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 --with-end-date-fix --study-definition study_definition_sameday_ab --index-date-range "2019-01-01 to 2022-06-01" --skip-existing --output-dir=output/measures --output-format=csv.gz

      outputs:
        highly_sensitive:
          cohort: output/measures/input_sameday_ab_*.csv.gz

  generate_measures_samedayab:
    run: cohortextractor:latest generate_measures --study-definition study_definition_sameday_ab --skip-existing --output-dir=output/measures
    needs: [generate_study_population_samedayab]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_samedayab_*.csv

  describe_same_day_ab:
    run: r:latest analysis/plot/same_day_covid_ab.R
    needs: [generate_measures_samedayab]
    outputs:
       moderately_sensitive:
        plot1: output/same_day_ab_prop_line_sgss.jpeg
        plot2: output/same_day_ab_prop_line_gp.jpeg

  generate_study_population_ab_extraction:
      run: cohortextractor:latest generate_cohort --study-definition study_definition_ab_extraction 
        --output-format=csv.gz
      outputs:
        highly_sensitive:
          cohort: output/input_ab_extraction.csv.gz

  generate_study_population_ab_extraction_condition:
      run: cohortextractor:latest generate_cohort --study-definition study_definition_ab_extraction_condition 
        --output-format=csv.gz
      outputs:
        highly_sensitive:
          cohort: output/input_ab_extraction_condition.csv.gz

  generate_study_population_ab_extraction_new:
      run: cohortextractor:latest generate_cohort --study-definition study_definition_ab_extraction_new 
        --output-format=csv.gz
      outputs:
        highly_sensitive:
          cohort: output/input_ab_extraction_new.csv.gz

  generate_study_population_antibiotic_Brit_2019:
      run: cohortextractor:latest generate_cohort --study-definition study_definition_antibiotic_Brit_2019
        --output-format=csv.gz
      outputs:
        highly_sensitive:
          cohort: output/input_antibiotic_Brit_2019.csv.gz     

  generate_study_population_antibiotic_Brit_2020:
      run: cohortextractor:latest generate_cohort --study-definition study_definition_antibiotic_Brit_2020
        --output-format=csv.gz
      outputs:
        highly_sensitive:
          cohort: output/input_antibiotic_Brit_2020.csv.gz      

  generate_study_population_antibiotic_Brit_2021:
      run: cohortextractor:latest generate_cohort --study-definition study_definition_antibiotic_Brit_2021
        --output-format=csv.gz
      outputs:
        highly_sensitive:
          cohort: output/input_antibiotic_Brit_2021.csv.gz   

  generate_study_population_antibiotic_Brit_2022:
      run: cohortextractor:latest generate_cohort --study-definition study_definition_antibiotic_Brit_2022
        --output-format=csv.gz
      outputs:
        highly_sensitive:
          cohort: output/input_antibiotic_Brit_2022.csv.gz 

  generate_study_population_antibiotic_OS_2019:
      run: cohortextractor:latest generate_cohort --study-definition study_definition_antibiotic_OS_2019
        --output-format=csv.gz
      outputs:
        highly_sensitive:
          cohort: output/input_antibiotic_OS_2019.csv.gz   

  generate_study_population_antibiotic_OS_2020:
      run: cohortextractor:latest generate_cohort --study-definition study_definition_antibiotic_OS_2020
        --output-format=csv.gz
      outputs:
        highly_sensitive:
          cohort: output/input_antibiotic_OS_2020.csv.gz 

  generate_study_population_antibiotic_OS_2021:
      run: cohortextractor:latest generate_cohort --study-definition study_definition_antibiotic_OS_2021
        --output-format=csv.gz
      outputs:
        highly_sensitive:
          cohort: output/input_antibiotic_OS_2021.csv.gz  

  generate_study_population_antibiotic_OS_2022:
      run: cohortextractor:latest generate_cohort --study-definition study_definition_antibiotic_OS_2022
        --output-format=csv.gz
      outputs:
        highly_sensitive:
          cohort: output/input_antibiotic_OS_2022.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

####### 2019 baseline table
  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
      highly_sensitive:
        cohort: output/measures/id_2019.csv

  extract_covrx_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covrx_2019
    needs: [describe_baseline_table_split_2019]
    outputs:
      highly_sensitive:
        cohort: output/measures/input_covrx_2019.csv 
  
  describe_covrx_2019:
    run: r:latest analysis/tables/covrx_2019.R
    needs: [extract_covrx_2019]
    outputs:
      moderately_sensitive:
        number: output/covrx_2019.txt


####### 2020 baseline table
  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
      highly_sensitive:
        cohort: output/measures/id_2020.csv
  
  extract_covrx_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covrx_2020
    needs: [describe_baseline_table_split_2020]
    outputs:
      highly_sensitive:
        cohort: output/measures/input_covrx_2020.csv 
    # check
  # describe_covrx_2020: 
  #   run: r:latest -e 'rmarkdown::render("analysis/process/covrx_check_2020.rmd", output_dir = "output/report")'
  #   needs: [extract_covrx_2021]
  #   outputs:
  #     moderately_sensitive:
  #       html: output/report/covrx_check_2020.html

  describe_covrx_2020:
    run: r:latest analysis/tables/covrx_2020.R
    needs: [extract_covrx_2020]
    outputs:
      moderately_sensitive:
        number: output/covrx_2020.txt

####### 2021 baseline table

  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
      highly_sensitive:
        cohort: output/measures/id_2021.csv
  
  extract_covrx_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covrx_2021
    needs: [describe_baseline_table_split_2021]
    outputs:
      highly_sensitive:
        cohort: output/measures/input_covrx_2021.csv 
  
  describe_covrx_2021:
    run: r:latest analysis/tables/covrx_2021.R
    needs: [extract_covrx_2021]
    outputs:
      moderately_sensitive:
        number: output/covrx_2021.txt

####### 2022 baseline table

  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
      highly_sensitive:
        cohort: output/measures/id_2022.csv
  
  extract_covrx_2022:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covrx_2022
    needs: [describe_baseline_table_split_2022]
    outputs:
      highly_sensitive:
        cohort: output/measures/input_covrx_2022.csv 
  
  describe_covrx_2022:
    run: r:latest analysis/tables/covrx_2022.R
    needs: [extract_covrx_2022]
    outputs:
      moderately_sensitive:
        number: output/covrx_2022.txt

##
  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
        table2: output/redacted/consultation_GP_rate_yr2.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_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

  generate_study_population_ab: #  Antibiotics_recorded_01
    run: cohortextractor:latest generate_cohort  --with-end-date-fix --study-definition study_definition_ab --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_ab_*.csv.gz
  
  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_ab]
    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: #  Antibiotics_recorded_03
    run: r:latest analysis/plot/ab_recorded_indication_plot_incident.R
    needs: [describe_ab_recoded_indication_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: #  Antibiotics_recorded_03
    run: r:latest analysis/plot/ab_recorded_indication_plot_prevalent.R
    needs: [describe_ab_recoded_indication_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 --with-end-date-fix --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:
        # plot1.1: output/redacted_v2/prevalent_AB_uti_top5.jpeg
        # plot1.2: output/redacted_v2/incident_AB_uti_top5.jpeg
        # plot2.1: output/redacted_v2/prevalent_AB_lrti_top5.jpeg
        # plot2.2: output/redacted_v2/incident_AB_lrti_top5.jpeg
        # plot3.1: output/redacted_v2/prevalent_AB_urti_top5.jpeg
        # plot3.2: output/redacted_v2/incident_AB_urti_top5.jpeg
        # plot4.1: output/redacted_v2/prevalent_AB_sinusitis_top5.jpeg
        # plot4.2: output/redacted_v2/incident_AB_sinusitis_top5.jpeg
        # plot5.1: output/redacted_v2/prevalent_AB_ot_externa_top5.jpeg
        # plot5.2: output/redacted_v2/incident_AB_ot_externa_top5.jpeg
        # plot6.1: output/redacted_v2/prevalent_AB_otmedia_top5.jpeg
        # plot6.2: output/redacted_v2/incident_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
        plot1: output/redacted_v2/prevalent_AB_top5.jpeg
        plot2: output/redacted_v2/incident_AB_top5.jpeg


  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_infection_abtype]
    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

  describe_TPP_broad_percentage: 
    run: r:latest analysis/xiaomin_ab/TPP_broad_percentage.R
    needs: [generate_measures_broad]
    outputs:
      moderately_sensitive:
        table1: output/TPP_broad_percentage.jpeg

  describe_TPP_Trim_Nitro_frequency: 
    run: r:latest analysis/xiaomin_ab/TPP_ab_frequency.R
    needs: [generate_study_population_ab_extraction]
    outputs:
      moderately_sensitive:
        table1: output/TPP_Trim_Nitro_frequency.csv

  describe_TPP_Trim_Nitro_frequency_condition: 
    run: r:latest analysis/xiaomin_ab/TPP_ab_frequency_condition.R
    needs: [generate_study_population_ab_extraction_condition]
    outputs:
      moderately_sensitive:
        table1: output/TPP_Trim_Nitro_frequency_condition.csv

#  describe_TPP_ab_per_mon: 
#    run: r:latest analysis/xiaomin_ab/TPP_ab_per_mon.R
#    needs: [generate_study_population_ab_extraction]
#    outputs:
#      moderately_sensitive:
#        table1: output/TPP_ab_month_2019.csv

  describe_TPP_Trim_Nitro_frequency_new: 
    run: r:latest analysis/xiaomin_ab/TPP_ab_frequency_new.R
    needs: [generate_study_population_ab_extraction_new]
    outputs:
      moderately_sensitive:
        table1: output/TPP_Trim_Nitro_frequency_new.csv

  describe_TPP_ab_Brit_2019_frequency_table: 
    run: r:latest analysis/xiaomin_ab/TPP_ab_Brit_2019_frequency.R
    needs: [generate_study_population_antibiotic_Brit_2019]
    outputs:
      moderately_sensitive:
        table1: output/TPP_ab_Brit_2019_frequency.csv
        table2: output/TPP_ab_Brit_2019_count.csv

  describe_TPP_ab_Brit_2020_frequency_table: 
    run: r:latest analysis/xiaomin_ab/TPP_ab_Brit_2020_frequency.R
    needs: [generate_study_population_antibiotic_Brit_2020]
    outputs:
      moderately_sensitive:
        table1: output/TPP_ab_Brit_2020_frequency.csv
        table2: output/TPP_ab_Brit_2020_count.csv

  describe_TPP_ab_Brit_2021_frequency_table: 
    run: r:latest analysis/xiaomin_ab/TPP_ab_Brit_2021_frequency.R
    needs: [generate_study_population_antibiotic_Brit_2021]
    outputs:
      moderately_sensitive:
        table1: output/TPP_ab_Brit_2021_frequency.csv
        table2: output/TPP_ab_Brit_2021_count.csv

  describe_TPP_ab_Brit_2022_frequency_table: 
    run: r:latest analysis/xiaomin_ab/TPP_ab_Brit_2022_frequency.R
    needs: [generate_study_population_antibiotic_Brit_2022]
    outputs:
      moderately_sensitive:
        table1: output/TPP_ab_Brit_2022_frequency.csv
        table2: output/TPP_ab_Brit_2022_count.csv

  describe_TPP_ab_OS_2019_frequency_table: 
    run: r:latest analysis/xiaomin_ab/TPP_ab_OS_2019_frequency.R
    needs: [generate_study_population_antibiotic_OS_2019]
    outputs:
      moderately_sensitive:
        table1: output/TPP_ab_OS_2019_count.csv

  describe_TPP_ab_OS_2020_frequency_table: 
    run: r:latest analysis/xiaomin_ab/TPP_ab_OS_2020_frequency.R
    needs: [generate_study_population_antibiotic_OS_2020]
    outputs:
      moderately_sensitive:
        table1: output/TPP_ab_OS_2020_count.csv

  describe_TPP_ab_OS_2021_frequency_table: 
    run: r:latest analysis/xiaomin_ab/TPP_ab_OS_2021_frequency.R
    needs: [generate_study_population_antibiotic_OS_2021]
    outputs:
      moderately_sensitive:
        table1: output/TPP_ab_OS_2021_count.csv

  describe_TPP_ab_OS_2022_frequency_table: 
    run: r:latest analysis/xiaomin_ab/TPP_ab_OS_2022_frequency.R
    needs: [generate_study_population_antibiotic_OS_2022]
    outputs:
      moderately_sensitive:
        table1: output/TPP_ab_OS_2022_count.csv

#### ab extraction: 2019
### generate study cohort with the date of each prescriptions
  generate_study_population_ab_type_2019: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ab_type_2019 --index-date-range "2019-01-01 to 2019-12-31" --skip-existing --output-dir=output/measures --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_ab_type_2019_*.csv.gz

  generate_study_population_ab_predictor_2019: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ab_predictor_2019 --index-date-range "2019-01-01 to 2019-12-31" --skip-existing --output-dir=output/measures --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_ab_predictor_2019_*.csv.gz

  generate_study_population_antibiotic_Brit_new_2019:
      run: cohortextractor:latest generate_cohort --study-definition study_definition_antibiotic_Brit_new_2019
        --output-format=csv.gz
      outputs:
        highly_sensitive:
          cohort: output/input_antibiotic_Brit_new_2019.csv.gz  

  describe_TPP_ab_Brit_new_2019_frequency_table: 
    run: r:latest analysis/xiaomin_ab/TPP_ab_Brit_2019_frequency_new.R
    needs: [generate_study_population_antibiotic_Brit_new_2019]
    outputs:
      moderately_sensitive:
        table1: output/TPP_ab_Brit_new_2019_frequency.csv
        table2: output/TPP_ab_Brit_new_2019_count.csv