Job request: 10258
- Organisation:
- University of Manchester
- Workspace:
- service_eval_work
- ID:
- mi6ztrb5iqzvy4cp
This page shows the technical details of what happened when authorised researcher Billy Zhong requested one or more actions to be run against real patient data in the project, within a secure environment.
By cross-referencing the indicated Requested Actions with the
Pipeline section below, you can infer what
security level
various outputs were written to. Outputs marked as
highly_sensitive
can never be viewed directly by a researcher; they can only
request that code runs against them. Outputs marked as
moderately_sensitive
can be viewed by an approved researcher by logging into a highly
secure environment. Only outputs marked as
moderately_sensitive
can be requested for release to the public, via a controlled
output review service.
Jobs
-
- Job identifier:
-
b6nkvgqlywnkv7as
Pipeline
Show project.yaml
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:
moderately_sensitive:
table1: output/df.m.model_asthma.csv
table2: output/df.m.model_cold.csv
table3: output/df.m.model_cough.csv
table4: output/df.m.model_copd.csv
table5: output/df.m.model_pneumonia.csv
table6: output/df.m.model_renal.csv
table7: output/df.m.model_sepsis.csv
table8: output/df.m.model_throat.csv
table9: output/df.m.model_uti.csv
table10: output/df.m.model_lrti.csv
table11: output/df.m.model_urti.csv
table12: output/df.m.model_sinusitis.csv
table13: output/df.m.model_ot_media.csv
table14: output/df.m.model_ot_externa.csv
table15: output/df.m.model_uncoded.csv
#############################################################################
describe_ITS_var_monthly_2_process:
run: r:latest analysis/process/ITS_var_monthly_2.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3]
outputs:
moderately_sensitive:
table1: output/df.m2.model_asthma.csv
table2: output/df.m2.model_cold.csv
table3: output/df.m2.model_cough.csv
table4: output/df.m2.model_copd.csv
table5: output/df.m2.model_pneumonia.csv
table6: output/df.m2.model_renal.csv
table7: output/df.m2.model_sepsis.csv
table8: output/df.m2.model_throat.csv
table9: output/df.m2.model_uti.csv
table10: output/df.m2.model_lrti.csv
table11: output/df.m2.model_urti.csv
table12: output/df.m2.model_sinusitis.csv
table13: output/df.m2.model_ot_media.csv
table14: output/df.m2.model_ot_externa.csv
table15: output/df.m2.model_uncoded.csv
#############################################################################
describe_ITS_model_monthly_2:
run: r:latest analysis/model/ITS_broad_model_monthly_2.R
needs: [describe_ITS_var_monthly_2_process]
outputs:
moderately_sensitive:
table1: output/its_main_plot_data_monthly_2.csv
plot1: output/forest_plot_broad_monthly_2.jpeg
plot2: output/predicted_plot_monthly_2.jpeg
table2: output/its_main_ORs_monthly_2.csv
#############################################################################
describe_ITS_model_monthly:
run: r:latest analysis/model/ITS_broad_model_monthly.R
needs: [describe_ITS_var_monthly_process]
outputs:
moderately_sensitive:
table1: output/its_main_plot_data_monthly.csv
plot1: output/forest_plot_broad_monthly.jpeg
plot2: output/predicted_plot_monthly.jpeg
table2: output/its_main_ORs_monthly.csv
#############################################################################
describe_ITS_var_uncoded_process:
run: r:latest analysis/process/ITS_var_uncoded.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3]
outputs:
moderately_sensitive:
table1: output/df.model_added_asthma.csv
table2: output/df.model_added_cold.csv
table3: output/df.model_added_cough.csv
table4: output/df.model_added_copd.csv
table5: output/df.model_added_pneumonia.csv
table6: output/df.model_added_renal.csv
table7: output/df.model_added_sepsis.csv
table8: output/df.model_added_throat.csv
table9: output/df.model_added_uti.csv
table10: output/df.model_added_lrti.csv
table11: output/df.model_added_urti.csv
table12: output/df.model_added_sinusitis.csv
table13: output/df.model_added_ot_media.csv
table14: output/df.model_added_ot_externa.csv
table15: output/df.model_added_uncoded.csv
#############################################################################
describe_ITS_model_uncoded:
run: r:latest analysis/model/ITS_broad_model_uncoded.R
needs: [describe_ITS_var_uncoded_process]
outputs:
moderately_sensitive:
table1: output/its_main_plot_data_uncoded.csv
plot1: output/forest_plot_broad_uncoded.jpeg
plot2: output/predicted_plot_uncoded.jpeg
table2: output/its_main_ORs_uncoded.csv
#############################################################################
describe_ITS_var_uncoded_without_A_process:
run: r:latest analysis/process/ITS_var_uncoded_without_A.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3]
outputs:
moderately_sensitive:
table1: output/df2.model_added_asthma.csv
table2: output/df2.model_added_cold.csv
table3: output/df2.model_added_cough.csv
table4: output/df2.model_added_copd.csv
table5: output/df2.model_added_pneumonia.csv
table6: output/df2.model_added_renal.csv
table7: output/df2.model_added_sepsis.csv
table8: output/df2.model_added_throat.csv
table9: output/df2.model_added_uti.csv
table10: output/df2.model_added_lrti.csv
table11: output/df2.model_added_urti.csv
table12: output/df2.model_added_sinusitis.csv
table13: output/df2.model_added_ot_media.csv
table14: output/df2.model_added_ot_externa.csv
table15: output/df2.model_added_uncoded.csv
#############################################################################
describe_ITS_model_uncoded_without_A:
run: r:latest analysis/model/ITS_broad_model_uncoded_without_A.R
needs: [describe_ITS_var_uncoded_without_A_process]
outputs:
moderately_sensitive:
table1: output/its_main_plot_data_uncoded_without_A.csv
plot1: output/forest_plot_broad_uncoded_without_A.jpeg
plot2: output/predicted_plot_uncoded_without_A.jpeg
table2: output/its_main_ORs_uncoded_without_A.csv
#############################################################################
describe_repeat_ab_table:
run: r:latest analysis/tables/repeat_ab_table.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:
table1: output/blt_repeat_ab.csv
table2: output/throat_ab.csv
table3: output/throat_ab_type.csv
describe_repeat_ab_table_2:
run: r:latest analysis/tables/repeat_ab_table_2.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:
table1: output/asthma_ab.csv
table2: output/asthma_ab_type.csv
table3: output/cold_ab.csv
table4: output/cold_ab_type.csv
table5: output/cough_ab.csv
table6: output/cough_ab_type.csv
table7: output/copd_ab.csv
table8: output/copd_ab_type.csv
table9: output/pneumonia_ab.csv
table10: output/pneumonia_ab_type.csv
table11: output/renal_ab.csv
table12: output/renal_ab_type.csv
table13: output/sepsis_ab.csv
table14: output/sepsis_ab_type.csv
table15: output/uti_ab.csv
table16: output/uti_ab_type.csv
table17: output/lrti_ab.csv
table18: output/lrti_ab_type.csv
table19: output/urti_ab.csv
table20: output/urti_ab_type.csv
table21: output/sinusitis_ab.csv
table22: output/sinusitis_ab_type.csv
table23: output/otmedia_ab.csv
table24: output/otmedia_ab_type.csv
table25: output/ot_externa_ab.csv
table26: output/ot_externa_ab_type.csv
describe_ab_throat:
run: r:latest analysis/plot/throat_ab.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3]
outputs:
moderately_sensitive:
table: output/ab_throat.csv
describe_broad_proportion:
run: r:latest analysis/plot/broad_proportion.R
needs: [describe_ab_recoded_broad_process]
outputs:
moderately_sensitive:
plot: output/broad_proportions_line.jpeg
table: output/broad_proportions.csv
describe_basic_record_process:
run: r:latest analysis/process/baseline_variables_transform.R
needs: [generate_study_population]
outputs:
highly_sensitive:
rds1: output/measures/basic_record_2019.rds
rds2: output/measures/basic_record_2020.rds
rds3: output/measures/basic_record_2021.rds
rds4: output/measures/basic_record_2022.rds
describe_check_broad_model_variable_2019:
run: r:latest analysis/model/broad_variable_transform_2019.R
needs: [describe_basic_record_process]
outputs:
highly_sensitive:
rds1: output/measures/model_variable_broad_2019_1.rds
describe_check_broad_model_variable_2019_2:
run: r:latest analysis/model/charlson_transform_2019.R
needs: [describe_basic_record_process]
outputs:
highly_sensitive:
talbe1: output/model_varibale_table_charlson_2019.csv
rds1: output/measures/model_variable_broad_2019_2.rds
describe_check_broad_model_variable_2020:
run: r:latest analysis/model/broad_variable_transform_2020.R
needs: [describe_basic_record_process]
outputs:
highly_sensitive:
rds1: output/measures/model_variable_broad_2020_1.rds
describe_check_broad_model_variable_2020_2:
run: r:latest analysis/model/charlson_transform_2020.R
needs: [describe_basic_record_process]
outputs:
highly_sensitive:
talbe1: output/model_varibale_table_charlson_2020.csv
rds1: output/measures/model_variable_broad_2020_2.rds
describe_check_broad_model_variable_2021:
run: r:latest analysis/model/broad_variable_transform_2021.R
needs: [describe_basic_record_process]
outputs:
highly_sensitive:
rds1: output/measures/model_variable_broad_2021_1.rds
describe_check_broad_model_variable_2021_2:
run: r:latest analysis/model/charlson_transform_2021.R
needs: [describe_basic_record_process]
outputs:
highly_sensitive:
talbe1: output/model_varibale_table_charlson_2021.csv
rds1: output/measures/model_variable_broad_2021_2.rds
describe_check_broad_model_variable_2022:
run: r:latest analysis/model/broad_variable_transform_2022.R
needs: [describe_basic_record_process]
outputs:
highly_sensitive:
rds1: output/measures/model_variable_broad_2022_1.rds
describe_check_broad_model_variable_2022_2:
run: r:latest analysis/model/charlson_transform_2022.R
needs: [describe_basic_record_process]
outputs:
highly_sensitive:
talbe1: output/model_varibale_table_charlson_2022.csv
rds1: output/measures/model_variable_broad_2022_2.rds
describe_broad_model_2019:
run: r:latest -e 'rmarkdown::render("analysis/model/broad_model_2019.Rmd", output_dir = "output/report")'
needs: [describe_check_broad_model_variable_2019, describe_check_broad_model_variable_2019_2, describe_ab_recoded_broad_process]
outputs:
moderately_sensitive:
html: output/report/broad_model_2019.html
describe_broad_model_covid:
run: r:latest -e 'rmarkdown::render("analysis/model/broad_model_covid.Rmd", output_dir = "output/report")'
needs: [describe_check_broad_model_variable_2020, describe_check_broad_model_variable_2020_2,
describe_check_broad_model_variable_2021, describe_check_broad_model_variable_2021_2,
describe_check_broad_model_variable_2022, describe_check_broad_model_variable_2022_2,
describe_ab_recoded_broad_process]
outputs:
moderately_sensitive:
html: output/report/broad_model_covid.html
# describe_descriptive_ab_broad:
# run: r:latest -e 'rmarkdown::render("analysis/model/descriptive_ab_broad.Rmd", output_dir = "output/report")'
# needs: [generate_measures]
# outputs:
# moderately_sensitive:
# html: output/report/descriptive_ab_broad.html
# describe_baseline_tb:
# run: r:latest -e 'rmarkdown::render("analysis/model/baseline_table_pat_one.Rmd", output_dir = "output/report")'
# needs: [describe_check_broad_model_variable_2019, describe_check_broad_model_variable_2019_2,
# describe_check_broad_model_variable_2020, describe_check_broad_model_variable_2020_2,
# describe_check_broad_model_variable_2021, describe_check_broad_model_variable_2021_2,
# describe_check_broad_model_variable_2022, describe_check_broad_model_variable_2022_2]
# outputs:
# moderately_sensitive:
# html: output/report/baseline_table_pat_one.html
# describe_baseline_tb_2019:
# run: r:latest -e 'rmarkdown::render("analysis/model/baseline_table_pat_one_2019.Rmd", output_dir = "output/report")'
# needs: [describe_check_broad_model_variable_2019, describe_check_broad_model_variable_2019_2]
# outputs:
# moderately_sensitive:
# html: output/report/baseline_table_pat_one_2019.html
# describe_baseline_tb_2020:
# run: r:latest -e 'rmarkdown::render("analysis/model/baseline_table_pat_one_2020.Rmd", output_dir = "output/report")'
# needs: [describe_check_broad_model_variable_2020, describe_check_broad_model_variable_2020_2]
# outputs:
# moderately_sensitive:
# html: output/report/baseline_table_pat_one_2020.html
# describe_baseline_tb_2021:
# run: r:latest -e 'rmarkdown::render("analysis/model/baseline_table_pat_one_2021.Rmd", output_dir = "output/report")'
# needs: [describe_check_broad_model_variable_2021, describe_check_broad_model_variable_2021_2]
# outputs:
# moderately_sensitive:
# html: output/report/baseline_table_pat_one_2021.html
# describe_baseline_tb_2022:
# run: r:latest -e 'rmarkdown::render("analysis/model/baseline_table_pat_one_2022.Rmd", output_dir = "output/report")'
# needs: [describe_check_broad_model_variable_2022, describe_check_broad_model_variable_2022_2]
# outputs:
# moderately_sensitive:
# html: output/report/baseline_table_pat_one_2022.html
# describe_ab_recoded_indication_process_plot: # Antibiotics_recorded_02: only indication/row
# run: r:latest analysis/process/ab_recorded_indication_transform_plot.R
# needs: [generate_study_population_antibiotics]
# outputs:
# highly_sensitive:
# rds1: output/measures/recorded_ab_indication_2019.rds
# rds2: output/measures/recorded_ab_indication_2020.rds
# rds3: output/measures/recorded_ab_indication_2021.rds
# rds4: output/measures/recorded_ab_indication_2022.rds
# describe_ab_recoded_indication_plot:
# run: r:latest analysis/plot/ab_recorded_indication_plot.R
# needs: [describe_ab_recoded_indication_process_plot]
# outputs:
# highly_sensitive:
# plot1: output/ab_recorded_indication_bar.jpeg
# plot2: output/ab_recorded_indication_line.jpeg
# csv: output/ab_recorded_indication.csv
generate_study_population_infection_abtype: # for ab types plot
run: cohortextractor:latest generate_cohort --study-definition study_definition_infection_abtype --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_abtype_*.csv.gz
describe_infection_abtype_process: # infection/row
run: r:latest analysis/process/infection_abtype_transform.R
needs: [generate_study_population_infection_abtype]
outputs:
highly_sensitive:
rds1: output/measures/abtype_uti.rds
rds2: output/measures/abtype_lrti.rds
rds3: output/measures/abtype_urti.rds
rds4: output/measures/abtype_sinusitis.rds
rds5: output/measures/abtype_ot_externa.rds
rds6: output/measures/abtype_otmedia.rds
describe_infection_abtype_plot: # incident+prevalent
run: r:latest analysis/plot/infection_abtype.R
needs: [describe_infection_abtype_process]
outputs:
moderately_sensitive:
plot1: output/abtype_uti.jpeg
plot2: output/abtype_lrti.jpeg
plot3: output/abtype_urti.jpeg
plot4: output/abtype_sinusitis.jpeg
plot5: output/abtype_ot_externa.jpeg
plot6: output/abtype_otmedia.jpeg
csv1: output/abtype_uti.csv
csv2: output/abtype_lrti.csv
csv3: output/abtype_urti.csv
csv4: output/abtype_sinusitis.csv
csv5: output/abtype_ot_externa.csv
csv6: output/abtype_otmedia.csv
describe_infection_abtype_plot_redacted: # incident+prevalent
run: r:latest analysis/redaction/infection_abtype.R
needs: [describe_infection_abtype_process]
outputs:
moderately_sensitive:
plot1: output/redacted/abtype_uti.jpeg
plot2: output/redacted/abtype_lrti.jpeg
plot3: output/redacted/abtype_urti.jpeg
plot4: output/redacted/abtype_sinusitis.jpeg
plot5: output/redacted/abtype_ot_externa.jpeg
plot6: output/redacted/abtype_otmedia.jpeg
csv1: output/redacted/abtype_uti_check.csv
csv2: output/redacted/abtype_lrti_check.csv
csv3: output/redacted/abtype_urti_check.csv
csv4: output/redacted/abtype_sinusitis_check.csv
csv5: output/redacted/abtype_ot_externa_check.csv
csv6: output/redacted/abtype_otmedia_check.csv
csv7: output/redacted/abtype_uti.csv
csv8: output/redacted/abtype_lrti.csv
csv9: output/redacted/abtype_urti.csv
csv10: output/redacted/abtype_sinusitis.csv
csv11: output/redacted/abtype_ot_externa.csv
csv12: output/redacted/abtype_otmedia.csv
describe_infection_abtype_plot_count: # output raw counts
run: r:latest analysis/redaction/infection_abtype_counts.R
needs: [describe_infection_abtype_process]
outputs:
moderately_sensitive:
plot1: output/redacted/count_abtype_uti.jpeg
plot2: output/redacted/count_abtype_lrti.jpeg
plot3: output/redacted/count_abtype_urti.jpeg
plot4: output/redacted/count_abtype_sinusitis.jpeg
plot5: output/redacted/count_abtype_ot_externa.jpeg
plot6: output/redacted/count_abtype_otmedia.jpeg
csv1: output/redacted/count_abtype_uti_check.csv
csv2: output/redacted/count_abtype_lrti_check.csv
csv3: output/redacted/count_abtype_urti_check.csv
csv4: output/redacted/count_abtype_sinusitis_check.csv
csv5: output/redacted/count_abtype_ot_externa_check.csv
csv6: output/redacted/count_abtype_otmedia_check.csv
csv7: output/redacted/count_abtype_uti.csv
csv8: output/redacted/count_abtype_lrti.csv
csv9: output/redacted/count_abtype_urti.csv
csv10: output/redacted/count_abtype_sinusitis.csv
csv11: output/redacted/count_abtype_ot_externa.csv
csv12: output/redacted/count_abtype_otmedia.csv
describe_infection_noAB_plot: # percentage
run: r:latest analysis/redaction/infection_v2_noAB.R
needs: [describe_infection_abtype_process]
outputs:
moderately_sensitive:
plot1: output/redacted_v2/noAB_uti.jpeg
plot2: output/redacted_v2/noAB_lrti.jpeg
plot3: output/redacted_v2/noAB_urti.jpeg
plot4: output/redacted_v2/noAB_sinusitis.jpeg
plot5: output/redacted_v2/noAB_ot_externa.jpeg
plot6: output/redacted_v2/noAB_otmedia.jpeg
csv1: output/redacted_v2/noAB_uti_check.csv
csv2: output/redacted_v2/noAB_lrti_check.csv
csv3: output/redacted_v2/noAB_urti_check.csv
csv4: output/redacted_v2/noAB_sinusitis_check.csv
csv5: output/redacted_v2/noAB_ot_externa_check.csv
csv6: output/redacted_v2/noAB_otmedia_check.csv
csv7: output/redacted_v2/noAB.csv
describe_infection_AB_plot: # percentage
run: r:latest analysis/redaction/infection_v2_AB.R
needs: [describe_infection_abtype_process]
outputs:
moderately_sensitive:
plot1: output/redacted_v2/AB_uti.jpeg
plot2: output/redacted_v2/AB_lrti.jpeg
plot3: output/redacted_v2/AB_urti.jpeg
plot4: output/redacted_v2/AB_sinusitis.jpeg
plot5: output/redacted_v2/AB_ot_externa.jpeg
plot6: output/redacted_v2/AB_otmedia.jpeg
csv1: output/redacted_v2/AB_uti_check.csv
csv2: output/redacted_v2/AB_lrti_check.csv
csv3: output/redacted_v2/AB_urti_check.csv
csv4: output/redacted_v2/AB_sinusitis_check.csv
csv5: output/redacted_v2/AB_ot_externa_check.csv
csv6: output/redacted_v2/AB_otmedia_check.csv
csv7: output/redacted_v2/AB.csv
infection_ab_ITS2_plot:
run: r:latest -e 'rmarkdown::render("analysis/model/infection_ab_ITS2_plot.rmd", output_dir = "output/report")'
needs: [describe_infection_noAB_plot]
outputs:
moderately_sensitive:
html: output/report/infection_ab_ITS2_plot.html
describe_infection_AB_plot_top3: # percentage
run: r:latest analysis/redaction/infection_v2_AB_top3.R
needs: [describe_infection_abtype_process]
outputs:
moderately_sensitive:
plot1: output/redacted_v2/AB_uti_top3.jpeg
plot2: output/redacted_v2/AB_lrti_top3.jpeg
plot3: output/redacted_v2/AB_urti_top3.jpeg
plot4: output/redacted_v2/AB_sinusitis_top3.jpeg
plot5: output/redacted_v2/AB_ot_externa_top3.jpeg
plot6: output/redacted_v2/AB_otmedia_top3.jpeg
csv1: output/redacted_v2/AB_uti_check_top3.csv
csv2: output/redacted_v2/AB_lrti_check_top3.csv
csv3: output/redacted_v2/AB_urti_check_top3.csv
csv4: output/redacted_v2/AB_sinusitis_check_top3.csv
csv5: output/redacted_v2/AB_ot_externa_check_top3.csv
csv6: output/redacted_v2/AB_otmedia_check_top3.csv
csv7: output/redacted_v2/AB_top3.csv
describe_infection_AB_plot_top5: # percentage
run: r:latest analysis/redaction/infection_v2_AB_top5.R
needs: [describe_infection_abtype_process]
outputs:
moderately_sensitive:
plot1: output/redacted_v2/AB_uti_top5.jpeg
plot2: output/redacted_v2/AB_lrti_top5.jpeg
plot3: output/redacted_v2/AB_urti_top5.jpeg
plot4: output/redacted_v2/AB_sinusitis_top5.jpeg
plot5: output/redacted_v2/AB_ot_externa_top5.jpeg
plot6: output/redacted_v2/AB_otmedia_top5.jpeg
csv1: output/redacted_v2/AB_uti_check_top5.csv
csv2: output/redacted_v2/AB_lrti_check_top5.csv
csv3: output/redacted_v2/AB_urti_check_top5.csv
csv4: output/redacted_v2/AB_sinusitis_check_top5.csv
csv5: output/redacted_v2/AB_ot_externa_check_top5.csv
csv6: output/redacted_v2/AB_otmedia_check_top5.csv
csv7: output/redacted_v2/AB_top5.csv
describe_broad_proportion_measure:
run: r:latest -e 'rmarkdown::render("analysis/model/descriptive_ab_broad_2.Rmd", output_dir = "output/report")'
needs: [generate_measures]
outputs:
moderately_sensitive:
html: output/report/descriptive_ab_broad_2.html
describe_broad_type_analysis:
run: r:latest -e 'rmarkdown::render("analysis/model/broad_type.Rmd", output_dir = "output/report")'
needs: [generate_measures]
outputs:
moderately_sensitive:
html: output/report/broad_type.html
describe_broad_percentage_op:
run: r:latest analysis/plot/broad_percentage_op.R
needs: [generate_measures_broad]
outputs:
moderately_sensitive:
plot1: output/broad_percentage_op.jpeg
# describe_broad_proportion_measure:
# run: r:latest analysis/plot/broad_proportion_measure.R
# needs: [generate_measures]
# outputs:
# moderately_sensitive:
# plot1: output/broad_proportions_overall.jpeg
# plot2: output/broad_proportions_practice.jpeg
describe_ab_check_2020:
run: r:latest -e 'rmarkdown::render("analysis/process/ab_check_2020.rmd", output_dir = "output/report")'
needs: [generate_study_population_antibiotics]
outputs:
moderately_sensitive:
html: output/report/ab_check_2020.html
#############################################################################
describe_ITS_var_monthly_without_A_process:
run: r:latest analysis/process/ITS_var_monthly_without_A.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3]
outputs:
moderately_sensitive:
table1: output/df.m.noA.model_asthma.csv
table2: output/df.m.noA.model_cold.csv
table3: output/df.m.noA.model_cough.csv
table4: output/df.m.noA.model_copd.csv
table5: output/df.m.noA.model_pneumonia.csv
table6: output/df.m.noA.model_renal.csv
table7: output/df.m.noA.model_sepsis.csv
table8: output/df.m.noA.model_throat.csv
table9: output/df.m.noA.model_uti.csv
table10: output/df.m.noA.model_lrti.csv
table11: output/df.m.noA.model_urti.csv
table12: output/df.m.noA.model_sinusitis.csv
table13: output/df.m.noA.model_ot_media.csv
table14: output/df.m.noA.model_ot_externa.csv
table15: output/df.m.noA.model_uncoded.csv
#############################################################################
describe_ITS_var_monthly_2_without_A_process:
run: r:latest analysis/process/ITS_var_monthly_2_without_A.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3]
outputs:
moderately_sensitive:
table1: output/df.m2.noA.model_asthma.csv
table2: output/df.m2.noA.model_cold.csv
table3: output/df.m2.noA.model_cough.csv
table4: output/df.m2.noA.model_copd.csv
table5: output/df.m2.noA.model_pneumonia.csv
table6: output/df.m2.noA.model_renal.csv
table7: output/df.m2.noA.model_sepsis.csv
table8: output/df.m2.noA.model_throat.csv
table9: output/df.m2.noA.model_uti.csv
table10: output/df.m2.noA.model_lrti.csv
table11: output/df.m2.noA.model_urti.csv
table12: output/df.m2.noA.model_sinusitis.csv
table13: output/df.m2.noA.model_ot_media.csv
table14: output/df.m2.noA.model_ot_externa.csv
table15: output/df.m2.noA.model_uncoded.csv
#############################################################################
describe_ITS_model_monthly_2_without_A:
run: r:latest analysis/model/ITS_broad_model_monthly_2_without_A.R
needs: [describe_ITS_var_monthly_2_without_A_process]
outputs:
moderately_sensitive:
table1: output/its_main_plot_data_monthly_2_without_A.csv
plot1: output/forest_plot_broad_monthly_2_without_A.jpeg
plot2: output/predicted_plot_monthly_2_without_A.jpeg
table2: output/its_main_ORs_monthly_2_without_A.csv
#############################################################################
describe_ITS_model_monthly_without_A:
run: r:latest analysis/model/ITS_broad_model_monthly_without_A.R
needs: [describe_ITS_var_monthly_without_A_process]
outputs:
moderately_sensitive:
table1: output/its_main_plot_data_monthly_without_A.csv
plot1: output/forest_plot_broad_monthly_without_A.jpeg
plot2: output/predicted_plot_monthly_without_A.jpeg
table2: output/its_main_ORs_monthly_without_A.csv
#############################################################################
describe_ITS_var_overall_process:
run: r:latest analysis/process/ITS_var_overall.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3]
outputs:
moderately_sensitive:
table1: output/df_model_overall.csv
table2: output/df_model_overall_18.csv
#############################################################################
describe_ITS_model_overall:
run: r:latest analysis/itsmodel/ITS_broad_model_overall.R
needs: [describe_ITS_var_overall_process]
outputs:
moderately_sensitive:
table1: output/its_main_plot_data_overall.csv
plot1: output/forest_plot_broad_overall_A.jpeg
plot2: output/forest_plot_broad_overall_B.jpeg
plot3: output/predicted_plot_overall.jpeg
table2: output/its_main_ORs_overall.csv
table3: output/its_main_INTORs_overall.csv
#############################################################################
describe_ITS_var_overall_without_A_process:
run: r:latest analysis/process/ITS_var_overall_without_A.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3]
outputs:
moderately_sensitive:
table1: output/df_noA_model_overall.csv
table2: output/df_noA_model_overall_18.csv
#############################################################################
describe_ITS_model_overall_without_A:
run: r:latest analysis/itsmodel/ITS_broad_model_overall_without_A.R
needs: [describe_ITS_var_overall_without_A_process]
outputs:
moderately_sensitive:
table1: output/noA_its_main_plot_data_overall.csv
plot1: output/noA_forest_plot_broad_overall_A.jpeg
plot2: output/noA_forest_plot_broad_overall_B.jpeg
plot3: output/noA_predicted_plot_overall.jpeg
table2: output/noA_its_main_ORs_overall.csv
table3: output/noA_its_main_INTORs_overall.csv
plot4: output/noA_all_plot.jpeg
#############################################################################
############################# monthly ######################################
#############################################################################
describe_ITS_var_overall_monthly_process:
run: r:latest analysis/process/ITS_var_overall_monthly.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3]
outputs:
moderately_sensitive:
table1: output/df_mon_model_overall.csv
table2: output/df_mon_model_overall_18.csv
#############################################################################
describe_ITS_model_overall_monthly:
run: r:latest analysis/itsmodel/ITS_broad_model_overall_monthly.R
needs: [describe_ITS_var_overall_monthly_process]
outputs:
moderately_sensitive:
table1: output/its_main_plot_data_overall_monthly.csv
plot1: output/forest_plot_broad_overall_monthly_A.jpeg
plot2: output/forest_plot_broad_overall_monthly_B.jpeg
plot3: output/predicted_plot_overall_monthly.jpeg
table2: output/its_main_ORs_overall_monthly.csv
table3: output/its_main_INTORs_overall_monthly.csv
plot4: output/all_plot_monthly.jpeg
#############################################################################
describe_ITS_var_overall_monthly_without_A_process:
run: r:latest analysis/process/ITS_var_overall_monthly_without_A.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3]
outputs:
moderately_sensitive:
table1: output/df_noA_mon_model_overall.csv
table2: output/df_noA_mon_model_overall_18.csv
#############################################################################
describe_ITS_model_overall_monthly_without_A:
run: r:latest analysis/itsmodel/ITS_broad_model_overall_monthly_without_A.R
needs: [describe_ITS_var_overall_monthly_without_A_process]
outputs:
moderately_sensitive:
table1: output/noA_its_main_plot_data_overall_monthly.csv
plot1: output/noA_forest_plot_broad_overall_monthly_A.jpeg
plot2: output/noA_forest_plot_broad_overall_monthly_B.jpeg
plot3: output/noA_predicted_plot_overall_monthly.jpeg
table2: output/noA_its_main_ORs_overall_monthly.csv
table3: output/noA_its_main_INTORs_overall_monthly.csv
plot4: output/noA_all_plot_monthly.jpeg
#############################################################################
describe_ITS_var_stratified_process:
run: r:latest analysis/process/ITS_stratified_var.R
needs: [describe_cleaning_process_2]
outputs:
moderately_sensitive:
table1: output/mon_stratified_broad.csv
table2: output/mon_stratified_repeat.csv
#############################################################################
describe_plot_by_coded:
run: r:latest analysis/itsmodel/plot_by_coded.R
needs: [describe_ITS_var_stratified_process]
outputs:
moderately_sensitive:
plot1: output/broad_all_group.jpeg
plot2: output/broad_incidental_group.jpeg
plot3: output/repeat_all_group.jpeg
plot4: output/repeat_incidental_group.jpeg
table1: output/broad_all_group_table.csv
table2: output/broad_incidental_group_table.csv
table3: output/repeat_all_group_table.csv
talbe4: output/repeat_incidental_group_table.csv
#############################################################################
describe_ITS_var_stratified_process_2:
run: r:latest analysis/process/ITS_stratified_var_2.R
needs: [describe_cleaning_process_2]
outputs:
moderately_sensitive:
table2: output/dt_incidental_cold.csv
table3: output/dt_incidental_cough.csv
table4: output/dt_incidental_copd.csv
table8: output/dt_incidental_throat.csv
table9: output/dt_incidental_uti.csv
table10: output/dt_incidental_lrti.csv
table11: output/dt_incidental_urti.csv
table12: output/dt_incidental_sinusitis.csv
table13: output/dt_incidental_ot_media.csv
table14: output/dt_incidental_ot_externa.csv
table16: output/dt_prevalent_cold.csv
table17: output/dt_prevalent_cough.csv
table18: output/dt_prevalent_copd.csv
table22: output/dt_prevalent_throat.csv
table23: output/dt_prevalent_uti.csv
table24: output/dt_prevalent_lrti.csv
table25: output/dt_prevalent_urti.csv
table26: output/dt_prevalent_sinusitis.csv
table27: output/dt_prevalent_ot_media.csv
table28: output/dt_prevalent_ot_externa.csv
#############################################################################
describe_ITS_var_stratified_process_3:
run: r:latest analysis/process/ITS_stratified_var_3.R
needs: [describe_cleaning_process_2]
outputs:
moderately_sensitive:
table2: output/repeat_incidental_cold.csv
table3: output/repeat_incidental_cough.csv
table4: output/repeat_incidental_copd.csv
table8: output/repeat_incidental_throat.csv
table9: output/repeat_incidental_uti.csv
table10: output/repeat_incidental_lrti.csv
table11: output/repeat_incidental_urti.csv
table12: output/repeat_incidental_sinusitis.csv
table13: output/repeat_incidental_ot_media.csv
table14: output/repeat_incidental_ot_externa.csv
#############################################################################
describe_ITS_repeat_incident:
run: r:latest analysis/itsmodel/ITS_repeat_incident.R
needs: [describe_ITS_var_stratified_process_3]
outputs:
moderately_sensitive:
table1: output/its_repeat_incident_predicted_data_table.csv
plot1: output/forest_repeat_incident_A.jpeg
plot2: output/forest_repeat_incident_B.jpeg
plot3: output/its_repeat_incident_predicted.jpeg
table2: output/its_repeat_incident_recovery_data_table.csv
table3: output/its_repeat_incident_changes_data_table.csv
plot4: output/conbined_repeat_incident.jpeg
#############################################################################
describe_ITS_var_broad_mon_overall_process:
run: r:latest analysis/process/ITS_stratified_var_4.R
needs: [describe_cleaning_process_2]
outputs:
moderately_sensitive:
table1: output/mon_overall_all_prescription.csv
table2: output/mon_overall_cold.csv
table3: output/mon_overall_cough.csv
#table4: output/mon_overall_copd.csv
#table5: output/mon_overall_throat.csv
table6: output/mon_overall_uti.csv
table7: output/mon_overall_lrti.csv
#table8: output/mon_overall_urti.csv
#table9: output/mon_overall_sinusitis.csv
table10: output/mon_overall_ot_media.csv
#table11: output/mon_overall_ot_externa.csv
describe_ITS_model_broad_mon_overall:
run: r:latest analysis/itsmodel/ITS_broad_mon_overall.R
needs: [describe_ITS_var_broad_mon_overall_process]
outputs:
moderately_sensitive:
plot1: output/mon_overall_predicted_plot.jpeg
plot2: output/mon_overall_forest_C.jpeg
plot3: output/mon_overall_forest_B.jpeg
plot4: output/mon_overall_combined.jpeg
table1: output/mon_overall_predicted_table.csv
table2: output/mon_overall_forest_B_table.csv
table3: output/mon_overall_forest_C_table.csv
extract_variables_extra_2019:
run: cohortextractor:latest generate_cohort --study-definition study_definition_extra_2019
needs: [describe_cleaning_process_2019]
outputs:
highly_sensitive:
cohort: output/input_extra_2019.csv
extract_variables_extra_2020:
run: cohortextractor:latest generate_cohort --study-definition study_definition_extra_2020
needs: [describe_cleaning_process_2020]
outputs:
highly_sensitive:
cohort: output/input_extra_2020.csv
extract_variables_extra_2021:
run: cohortextractor:latest generate_cohort --study-definition study_definition_extra_2021
needs: [describe_cleaning_process_2021]
outputs:
highly_sensitive:
cohort: output/input_extra_2021.csv
extract_variables_2019:
run: cohortextractor:latest generate_cohort --study-definition study_definition_demographic_2019
needs: [describe_cleaning_process_2019]
outputs:
highly_sensitive:
cohort: output/input_demographic_2019.csv
extract_test:
run: r:latest analysis/process/cleaning_id_extraction_test.R
needs: [extract_variables_2019,describe_cleaning_process_2019]
outputs:
moderately_sensitive:
plot1: output/extraction_test.csv
extract_variables_2020:
run: cohortextractor:latest generate_cohort --study-definition study_definition_demographic_2020
needs: [describe_cleaning_process_2020]
outputs:
highly_sensitive:
cohort: output/input_demographic_2020.csv
extract_variables_2021:
run: cohortextractor:latest generate_cohort --study-definition study_definition_demographic_2021
needs: [describe_cleaning_process_2021]
outputs:
highly_sensitive:
cohort: output/input_demographic_2021.csv
describe_prepare_var_2019_process:
run: r:latest analysis/multinomial/prepare_var_2019.R
needs: [extract_variables_2019]
outputs:
moderately_sensitive:
table1: output/prepare_var_count_2019.csv
table2: output/blt_var_2019.csv
highly_sensitive:
cohort: output/prepared_var_2019.csv
describe_prepare_var_2020_process:
run: r:latest analysis/multinomial/prepare_var_2020.R
needs: [extract_variables_2020]
outputs:
moderately_sensitive:
table1: output/prepare_var_count_2020.csv
table2: output/blt_var_2020.csv
highly_sensitive:
cohort: output/prepared_var_2020.csv
describe_prepare_var_2021_process:
run: r:latest analysis/multinomial/prepare_var_2021.R
needs: [extract_variables_2021]
outputs:
moderately_sensitive:
table1: output/prepare_var_count_2021.csv
table2: output/blt_var_2021.csv
highly_sensitive:
cohort: output/prepared_var_2021.csv
######## multinomial #########
describe_predict_model_var_process:
run: r:latest analysis/multinomial/predict_model_var.R
needs: [describe_prepare_var_2019_process,describe_prepare_var_2020_process,
describe_prepare_var_2021_process,describe_cleaning_process_2]
outputs:
moderately_sensitive:
table1: output/throat_count.csv
table2: output/urti_count.csv
table3: output/sinusitis_count.csv
table4: output/ot_externa_count.csv
table5: output/otmedia_count.csv
table6: output/copd_count.csv
table7: output/cough_count.csv
table8: output/pneumonia_count.csv
table9: output/lrti_count.csv
table10: output/uti_count.csv
highly_sensitive:
cohort1: output/throat_outcome.csv
cohort2: output/urti_outcome.csv
cohort3: output/sinusitis_outcome.csv
cohort4: output/ot_externa_outcome.csv
cohort5: output/otmedia_outcome.csv
cohort6: output/copd_outcome.csv
cohort7: output/cough_outcome.csv
cohort8: output/pneumonia_outcome.csv
cohort9: output/lrti_outcome.csv
cohort10: output/uti_outcome.csv
throat_appro_model:
run: r:latest -e 'rmarkdown::render("analysis/multinomial/throat_appro_model.Rmd", output_dir = "output/report")'
needs: [describe_predict_model_var_process]
outputs:
moderately_sensitive:
html: output/report/throat_appro_model.html
urti_appro_model:
run: r:latest -e 'rmarkdown::render("analysis/multinomial/urti_appro_model.Rmd", output_dir = "output/report")'
needs: [describe_predict_model_var_process]
outputs:
moderately_sensitive:
html: output/report/urti_appro_model.html
sinusitis_appro_model:
run: r:latest -e 'rmarkdown::render("analysis/multinomial/sinusitis_appro_model.Rmd", output_dir = "output/report")'
needs: [describe_predict_model_var_process]
outputs:
moderately_sensitive:
html: output/report/sinusitis_appro_model.html
ot_externa_appro_model:
run: r:latest -e 'rmarkdown::render("analysis/multinomial/ot_externa_appro_model.Rmd", output_dir = "output/report")'
needs: [describe_predict_model_var_process]
outputs:
moderately_sensitive:
html: output/report/ot_externa_appro_model.html
otmedia_appro_model:
run: r:latest -e 'rmarkdown::render("analysis/multinomial/otmedia_appro_model.Rmd", output_dir = "output/report")'
needs: [describe_predict_model_var_process]
outputs:
moderately_sensitive:
html: output/report/otmedia_appro_model.html
copd_appro_model:
run: r:latest -e 'rmarkdown::render("analysis/multinomial/copd_appro_model.Rmd", output_dir = "output/report")'
needs: [describe_predict_model_var_process]
outputs:
moderately_sensitive:
html: output/report/copd_appro_model.html
cough_appro_model:
run: r:latest -e 'rmarkdown::render("analysis/multinomial/cough_appro_model.Rmd", output_dir = "output/report")'
needs: [describe_predict_model_var_process]
outputs:
moderately_sensitive:
html: output/report/cough_appro_model.html
pneumonia_appro_model:
run: r:latest -e 'rmarkdown::render("analysis/multinomial/pneumonia_appro_model.Rmd", output_dir = "output/report")'
needs: [describe_predict_model_var_process]
outputs:
moderately_sensitive:
html: output/report/pneumonia_appro_model.html
uti_appro_model:
run: r:latest -e 'rmarkdown::render("analysis/multinomial/uti_appro_model.Rmd", output_dir = "output/report")'
needs: [describe_predict_model_var_process]
outputs:
moderately_sensitive:
html: output/report/uti_appro_model.html
lrti_appro_model:
run: r:latest -e 'rmarkdown::render("analysis/multinomial/lrti_appro_model.Rmd", output_dir = "output/report")'
needs: [describe_predict_model_var_process]
outputs:
moderately_sensitive:
html: output/report/lrti_appro_model.html
describe_cohort_3_var_process:
run: r:latest analysis/multinomial/cohort_3_var.R
needs: [describe_cohort_1_rds]
outputs:
moderately_sensitive:
table1: output/repeat_overall_tab.csv
table2: output/repeat_incident_tab.csv
table3: output/cohort_2_count.csv
table4: output/cohort_3_count.csv
table5: output/cohort_2_pat_one.csv
table6: output/cohort_3_pat_one.csv
describe_cohort_1_var_process:
run: r:latest analysis/itsmodel/cohort_1_var.R
needs: [describe_cohort_1_rds]
outputs:
moderately_sensitive:
table7: output/cohort_1_count.csv
table1: output/cohort_1_overall_blt_2019.csv
table2: output/cohort_1_blt_2019.csv
table3: output/cohort_1_overall_blt_2020.csv
table4: output/cohort_1_blt_2020.csv
table5: output/cohort_1_overall_blt_2021.csv
table6: output/cohort_1_blt_2021.csv
describe_cohort_1_rds:
run: r:latest analysis/description/var_rds_prepare.R
needs: [describe_prepare_var_2019_process,describe_prepare_var_2020_process,
describe_prepare_var_2021_process,describe_cleaning_process_2]
outputs:
highly_sensitive:
rds1: output/measures/cohort_1.rds
describe_descriptive_figure_process:
run: r:latest analysis/description/figure.R
needs: [describe_cohort_1_rds]
outputs:
moderately_sensitive:
figure1: output/figure_age_strata.jpeg
figure2: output/figure_sex_strata.jpeg
figure3: output/figure_region_strata.jpeg
table1: output/figure_age_strata_table.csv
table2: output/figure_sex_strata_table.csv
table3: output/figure_region_strata_table.csv
describe_descriptive_repeat_figure_process:
run: r:latest analysis/description/repeat_figure.R
needs: [describe_cohort_1_rds]
outputs:
moderately_sensitive:
figure1: output/figure_2_age_strata.jpeg
figure2: output/figure_2_sex_strata.jpeg
figure3: output/figure_2_region_strata.jpeg
table1: output/figure_2_age_strata_table.csv
table2: output/figure_2_sex_strata_table.csv
table3: output/figure_2_region_strata_table.csv
describe_descriptive_cold_figure_process:
run: r:latest analysis/description/cold_figure.R
needs: [describe_cohort_1_rds]
outputs:
moderately_sensitive:
figure1: output/figure_cold_repeat.jpeg
table1: output/figure_cold_repeat_table.csv
describe_its_repeat_var_process:
run: r:latest analysis/description/its_repeat_var.R
needs: [describe_cohort_1_rds]
outputs:
moderately_sensitive:
table1: output/dt_repeat_overall.csv
table2: output/dt_repeat_incidental.csv
describe_ITS_repeat_compare:
run: r:latest analysis/itsmodel/ITS_repeat_compare.R
needs: [describe_its_repeat_var_process]
outputs:
moderately_sensitive:
table1: output/its_repeat_compare_predicted_table.csv
plot1: output/forest_repeat_compare_B.jpeg
plot2: output/forest_repeat_compare_C.jpeg
plot3: output/its_repeat_compare_predicted.jpeg
table2: output/its_repeat_compare_changes_table.csv
table3: output/its_repeat_compare_recovery_table.csv
plot4: output/forest_repeat_compare_BC.jpeg
describe_prepare_var_2019_extra_process:
run: r:latest analysis/multinomial/prepare_var_2019_extra.R
needs: [extract_variables_extra_2019]
outputs:
moderately_sensitive:
table2: output/var_extra_blt_2019.csv
highly_sensitive:
cohort: output/prepared_var_extra_2019.csv
describe_prepare_var_2020_extra_process:
run: r:latest analysis/multinomial/prepare_var_2020_extra.R
needs: [extract_variables_extra_2020]
outputs:
moderately_sensitive:
table2: output/var_extra_blt_2020.csv
highly_sensitive:
cohort: output/prepared_var_extra_2020.csv
describe_prepare_var_2021_extra_process:
run: r:latest analysis/multinomial/prepare_var_2021_extra.R
needs: [extract_variables_extra_2021]
outputs:
moderately_sensitive:
table2: output/var_extra_blt_2021.csv
highly_sensitive:
cohort: output/prepared_var_extra_2021.csv
describe_descriptive_figure_for_se_process:
run: r:latest analysis/description/figure_for_se.R
needs: [describe_cohort_1_rds]
outputs:
moderately_sensitive:
figure1: output/figure_broad_1.jpeg
figure2: output/figure_broad_2.jpeg
figure3: output/figure_broad_3.jpeg
table1: output/figure_broad_1_table.csv
table2: output/figure_broad_2_table.csv
table3: output/figure_broad_3_table.csv
describe_descriptive_figure_for_se_65_process:
run: r:latest analysis/description/figure_for_se_65.R
needs: [describe_cohort_1_rds]
outputs:
moderately_sensitive:
figure1: output/figure_broad_65_1.jpeg
figure2: output/figure_broad_65_2.jpeg
figure3: output/figure_broad_65_3.jpeg
table1: output/figure_broad_65_1_table.csv
table2: output/figure_broad_65_2_table.csv
table3: output/figure_broad_65_3_table.csv
describe_predict_model_overall_var_process:
run: r:latest analysis/multinomial/predict_model_overall_var.R
needs: [describe_cohort_1_rds]
outputs:
highly_sensitive:
cohort1: output/ten_infection_outcome.csv
overall_appro_model:
run: r:latest -e 'rmarkdown::render("analysis/multinomial/overall_appro_model.Rmd", output_dir = "output/report")'
needs: [describe_predict_model_overall_var_process]
outputs:
moderately_sensitive:
html: output/report/overall_appro_model.html
##### check trimethoprim/nitrofurantonin
generate_study_population_uti_ab_check:
run: cohortextractor:latest generate_cohort --study-definition study_definition_uti_ab_check --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_uti_ab_check_*.csv.gz
generate_measures_uti_ab_check:
run: cohortextractor:latest generate_measures --study-definition study_definition_uti_ab_check --skip-existing --output-dir=output/measures
needs: [generate_study_population_uti_ab_check]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_ratio_*.csv
describe_uti_ab_check:
run: r:latest analysis/plot/uti_ab_check.R
needs: [describe_ab_type_process_1,describe_ab_type_process_2,describe_ab_type_process_3] # transfrom & define all variables
outputs:
moderately_sensitive:
plot1: output/uti_ab_check_bar.jpeg
plot2: output/uti_ab_check_line.jpeg
plot3: output/uti_ab_check_bar_2.jpeg
csv: output/uti_ab_check.csv
describe_uti_ab_check_2:
run: r:latest analysis/plot/uti_ab_check_2.R
needs: [generate_measures_uti_ab_check] # transfrom & define all variables
outputs:
moderately_sensitive:
plot1: output/uti_ab_ratio_check_line.jpeg
plot2: output/uti_ab_ratio_check_line2.jpeg
plot3: output/uti_ab_ratio_check_line3.jpeg
csv: output/uti_ab_ratio_check.csv
generate_study_population_uti_ab_check_op: #open prescribing
run: cohortextractor:latest generate_cohort --study-definition study_definition_uti_ab_check_op --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_uti_ab_check_op_*.csv.gz
generate_measures_uti_ab_check_op:
run: cohortextractor:latest generate_measures --study-definition study_definition_uti_ab_check_op --skip-existing --output-dir=output/measures
needs: [generate_study_population_uti_ab_check_op]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_ratio_op_*.csv
describe_uti_ab_check_2_op:
run: r:latest analysis/plot/uti_ab_check_2_op.R
needs: [generate_measures_uti_ab_check_op] # transfrom & define all variables
outputs:
moderately_sensitive:
plot1: output/uti_ab_ratio_check_line_op.jpeg
plot2: output/uti_ab_ratio_check_line2_op.jpeg
plot3: output/uti_ab_ratio_check_line3_op.jpeg
csv: output/uti_ab_ratio_check_op.csv
describe_region: # check region & age
run: r:latest -e 'rmarkdown::render("analysis/region.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [generate_study_population]
outputs:
moderately_sensitive:
html: output/region.html
describe_age: # check region & age
run: r:latest -e 'rmarkdown::render("analysis/age.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [generate_study_population]
outputs:
moderately_sensitive:
html: output/age.html
generate_study_population_uti_ab_check_oc: #openCodelit
run: cohortextractor:latest generate_cohort --study-definition study_definition_uti_ab_check_oc --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_uti_ab_check_oc_*.csv.gz
generate_measures_uti_ab_check_oc:
run: cohortextractor:latest generate_measures --study-definition study_definition_uti_ab_check_oc --skip-existing --output-dir=output/measures
needs: [generate_study_population_uti_ab_check_oc]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_ratio_oc_*.csv
describe_uti_ab_check_2_oc:
run: r:latest analysis/plot/uti_ab_check_2_oc.R
needs: [generate_measures_uti_ab_check_oc] # transfrom & define all variables
outputs:
moderately_sensitive:
plot1: output/uti_ab_ratio_check_line_oc.jpeg
plot2: output/uti_ab_ratio_check_line2_oc.jpeg
plot3: output/uti_ab_ratio_check_line3_oc.jpeg
csv: output/uti_ab_ratio_check_oc.csv
generate_study_population_uti_ab_check_19: # 2019-01
run: cohortextractor:latest generate_cohort --study-definition study_definition_uti_ab_check_19 --index-date-range "2019-01-01 to 2019-02-01 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_uti_ab_check_19_*.csv.gz
generate_measures_uti_ab_check_19:
run: cohortextractor:latest generate_measures --study-definition study_definition_uti_ab_check_19 --skip-existing --output-dir=output/measures
needs: [generate_study_population_uti_ab_check_19]
outputs:
moderately_sensitive:
measure_csv1: output/measures/measure_uti_ab_check_19_*.csv
describe_cohort_1_repeat_check_process:
run: r:latest analysis/description/cohort_1_repeat_check.R
needs: [describe_cohort_1_rds]
outputs:
moderately_sensitive:
table1: output/all_record_count.csv
table2: output/cohort_1_all_record.csv
table3: output/cohort_1_record_2019.csv
table4: output/count_record_2019.csv
table5: output/cohort_1_record_2020.csv
table6: output/count_record_2020.csv
table7: output/cohort_1_record_2021.csv
table8: output/count_record_2021.csv
describe_age_sex_ab_check_process:
run: r:latest analysis/description/age_sex_ab_check.R
needs: [describe_cohort_1_rds]
outputs:
moderately_sensitive:
table1: output/age_sex_ab_check.csv
table2: output/age_sex_ab_check_2019.csv
table3: output/age_sex_ab_check_2020.csv
table4: output/age_sex_ab_check_2021.csv
describe_cohort_1_indication_strata_figure_process:
run: r:latest analysis/description/cohort_1_indication_strata_repeat.R
needs: [describe_cohort_1_rds]
outputs:
moderately_sensitive:
figure1: output/cohort_1_indication_strata.jpeg
table1: output/cohort_1_indication_strata_table.csv
describe_cohort_2_incident_strata_figure_process:
run: r:latest analysis/description/cohort_2_incident_strata_repeat.R
needs: [describe_cohort_1_rds]
outputs:
moderately_sensitive:
figure1: output/cohort_2_incident_strata.jpeg
table1: output/cohort_2_incident_strata_table.csv
describe_cohort_2_strata_figure_process:
run: r:latest analysis/description/cohort_2_strata_repeat.R
needs: [describe_cohort_1_rds]
outputs:
moderately_sensitive:
figure1: output/cohort_2_age_strata.jpeg
figure2: output/cohort_2_sex_strata.jpeg
figure3: output/cohort_2_region_strata.jpeg
table1: output/cohort_2_age_strata_table.csv
table2: output/cohort_2_sex_strata_table.csv
table3: output/cohort_2_region_strata_table.csv
describe_TPP_ab_frequency_table:
run: r:latest analysis/xiaomin_ab/TPP_ab_frequency_table.R
needs: [generate_measures_broad]
outputs:
moderately_sensitive:
table1: output/TPP_ab_frequency_table.csv
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 29:13:41
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- service_eval_work
- Requested by
- Billy Zhong
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 63fe1c6
- Requested actions
-
-
generate_study_population_broad_comparison
-