broad_prescriptions_by_age_noA.jpeg
plot2: output/broad_proportion_by_age_noA.jpeg
describe_amoxicillin_by_age:
run: r:latest analysis/plot/amoxicillin_percentage_by_age.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3,describe_ab_type_process_pre]
outputs:
moderately_sensitive:
plot1: output/amoxicillin_prescriptions_by_age.jpeg
plot2: output/amoxicillin_proportion_by_age.jpeg
# describe_same_day_ab_gp:
# run: r:latest analysis/plot/same_day_covid_ab_gp.R
# needs: [generate_measures]
# outputs:
# moderately_sensitive:
# plot: output/same_day_ab_prop_line_gp.jpeg
generate_study_population_antibiotics: # Antibiotics_recorded_01
run: cohortextractor:latest generate_cohort --study-definition study_definition_antibiotics --index-date-range "2019-01-01 to today" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_antibiotics_*.csv.gz
### generate study cohort with the date of each prescriptions
generate_study_population_antibiotics_tpye:
run: cohortextractor:latest generate_cohort --study-definition study_definition_antibiotics_type --index-date-range "2019-01-01 to today" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_antibiotics_type_*.csv.gz
### generate study cohort three months before 2019-01-01 to get the incident infection information
generate_study_population_antibiotics_tpye_pre:
run: cohortextractor:latest generate_cohort --study-definition study_definition_antibiotics_type_pre --index-date-range "2018-01-01 to 2018-12-31" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_antibiotics_type_pre_*.csv.gz
### generate study cohort with the date of each infection
generate_study_population_infection_all:
run: cohortextractor:latest generate_cohort --study-definition study_definition_infection_all --index-date-range "2019-01-01 to today" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_infection_all_*.csv.gz
### generate study cohort three months before 2019-01-01 to get the incident infection information
generate_study_population_infection_all_pre:
run: cohortextractor:latest generate_cohort --study-definition study_definition_infection_all_pre --index-date-range "2018-10-01 to 2018-12-31" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_infection_all_pre_*.csv.gz
generate_study_population_antibiotics_covid: # Ab for covid
run: cohortextractor:latest generate_cohort --study-definition study_definition_antibiotics_covid --index-date-range "2019-01-01 to today" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_antibiotics_covid_*.csv.gz
describe_ab_recoded_covid_process:
run: r:latest analysis/process/ab_covid_transform.R
needs: [generate_study_population_antibiotics_covid]
outputs:
highly_sensitive:
rds1: output/measures/recorded_ab_covid_2019.rds
rds2: output/measures/recorded_ab_covid_2020.rds
rds3: output/measures/recorded_ab_covid_2021.rds
# rds4: output/measures/recorded_ab_covid_2022.rds
# used describe_ab_recoded_broad_process instead
# describe_ab_recoded_indication_process: # Antibiotics_recorded_02: generate prescription-level dataset
# run: r:latest analysis/process/ab_recorded_indication_transform.R
# needs: [generate_study_population_antibiotics_antibiotics]
# outputs:
# highly_sensitive:
# rds1: output/measures/recorded_ab_2019.rds
# rds2: output/measures/recorded_ab_2020.rds
# rds3: output/measures/recorded_ab_2021.rds
# rds4: output/measures/recorded_ab_2022.rds
describe_ab_recoded_indication_plot_incident:
run: r:latest analysis/plot/ab_recorded_indication_plot_incident.R
needs: [describe_ab_recoded_broad_process] # transfrom & define all variables
outputs:
moderately_sensitive:
plot1: output/ab_recorded_incident_bar.jpeg
plot2: output/ab_recorded_incident_line.jpeg
plot3: output/ab_recorded_incident_bar_2.jpeg
csv: output/ab_recorded_incident.csv
describe_ab_recoded_indication_plot_prevalent:
run: r:latest analysis/plot/ab_recorded_indication_plot_prevalent.R
needs: [describe_ab_recoded_broad_process]
outputs:
moderately_sensitive:
plot1: output/ab_recorded_prevalent_bar.jpeg
plot2: output/ab_recorded_prevalent_line.jpeg
plot3: output/ab_recorded_prevalent_bar_2.jpeg
csv: output/ab_recorded_prevalent.csv
ab_recoded_indication_ITS2_plot: # overall, incident, prevalent
run: r:latest -e 'rmarkdown::render("analysis/model/ab_recoded_indication_ITS2_plot.rmd", output_dir = "output/report")'
needs: [describe_ab_recoded_indication_plot_prevalent,describe_ab_recoded_indication_plot_incident]
outputs:
moderately_sensitive:
html: output/report/ab_recoded_indication_ITS2_plot.html
describe_ab_recoded_covid_plot_incident: # ab prescription on covid infection date
run: r:latest analysis/plot/ab_recorded_covid_plot_incident.R
needs: [describe_ab_recoded_covid_process]
outputs:
moderately_sensitive:
plot1: output/ab_recorded_covid_incident_bar.jpeg
plot2: output/ab_recorded_covid_incident_line.jpeg
csv: output/ab_recorded_covid_incident.csv
describe_ab_recoded_covid_plot_prevalent:
run: r:latest analysis/plot/ab_recorded_covid_plot_prevalent.R
needs: [describe_ab_recoded_covid_process]
outputs:
moderately_sensitive:
plot1: output/ab_recorded_covid_prevalent_bar.jpeg
plot2: output/ab_recorded_covid_prevalent_line.jpeg
csv: output/ab_recorded_covid_prevalent.csv
describe_ab_recoded_covid_all_plot_incident: # combind all indication and covid
run: r:latest analysis/plot/ab_recorded_indic_plus_covid_plot_incident.R
needs: [describe_ab_recoded_covid_plot_incident,describe_ab_recoded_indication_plot_incident]
outputs:
moderately_sensitive:
plot1: output/ab_recorded_covid_indication_incident_bar.jpeg
plot2: output/ab_recorded_covid_indication_incident_line.jpeg
csv: output/ab_recorded_covid_indication_incident.csv
describe_ab_recoded_covid_all_plot_prevalent:
run: r:latest analysis/plot/ab_recorded_indic_plus_covid_plot_prevalent.R
needs: [describe_ab_recoded_covid_plot_prevalent,describe_ab_recoded_indication_plot_prevalent]
outputs:
moderately_sensitive:
plot1: output/ab_recorded_covid_indication_prevalent_bar.jpeg
plot2: output/ab_recorded_covid_indication_prevalent_line.jpeg
csv: output/ab_recorded_covid_indication_prevalent.csv
describe_ab_recoded_broad_process:
run: r:latest analysis/process/broad_transform.R
needs: [generate_study_population_antibiotics]
outputs:
highly_sensitive:
rds1: output/measures/recorded_ab_broad_2019.rds
rds2: output/measures/recorded_ab_broad_2020.rds
rds3: output/measures/recorded_ab_broad_2021.rds
rds4: output/measures/recorded_ab_broad_2022.rds
###### ab record transform process ######
describe_ab_type_process_1:
run: r:latest analysis/process/ab_type_transform_1.R
needs: [generate_study_population_antibiotics_tpye]
outputs:
highly_sensitive:
rds1: output/measures/ab_type_2019.rds
rds2: output/measures/ab_type_2020.rds
describe_ab_type_process_2:
run: r:latest analysis/process/ab_type_transform_2.R
needs: [generate_study_population_antibiotics_tpye]
outputs:
highly_sensitive:
rds1: output/measures/ab_type_2021.rds
# rds2: output/measures/ab_type_2022.rds
describe_ab_type_process_3:
run: r:latest analysis/process/ab_type_transform_3.R
needs: [generate_study_population_antibiotics_tpye]
outputs:
highly_sensitive:
rds1: output/measures/ab_type_2022.rds
describe_ab_type_process_pre:
run: r:latest analysis/process/ab_type_transform_pre.R
needs: [generate_study_population_antibiotics_tpye_pre]
outputs:
highly_sensitive:
rds1: output/measures/ab_type_pre.rds
###### infection record transform process ######
describe_infection_all_process_1:
run: r:latest analysis/process/ab_infection_all_transform_1.R
needs: [generate_study_population_infection_all]
outputs:
highly_sensitive:
rds1: output/measures/infect_all_2019.rds
rds2: output/measures/infect_all_2020.rds
rds3: output/measures/infect_all_2021.rds
describe_infection_all_process_2:
run: r:latest analysis/process/ab_infection_all_transform_2.R
needs: [generate_study_population_infection_all]
outputs:
highly_sensitive:
rds1: output/measures/infect_all_2022.rds
describe_infection_all_process_pre:
run: r:latest analysis/process/ab_infection_all_transform_pre.R
needs: [generate_study_population_infection_all_pre]
outputs:
highly_sensitive:
rds1: output/measures/infect_all_pre.rds
#############################################################################
describe_cleaning_process:
run: r:latest analysis/process/cleaning_process.R
needs: [describe_infection_all_process_1,describe_infection_all_process_2,describe_infection_all_process_pre,
describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3,describe_ab_type_process_pre]
outputs:
highly_sensitive:
rds1: output/measures/cleaned_ab_infection.rds
describe_cleaning_process_2:
run: r:latest analysis/process/cleaning_process_2.R
needs: [describe_cleaning_process]
outputs:
highly_sensitive:
rds1: output/measures/cleaned_indication_ab.rds
describe_cleaning_process_3:
run: r:latest analysis/process/cleaning_id_extraction.R
needs: [describe_cleaning_process_2]
outputs:
highly_sensitive:
talbe1: output/ab_id_date.csv
describe_cleaning_process_2019:
run: r:latest analysis/process/cleaning_id_extraction_2019.R
needs: [describe_cleaning_process_2]
outputs:
highly_sensitive:
talbe1: output/ab_id_date_2019.csv
moderately_sensitive:
table1: output/num_pats_count.csv
describe_cleaning_process_2020:
run: r:latest analysis/process/cleaning_id_extraction_2020.R
needs: [describe_cleaning_process_2]
outputs:
highly_sensitive:
talbe1: output/ab_id_date_2020.csv
moderately_sensitive:
table1: output/num_pats_count_2020.csv
describe_cleaning_process_2021:
run: r:latest analysis/process/cleaning_id_extraction_2021.R
needs: [describe_cleaning_process_2]
outputs:
highly_sensitive:
talbe1: output/ab_id_date_2021.csv
moderately_sensitive:
table1: output/num_pats_count_2021.csv
describe_ab_table:
run: r:latest analysis/tables/repeat_ab_all_record.R
needs: [describe_cleaning_process]
outputs:
moderately_sensitive:
table1: output/same_day_ab_by_infection.csv
table2: output/incidental_repeat_ab_table.csv
#############################################################################
describe_ITS_var_process:
run: r:latest analysis/process/ITS_var.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3]
outputs:
moderately_sensitive:
table1: output/df.model_asthma.csv
table2: output/df.model_cold.csv
table3: output/df.model_cough.csv
table4: output/df.model_copd.csv
table5: output/df.model_pneumonia.csv
table6: output/df.model_renal.csv
table7: output/df.model_sepsis.csv
table8: output/df.model_throat.csv
table9: output/df.model_uti.csv
table10: output/df.model_lrti.csv
table11: output/df.model_urti.csv
table12: output/df.model_sinusitis.csv
table13: output/df.model_ot_media.csv
table14: output/df.model_ot_externa.csv
#############################################################################
describe_ITS_model:
run: r:latest analysis/model/ITS_broad_model.R
needs: [describe_ITS_var_process]
outputs:
moderately_sensitive:
table1: output/its_main_plot_data.csv
plot1: output/forest_plot_broad.jpeg
plot2: output/predicted_plot.jpeg
table2: output/its_main_ORs.csv
#############################################################################
describe_ITS_var_process_2:
run: r:latest analysis/process/ITS_var_2.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3]
outputs:
moderately_sensitive:
table1: output/df.2.model_asthma.csv
table2: output/df.2.model_cold.csv
table3: output/df.2.model_cough.csv
table4: output/df.2.model_copd.csv
table5: output/df.2.model_pneumonia.csv
table6: output/df.2.model_renal.csv
table7: output/df.2.model_sepsis.csv
table8: output/df.2.model_throat.csv
table9: output/df.2.model_uti.csv
table10: output/df.2.model_lrti.csv
table11: output/df.2.model_urti.csv
table12: output/df.2.model_sinusitis.csv
table13: output/df.2.model_ot_media.csv
table14: output/df.2.model_ot_externa.csv
#############################################################################
describe_ITS_model_2:
run: r:latest analysis/model/ITS_broad_model_2.R
needs: [describe_ITS_var_process_2]
outputs:
moderately_sensitive:
table1: output/its_main_plot_data_2.csv
plot1: output/forest_plot_broad_2.jpeg
plot2: output/predicted_plot_2.jpeg
table2: output/its_main_ORs_2.csv
#############################################################################
describe_ITS_var_without_A_process:
run: r:latest analysis/process/ITS_var_without_Amoxicillin.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3]
outputs:
moderately_sensitive:
table1: output/df2.model_asthma.csv
table2: output/df2.model_cold.csv
table3: output/df2.model_cough.csv
table4: output/df2.model_copd.csv
table5: output/df2.model_pneumonia.csv
table6: output/df2.model_renal.csv
table7: output/df2.model_sepsis.csv
table8: output/df2.model_throat.csv
table9: output/df2.model_uti.csv
table10: output/df2.model_lrti.csv
table11: output/df2.model_urti.csv
table12: output/df2.model_sinusitis.csv
table13: output/df2.model_ot_media.csv
table14: output/df2.model_ot_externa.csv
#############################################################################
describe_ITS_model_without_Amoxicillin:
run: r:latest analysis/model/ITS_broad_model_without_Amoxicillin.R
needs: [describe_ITS_var_without_A_process]
outputs:
moderately_sensitive:
table1: output/its_main_plot_data_noA.csv
plot1: output/forest_plot_broad_noA.jpeg
plot2: output/predicted_plot_noA.jpeg
table2: output/its_main_ORs_noA.csv
#############################################################################
describe_ITS_var_monthly_process:
run: r:latest analysis/process/ITS_var_monthly.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3]
outputs: