project.yaml

version: '3.0'

expectations:
  population_size: 50000

actions:

### 1.  Extract the cohort

  ## use the Measure function to allow data for different time periods to be extracted in the same study population:  --index-date-range ""yyyy-mm-dd"" --output-format feather 
  generate_study_population_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2015-03-01" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_all_2015-03-01.feather  

  generate_study_population_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2016-03-01" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_all_2016-03-01.feather  

  generate_study_population_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2017-03-01" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_all_2017-03-01.feather  
        
  generate_study_population_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2018-03-01" --output-format feather 
    outputs:
      highly_sensitive:
        cohort: output/data/input_all_2018-03-01.feather  
        
        
  generate_study_population_5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2019-03-01" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_all_2019-03-01.feather        
        
  generate_study_population_6:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2020-03-01" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_all_2020-03-01.feather  
   
  generate_study_population_7:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-dir=output/data --index-date-range "2021-03-01" --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/data/input_all_2021-03-01.feather  
 
 

  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output/data --output-format=feather 
    outputs:
      highly_sensitive:
        cohort: output/data/input_ethnicity.feather
        
      
        
  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py --output-dir=output/data --output-format feather
    needs: [generate_study_population_1, generate_study_population_2, generate_study_population_3, generate_study_population_4, generate_study_population_5, generate_study_population_6, generate_study_population_7, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/data/input*.feather

  generate_study_population_dm1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_dm_meds --output-dir=output/data --index-date-range "2015-03-01" 
    outputs:
      highly_sensitive:
        cohort: output/data/input_dm_meds_2015-03-01.csv

  generate_study_population_dm2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_dm_meds --output-dir=output/data --index-date-range "2016-03-01" 
    outputs:
      highly_sensitive:
        cohort: output/data/input_dm_meds_2016-03-01.csv

  generate_study_population_dm3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_dm_meds --output-dir=output/data --index-date-range "2017-03-01" 
    outputs:
      highly_sensitive:
        cohort: output/data/input_dm_meds_2017-03-01.csv

  generate_study_population_dm4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_dm_meds --output-dir=output/data --index-date-range "2018-03-01" 
    outputs:
      highly_sensitive:
        cohort: output/data/input_dm_meds_2018-03-01.csv

  generate_study_population_dm5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_dm_meds --output-dir=output/data --index-date-range "2019-03-01" 
    outputs:
      highly_sensitive:
        cohort: output/data/input_dm_meds_2019-03-01.csv

  generate_study_population_dm6:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_dm_meds --output-dir=output/data --index-date-range "2020-03-01" 
    outputs:
      highly_sensitive:
        cohort: output/data/input_dm_meds_2020-03-01.csv

  generate_study_population_dm7:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_dm_meds --output-dir=output/data --index-date-range "2021-03-01" 
    outputs:
      highly_sensitive:
        cohort: output/data/input_dm_meds_2021-03-01.csv
###  Develop yearly BMI data sets to de-duplicate data and calculate median BMI each year.   Feather format to reduce data quantity.


  join_meds:
    run: r:latest analysis/add_medication.R --output-dir=output/data --output-format feather
    needs: [join_ethnicity, generate_study_population_dm1, generate_study_population_dm2, generate_study_population_dm3, generate_study_population_dm4, generate_study_population_dm5, generate_study_population_dm6, generate_study_population_dm7]
    outputs:
      highly_sensitive:
        cohort1: output/data/complete_meds_2015.feather
        cohort2: output/data/complete_meds_2016.feather
        cohort3: output/data/complete_meds_2017.feather
        cohort4: output/data/complete_meds_2018.feather
        cohort5: output/data/complete_meds_2019.feather
        cohort6: output/data/complete_meds_2020.feather
        cohort7: output/data/complete_meds_2021.feather





  generate_BMI_2015_data:
    run: r:latest analysis/BMI_2015.R --output-dir=output/data --output-format feather
    needs: [join_meds]
    outputs:
      highly_sensitive:
        cohort1: output/data/BMI_complete_median_2015.feather
        cohort2: output/data/BMI_complete_long_2015.feather
      moderately_sensitive:
        table1:  output/data/BMI_data_checks_2015.csv


  generate_BMI_2016_data:
    run: r:latest analysis/BMI_2016.R --output-dir=output/data --output-format feather
    needs: [join_meds]
    outputs:
      highly_sensitive:
        cohort1: output/data/BMI_complete_median_2016.feather
        cohort2: output/data/BMI_complete_long_2016.feather
      moderately_sensitive:
        table1:  output/data/BMI_data_checks_2016.csv

  
  generate_BMI_2017_data:
    run: r:latest analysis/BMI_2017.R --output-dir=output/data --output-format feather
    needs: [join_meds]
    outputs:
      highly_sensitive:
        cohort1: output/data/BMI_complete_median_2017.feather
        cohort2: output/data/BMI_complete_long_2017.feather
      moderately_sensitive:
        table1:  output/data/BMI_data_checks_2017.csv
        
   
   
   
  generate_BMI_2019_data:
    run: r:latest analysis/BMI_2019.R --output-dir=output/data --output-format feather
    needs: [join_meds]
    outputs:
      highly_sensitive:
        cohort1: output/data/BMI_complete_median_2019.feather
        cohort2: output/data/BMI_complete_long_2019.feather
      moderately_sensitive:
        table1:  output/data/BMI_data_checks_2019.csv


  generate_BMI_2021_data:
    run: r:latest analysis/BMI_2021.R --output-dir=output/data --output-format feather
    needs: [join_meds]
    outputs:
      highly_sensitive:
        cohort1: output/data/BMI_complete_median_2021.feather
        cohort2: output/data/BMI_complete_long_2021.feather
      moderately_sensitive:
        table1:  output/data/BMI_data_checks_2021.csv


  generate_BMI_2018_data:
    run: r:latest analysis/BMI_2018.R --output-dir=output/data --output-format feather
    needs: [join_meds]
    outputs:
      highly_sensitive:
        cohort1: output/data/BMI_complete_median_2018.feather
        cohort2: output/data/BMI_complete_long_2018.feather
      moderately_sensitive:
        table1:  output/data/BMI_data_checks_2018.csv


  generate_BMI_2020_data:
    run: r:latest analysis/BMI_2020.R --output-dir=output/data --output-format feather
    needs: [join_meds]
    outputs:
      highly_sensitive:
        cohort1: output/data/BMI_complete_median_2020.feather
        cohort2: output/data/BMI_complete_long_2020.feather
      moderately_sensitive:
        table1:  output/data/BMI_data_checks_2020.csv


# Append yearly data sets to produce a complete data set for analysis of change in trends

  generate_complete_median_BMI_data:
    run: r:latest analysis/BMI_median_combine_datasets.R --output-dir=output/data --output-format feather
    needs: [generate_BMI_2015_data, generate_BMI_2016_data, generate_BMI_2017_data, generate_BMI_2018_data, generate_BMI_2019_data, generate_BMI_2020_data, generate_BMI_2021_data ]
    outputs:
      highly_sensitive:
        cohort1: output/data/BMI_complete_median.feather


  generate_complete_long_BMI_data:
    run: r:latest analysis/BMI_complete_long.R --output-dir=output/data --output-format feather
    needs: [generate_BMI_2015_data, generate_BMI_2016_data, generate_BMI_2017_data, generate_BMI_2018_data, generate_BMI_2019_data, generate_BMI_2020_data, generate_BMI_2021_data ]
    outputs:
      highly_sensitive:
        cohort1: output/data/all_bmi_long.feather

  generate_BMI_trajectories_data1:
    run: r:latest analysis/BMI_change_1.R --output-dir=output/data --output-format feather
    needs: [generate_complete_long_BMI_data]
    outputs:
      highly_sensitive:
        cohort1: output/data/BMI_demog.feather     
        cohort2: output/data/BMI_all_long_sample.feather 

  generate_BMI_trajectories_data2:
    run: r:latest analysis/BMI_change_2.R --output-dir=output/data --output-format feather
    needs: [generate_BMI_trajectories_data1]
    outputs:
      highly_sensitive:
        cohort1: output/data/BMI_trajectories.feather     

  generate_BMI_trajectories_data3:
    run: r:latest analysis/BMI_change_3.R --output-dir=output/data --output-format feather
    needs: [generate_BMI_trajectories_data2, generate_BMI_trajectories_data1]
    outputs:
      highly_sensitive:
        cohort1: output/data/BMI_trajectories_final.feather 

  BMI_trajectories_demographics_correction:
    run: r:latest analysis/BMI_change_demographic_correction.R --output-dir=output/data --output-format feather
    needs: [generate_BMI_trajectories_data3, generate_complete_long_BMI_data]
    outputs:
      highly_sensitive:
        cohort1: output/data/BMI_trajectories_final_demog.feather
      moderately_sensitive:
        table1: output/data/BMI_traj_demog.html

########################################
## POPULATION DEMOGRAPHICS
#######################################
  demographics_analysis_pop:
    run: r:latest analysis/pop_demographics/pop_demographics_total_pop.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/demographics_study_population.csv

  demographics_had_bmi:
    run: r:latest analysis/pop_demographics/pop_demographics_had_bmi.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/demographics_had_bmi.csv

  demographics_t2dm:
    run: r:latest analysis/pop_demographics/pop_demographics_t2dm.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/demographics_study_population_t2dm.csv
        table2: output/data/demographics_had_bmi_t2dm.csv

  demographics_t1dm:
    run: r:latest analysis/pop_demographics/pop_demographics_t1dm.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/demographics_study_population_t1dm.csv
        table2: output/data/demographics_had_bmi_t1dm.csv

  demographics_hypertension:
    run: r:latest analysis/pop_demographics/pop_demographics_hypertension.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/demographics_study_population_hypertension.csv
        table2: output/data/demographics_had_bmi_hypertension.csv

  demographics_bmi_change_all:
    run: r:latest analysis/pop_demographics/pop_demographics_bmi_change_all.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive:
        table1: output/data/demographics_bmi_change_analysis_all.csv


  demographics_bmi_change_lowbmiexc:
    run: r:latest analysis/pop_demographics/pop_demographics_bmi_change_lowbmiexc.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive:
        table1: output/data/demographics_bmi_change_analysis_lowbmiexc.csv

  demographics_bmi_change_t2dm:
    run: r:latest analysis/pop_demographics/pop_demographics_bmi_change_t2dm.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive:
        table1: output/data/demographics_bmi_change_analysis_all_t2dm.csv
        table2: output/data/demographics_bmi_change_analysis_lowbmiexc_t2dm.csv


  demographics_bmi_change_t1dm:
    run: r:latest analysis/pop_demographics/pop_demographics_bmi_change_t1dm.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive:
        table1: output/data/demographics_bmi_change_analysis_all_t1dm.csv
        table2: output/data/demographics_bmi_change_analysis_lowbmiexc_t1dm.csv

  demographics_bmi_change_hypertension:
    run: r:latest analysis/pop_demographics/pop_demographics_bmi_change_hypertension.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive:
        table1: output/data/demographics_bmi_change_analysis_all_hypertension.csv
        table2: output/data/demographics_bmi_change_analysis_lowbmiexc_hypertension.csv

#########################################################
## TOP DECILE: BMI_ CHANGE
##########################################################
  topdecile_bmi_change_univariate:
    run: r:latest analysis/bmi_trajectory/top_decile_change/top_decile_change_univariate.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive:
        table1: output/data/change_90th_univariate_lowbmiexc.csv
        table2: output/data/change_deciles_lowbmiexc.csv
        table3: output/data/change_90th_counts_lowbmiexc.csv

  topdecile_bmi_change_age_adjusted:
    run: r:latest analysis/bmi_trajectory/top_decile_change/top_decile_change_age_adjusted.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive:
        table1: output/data/change_90th_age_adjusted_lowbmiexc.csv
        table2: output/data/change_90th_wald_age.csv

  topdecile_bmi_change_sex_adjusted:
    run: r:latest analysis/bmi_trajectory/top_decile_change/top_decile_change_sex_adjusted.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive:
        table1: output/data/change_90th_sex_adjusted_lowbmiexc.csv
        table2: output/data/change_90th_wald_sex.csv


  topdecile_bmi_change_age_sex_adjusted:
    run: r:latest analysis/bmi_trajectory/top_decile_change/top_decile_change_age_sex_adjusted.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive:
        table1: output/data/change_90th_age_sex_adjusted_lowbmiexc.csv
        table2: output/data/change_90th_wald_age_sex.csv

##################################################################
### >> HAD_BMI ANALYSIS
######################################################################
# who had_bmi measured: 
  generate_had_bmi_proportion_2019:
    run: r:latest analysis/had_bmi_proportions_2019.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/proportion_had_bmi_2019.csv
  
  generate_had_bmi_proportion_2020:
    run: r:latest analysis/had_bmi_proportions_2020.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/proportion_had_bmi_2020.csv
  
  generate_had_bmi_proportion_2021:
    run: r:latest analysis/had_bmi_proportions_2021.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/proportion_had_bmi_2021.csv
 
## Look at odds of having BMI across the years
  had_bmi_2019_2021_models1:
    run: r:latest analysis/had_bmi_check/had_bmi_all_years_models.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/had_bmi_2019_21_models_1.csv

  had_bmi_2019_2021_models1_counts:
    run: r:latest analysis/had_bmi_check/had_bmi_all_years_models_counts.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/had_bmi_2019_21_models_1_counts.csv
        table2: output/data/had_bmi_2019_21_models_1_demographics.csv

  had_bmi_2019_2021_models_comorbidities:
    run: r:latest analysis/had_bmi_check/had_bmi_all_years_comorbidities_models.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/had_bmi_2019_21_comorbidity_models.csv
        table2: output/data/had_bmi_2019_21_comorbidity_models_counts.csv


  had_bmi_2019_2021_proportions:
    run: r:latest analysis/had_bmi_check/had_bmi_all_years_prop_chi.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/proportion_had_bmi_2019_2021.csv
        table2: output/data/proportion_had_bmi_2019_2021_chisquare.csv


## check the output from the cohort extractor 'had_bmi'

  had_bmi_proportion_2019_check:
    run: r:latest analysis/had_bmi_check/had_bmi_check_2019.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/proportion_had_bmi_check_2019.csv
        table2: output/data/had_bmi_numbers_check.csv

#########################################################
## PROPORTION OBESE ANALYSIS

  generate_obese_proportion_2019:
    run: r:latest analysis/obese_proportions_2019.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/proportion_obese_2019.csv


  generate_obese_proportion_2020:
    run: r:latest analysis/obese_proportions_2020.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/proportion_obese_2020.csv

  generate_obese_proportion_2021:
    run: r:latest analysis/obese_proportions_2021.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/proportion_obese_2021.csv






 ######################################################################################
 # >> Median BMI Analysis
 
 #######################################################################################

  
  
  # generate summary stats of median BMI by exposures
  generate_median_summary_stats:
    run: r:latest analysis/BMI_median_summary_stats.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/median_bmi_summary_table_demographic.csv
        table2: output/data/median_bmi_summary_table_covariates.csv
        
        
        
  ## tables of median BMI and range
  generate_median_bmi_range_2015:
    run: r:latest analysis/median_range_bmi/median_range_2015.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/median_range_bmi_2015.csv

  generate_median_bmi_range_2016:
    run: r:latest analysis/median_range_bmi/median_range_2016.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/median_range_bmi_2016.csv

  generate_median_bmi_range_2017:
    run: r:latest analysis/median_range_bmi/median_range_2017.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/median_range_bmi_2017.csv

  generate_median_bmi_range_2018:
    run: r:latest analysis/median_range_bmi/median_range_2018.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/median_range_bmi_2018.csv

  generate_median_bmi_range_2019:
    run: r:latest analysis/median_range_bmi/median_range_2019.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/median_range_bmi_2019.csv

  generate_median_bmi_range_2020:
    run: r:latest analysis/median_range_bmi/median_range_2020.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/median_range_bmi_2020.csv


  generate_median_bmi_range_2021:
    run: r:latest analysis/median_range_bmi/median_range_2021.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/median_range_bmi_2021.csv



  combine_median_range_BMI:
    run: r:latest analysis/median_range_bmi/combine_median_range_BMI.R --output-dir=output/data 
    needs: [generate_median_bmi_range_2021, generate_median_bmi_range_2020, generate_median_bmi_range_2019, generate_median_bmi_range_2018, generate_median_bmi_range_2017, generate_median_bmi_range_2016, generate_median_bmi_range_2015]
    outputs:
      moderately_sensitive:
        table1: output/data/median_range_bmi_2015_2021.csv


## Proportion Obese
  proportion_obese_2015:
    run: r:latest analysis/proportion_obese/proportion_obese_2015.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/obese_2015.csv

  proportion_obese_2016:
    run: r:latest analysis/proportion_obese/proportion_obese_2016.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/obese_2016.csv


  proportion_obese_2017:
    run: r:latest analysis/proportion_obese/proportion_obese_2017.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/obese_2017.csv

  proportion_obese_2018:
    run: r:latest analysis/proportion_obese/proportion_obese_2018.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/obese_2018.csv

  proportion_obese_2019:
    run: r:latest analysis/proportion_obese/proportion_obese_2019.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/obese_2019.csv

  proportion_obese_2020:
    run: r:latest analysis/proportion_obese/proportion_obese_2020.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/obese_2020.csv

  proportion_obese_2021:
    run: r:latest analysis/proportion_obese/proportion_obese_2021.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/obese_2021.csv

########## BMI_trajectory_data

  proportion_complete_bmi_trajectory:
    run: r:latest analysis/proportion_complete_BMI_trajectory.R --output-dir=output/data 
    needs: [BMI_trajectories_demographics_correction]
    outputs:
      moderately_sensitive:
        table1: output/data/complete_bmi_trajectories_proportions.csv

  bmi_change_plots:
    run: r:latest analysis/BMI_change_plot.R --output-dir=output/data 
    needs: [BMI_trajectories_demographics_correction]
    outputs:
      moderately_sensitive:
        table1: output/data/short_bmi_change_summary.csv
        chart1: output/bmi_change_plot.png
        chart2: output/bmi_change_plot_age.png
        chart3: output/bmi_change_plot_counts.png
        chart4: output/bmi_change_plot_age_precovid_counts.png
        chart5: output/bmi_change_plot_age_postcovid_counts.png


  bmi_change_extremes:
    run: r:latest analysis/BMI_change_check_extremes.R --output-dir=output/data 
    needs: [BMI_trajectories_demographics_correction]
    outputs:
      moderately_sensitive:
        table1: output/data/short_bmi_change_extremes.csv


  bmi_timeinterval_check:
    run: r:latest analysis/check_timeintervals_BMI_change.R --output-dir=output/data 
    needs: [generate_BMI_trajectories_data3]
    outputs:
      moderately_sensitive:
        table1: output/data/bmi_timeinterval_check.csv
        table2: output/data/time1_error.csv


  pandemic_bmi_changes:
    run: r:latest analysis/BMI_change_pandemic.R --output-dir=output/data 
    needs: [BMI_trajectories_demographics_correction]
    outputs:
      moderately_sensitive:
        table1: output/data/prepandemic_bmi_change_per_year.csv
        table2: output/data/postpandemic_bmi_change_per_year.csv
  

  pandemic_bmi_trajectory_plots:
    run: r:latest analysis/BMI_change_postcovid_plots.R --output-dir=output/data 
    needs: [BMI_trajectories_demographics_correction]
    outputs:
      highly_sensitive:
        table1: output/data/BMI_trajectory_data.feather
        table2: output/data/BMI_trajectory_data_filtered.feather
      moderately_sensitive:
        chart1: output/precovid_stable_bmi.png
        chart2: output/precovid_slow_inc_bmi.png
        chart3: output/precovid_mod_inc_bmi.png
        chart4: output/precovid_rapid_inc_bmi.png


## violin plots to see distribution before filtering
  postcovid_BMI_change_plots: 
    run: r:latest analysis/bmi_change_postcovid_distribution_plots.R --output-dir=output/data 
    needs: [pandemic_bmi_trajectory_plots]
    outputs:
      moderately_sensitive:
        chart1: output/SMI_postcovid_trajectory.png
        chart2: output/region_postcovid_trajectory.png
        chart3: output/precovid_traj_postcovid_trajectory.png
        chart4: output/bmi_postcovid_trajectory.png
        chart5: output/LD_postcovid_trajectory.png
        chart6: output/imd_postcovid_trajectory.png
        chart7: output/hypertension_postcovid_trajectory.png
        chart8: output/ethnic_postcovid_trajectory.png
        chart9: output/diabetes2_postcovid_trajectory.png
        chart10: output/diabetes1_postcovid_trajectory.png
        chart11: output/depression_postcovid_trajectory.png
        chart12: output/age_postcovid_trajectory.png

## stacked column charts showing proportion in different BMI change categories
  bmi_change_category_proportion_plots: 
    run: r:latest analysis/BMI_change_category_prop_plots.R --output-dir=output/data 
    needs: [BMI_trajectories_demographics_correction]
    outputs:
      highly_sensitive: 
        table1: output/data/BMI_trajectory_data_long.feather
      moderately_sensitive:
        chart1: output/category_bmi_change_depression.png
        chart2: output/category_bmi_change_ethnicity.png
        chart3: output/category_bmi_change_learning_diff.png
        chart4: output/category_bmi_change_region.png
        chart5: output/category_bmi_change_sex.png
        chart6: output/category_bmi_change_serious_mental.png
        chart7: output/category_bmi_change_t1dm.png
        chart8: output/category_bmi_change_t2dm.png
        chart9: output/category_bmi_change_imd.png
        chart10: output/category_bmi_change_hypertension.png

## description proportions in each change group
  bmi_change_groups_description: 
    run: r:latest analysis/bmi_trajectory/BMI_change_category_description.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/precovid_bmichange_description.csv
        table2: output/data/postcovid_bmichange_description.csv


## logistic regression predictors of rapid bmi change in pre and post covid period
  bmi_change_univariate: 
    run: r:latest analysis/BMI_change_rapid_univariate.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/rapid_bmi_change_univariate.csv
        table2: output/data/rapid_bmi_change_popcharac.csv

  bmi_change_age_adjusted: 
    run: r:latest analysis/BMI_change_rapid_age_model.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/rapid_bmi_change_age_adjusted.csv

## Predictors of rapid bmi change with cancer and low pre pandemic weight removed. 
  bmi_change_univariate_lowbmiexcluded: 
    run: r:latest analysis/BMI_change_rapid_lowbmi_excluded_univariate.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/rapid_bmi_change_cancerandlowbmi_removed_univariate.csv
        table2: output/data/rapid_bmi_change_cancerandlowbmi_removed_popcharac.csv

  bmi_change_age_adjusted_lowbmiexcluded: 
    run: r:latest analysis/BMI_change_rapid_lowbmi_excluded_age_models.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/rapid_bmi_change_cancerandlowbmi_removed_age_adjusted.csv

### RAPID CHANGE BMI - ADJUSTED MODELS
  bmi_rapid_change_sex_adjusted_lowbmiexcluded: 
    run: r:latest analysis/bmi_trajectory/rapid_bmi_change/rapid_change_cancerlowbmiexc_sex_adj.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/rapid_bmi_change_cancerandlowbmi_removed_sex_adjusted.csv


  bmi_rapid_change_imd_adjusted_lowbmiexcluded: 
    run: r:latest analysis/bmi_trajectory/rapid_bmi_change/rapid_change_cancerlowbmiexc_imd_adj.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/rapid_bmi_change_cancerandlowbmi_removed_imd_adjusted.csv

  bmi_rapid_change_ethnic_adjusted_lowbmiexcluded: 
    run: r:latest analysis/bmi_trajectory/rapid_bmi_change/rapid_change_cancerlowbmiexc_ethnic_adj.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/rapid_bmi_change_cancerandlowbmi_removed_ethnic_adjusted.csv


  bmi_rapid_change_sexage_adjusted_lowbmiexcluded: 
    run: r:latest analysis/bmi_trajectory/rapid_bmi_change/rapid_change_cancerlowbmiec_sexage_adj.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/rapid_bmi_change_cancerandlowbmi_removed_sexage_adjusted.csv

  bmi_rapid_change_imdsexage_adjusted_lowbmiexcluded: 
    run: r:latest analysis/bmi_trajectory/rapid_bmi_change/rapid_change_cancerlowbmiexc_imdsexage_adj.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/rapid_bmi_change_cancerandlowbmi_removed_imdsexage_adjusted.csv

  bmi_rapid_change_imdsexageethnic_adjusted_lowbmiexcluded: 
    run: r:latest analysis/bmi_trajectory/rapid_bmi_change/rapid_change_cancerlowbmiexc_imdsexageethnic_adj.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/rapid_bmi_change_cancerandlowbmi_removed_imdsexageethnic_adjusted.csv

## Top decile weight gain all
## TOP decile weight gain
  bmi_gain_top_decile_univariate.R: 
    run: r:latest analysis/bmi_trajectory/top_decile/top_decile_weightgain_univariate.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/weightgain_90th_popcharac.csv
        table2: output/data/weightgain_90th_univariate.csv
        table3: output/data/yearly_bmi_change_deciles.csv

  bmi_gain_top_decile_age: 
    run: r:latest analysis/bmi_trajectory/top_decile/top_decile_weightgain_age_adj.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/weightgain_90th_age_adj.csv

  bmi_gain_top_decile_sex: 
    run: r:latest analysis/bmi_trajectory/top_decile/top_decile_weightgain_sex_adj.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/weightgain_90th_sex_adj.csv

  bmi_gain_top_decile_imd: 
    run: r:latest analysis/bmi_trajectory/top_decile/top_decile_weightgain_imd_adj.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/weightgain_90th_imd_adj.csv

  bmi_gain_top_decile_eth: 
    run: r:latest analysis/bmi_trajectory/top_decile/top_decile_weightgain_ethnicity_adj.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/weightgain_90th_ethnicity_adj.csv

  bmi_gain_top_decile_agesex: 
    run: r:latest analysis/bmi_trajectory/top_decile/top_decile_weightgain_agesex.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/weightgain_90th_agesex_adj.csv


## change in BMI trajectory pre and post covid
  bmi_trajectory_change_summary: 
    run: r:latest analysis/BMI_change_diff_trajectories_summary.R --output-dir=output/data 
    needs: [BMI_trajectories_demographics_correction]
    outputs:
      highly_sensitive: 
        cohort1: output/data/BMI_trajectory_models_data.feather
      moderately_sensitive: 
        table1: output/data/mean_bmi_traj_change.csv
        chart1: output/change_bmi_trajectories.png
        chart2: output/change_bmi_trajectories_counts.png

  bmi_trajectory_change_summary_DWMP:
    run: r:latest analysis/BMI_change_diff_traj_summ_DWMP_groups.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/mean_bmi_traj_change_hypertension.csv
        table2: output/data/mean_bmi_traj_change_t2dm.csv
        table3: output/data/mean_bmi_traj_change_t1dm.csv


  bmi_trajectory_change_summary_mentalhealth_2:
    run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_change_traj_summ_mentalhealthLD_groups.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/mean_bmi_traj_change_depression.csv
        table2: output/data/mean_bmi_traj_change_learning_disability.csv
        table3: output/data/mean_bmi_traj_change_psychosis_schiz_bipolar.csv




  bmi_trajectory_change_model_univariate: 
    run: r:latest analysis/BMI_change_diff_trajectories_univariate.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/univariate_bmi_trajectory_change.csv
        table2: output/data/univariate_bmi_trajectory_change_hypertension.csv
        table3: output/data/univariate_bmi_trajectory_change_T1DM.csv
        table4: output/data/univariate_bmi_trajectory_change_T2DM.csv

  bmi_trajectory_change_model_age: 
    run: r:latest analysis/BMI_change_diff_trajectories_age_model.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/age_adjusted_bmi_trajectory_change.csv
        table2: output/data/age_adjusted_bmi_trajectory_change_hypertension.csv
        table3: output/data/age_adjusted_bmi_trajectory_change_T1DM.csv
        table4: output/data/age_adjusted_bmi_trajectory_change_T2DM.csv


  redact_bmi_trajectory_change_T1DM:
    run: r:latest analysis/redact_bmi_trajectory_change_T1DM.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary_DWMP, bmi_trajectory_change_model_univariate, bmi_trajectory_change_model_age]
    outputs:
      moderately_sensitive: 
        table1: output/data/mean_bmi_traj_change_t1dm_redacted.csv
        table2: output/data/univariate_bmi_traj_change_t1dm_redacted.csv
        table3: output/data/age_adj_bmi_traj_change_t1dm_redacted.csv

  bmi_trajectory_change_pop_with_depression: 
    run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_traj_change_lowbmi_exc_depression_models.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/depression_lowbmi_excluded_bmi_trajectory_change_univariate.csv
        table2: output/data/depression_lowbmi_excluded_bmi_trajectory_change_sex_adj.csv
        table3: output/data/depression_lowbmi_excluded_bmi_trajectory_change_age_adj.csv
        table4: output/data/depression_lowbmi_excluded_bmi_trajectory_change_ethnicity_adj.csv
        table5: output/data/depression_lowbmi_excluded_bmi_trajectory_change_imd_adj.csv
        table6: output/data/depression_lowbmi_excluded_bmi_trajectory_change_sexage_adj.csv
        table7: output/data/depression_lowbmi_excluded_bmi_trajectory_change_sexageimd_adj.csv
        table8: output/data/depression_lowbmi_excluded_bmi_trajectory_change_sexageeth_adj.csv
        table9: output/data/depression_lowbmi_excluded_bmi_trajectory_change_sexageethimd_adj.csv



  bmi_trajectory_change_pop_with_learning_diff: 
    run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_traj_change_lowbmi_exc_learning_diff_models.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_univariate.csv
        table2: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_sex_adj.csv
        table3: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_age_adj.csv
        table4: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_ethnicity_adj.csv
        table5: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_imd_adj.csv
        table6: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_sexage_adj.csv
        table7: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_sexageimd_adj.csv
        table8: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_sexageeth_adj.csv
        table9: output/data/learning_diff_lowbmi_excluded_bmi_trajectory_change_sexageethimd_adj.csv

  bmi_trajectory_change_pop_with_SMI: 
    run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_traj_change_lowbmi_exc_SMI_models.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_univariate.csv
        table2: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sex_adj.csv
        table3: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_age_adj.csv
        table4: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_ethnicity_adj.csv
        table5: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_imd_adj.csv
        table6: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sexage_adj.csv
        table7: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sexageimd_adj.csv
        table8: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sexageeth_adj.csv
        table9: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sexageethimd_adj.csv

  bmi_trajectory_change_pop_with_SMI_redact: 
    run: r:latest analysis/bmi_trajectory/trajectory_change/redact_SMI_traj_change.R --output-dir=output/data 
    needs: [bmi_trajectory_change_pop_with_SMI, bmi_trajectory_change_summary_mentalhealth_2]
    outputs:
      moderately_sensitive: 
        table1: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_univariate_redact.csv
        table2: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sex_adj_redact.csv
        table3: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_age_adj_redact.csv
        table4: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_ethnicity_adj_redact.csv
        table5: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_imd_adj_redact.csv
        table6: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sexage_adj_redact.csv
        table7: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sexageimd_adj_redact.csv
        table8: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sexageeth_adj_redact.csv
        table9: output/data/SMI_lowbmi_excluded_bmi_trajectory_change_sexageethimd_adj_redact.csv
        table10: output/data/mean_bmi_traj_change_psychosis_schiz_bipolar_redact.csv



## trajectory change calculations - with prepandemic underweight and cancer excluded
  bmi_trajectory_change_summary_lowbmi_excluded:
    run: r:latest analysis/BMI_change_diff_traj_summ_cancerandlowbmi_removed.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/mean_bmi_traj_change_cancerandlowbmi_removed_hypertension.csv
        table2: output/data/mean_bmi_traj_change_cancerandlowbmi_removed_t2dm.csv
        table3: output/data/mean_bmi_traj_change_cancerandlowbmi_removed_t1dm.csv
        table4: output/data/mean_bmi_traj_change_cancerandlowbmi_removed.csv

  bmi_trajectory_change_lowbmi_excluded_univariate: 
    run: r:latest analysis/BMI_trajectory_change_lowbmi_excluded_univariate.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/univariate_lowbmi_excluded_bmi_trajectory_change.csv
        table2: output/data/univariate_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
        table3: output/data/univariate_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
        table4: output/data/univariate_lowbmi_excluded_bmi_trajectory_change_T2DM.csv

  bmi_trajectory_change_lowbmi_excluded_age_adjusted: 
    run: r:latest analysis/BMI_trajectory_change_lowbmi_excluded_age_adjusted.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/age_adjusted_lowbmi_excluded_bmi_trajectory_change.csv
        table2: output/data/age_adjusted_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
        table3: output/data/age_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
        table4: output/data/age_adjusted_lowbmi_excluded_bmi_trajectory_change_T2DM.csv

## adjusted models
  bmi_trajectory_change_lowbmi_excluded_sex_adjusted: 
    run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_trajectory_change_lowbmi_excluded_sex_adjusted.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/sex_adjusted_lowbmi_excluded_bmi_trajectory_change.csv
        table2: output/data/sex_adjusted_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
        table3: output/data/sex_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
        table4: output/data/sex_adjusted_lowbmi_excluded_bmi_trajectory_change_T2DM.csv

  bmi_trajectory_change_lowbmi_excluded_imd_adjusted: 
    run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_trajectory_change_lowbmi_excluded_imd_adjusted.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/imd_adjusted_lowbmi_excluded_bmi_trajectory_change.csv
        table2: output/data/imd_adjusted_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
        table3: output/data/imd_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
        table4: output/data/imd_adjusted_lowbmi_excluded_bmi_trajectory_change_T2DM.csv

  bmi_trajectory_change_lowbmi_excluded_ethnic_adjusted: 
    run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_trajectory_change_lowbmi_excluded_ethnic_adjusted.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/ethnic_adjusted_lowbmi_excluded_bmi_trajectory_change.csv
        table2: output/data/ethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
        table3: output/data/ethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
        table4: output/data/ethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T2DM.csv





  bmi_trajectory_change_lowbmi_excluded_sexage_adjusted: 
    run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_trajectory_change_lowbmi_excluded_sexage_adjusted.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/sexage_adjusted_lowbmi_excluded_bmi_trajectory_change.csv
        table2: output/data/sexage_adjusted_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
        table3: output/data/sexage_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
        table4: output/data/sexage_adjusted_lowbmi_excluded_bmi_trajectory_change_T2DM.csv

  bmi_trajectory_change_lowbmi_excluded_sexageimd_adjusted: 
    run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_trajectory_change_lowbmi_excluded_sexageimd_adjusted.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/sexageimd_adjusted_lowbmi_excluded_bmi_trajectory_change.csv
        table2: output/data/sexageimd_adjusted_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
        table3: output/data/sexageimd_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
        table4: output/data/sexageimd_adjusted_lowbmi_excluded_bmi_trajectory_change_T2DM.csv

  bmi_trajectory_change_lowbmi_excluded_sexageethnic_adjusted: 
    run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_trajectory_change_lowbmi_excluded_sexageethnic_adjusted.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/sexageethnic_adjusted_lowbmi_excluded_bmi_trajectory_change.csv
        table2: output/data/sexageethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
        table3: output/data/sexageethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
        table4: output/data/sexageethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T2DM.csv



  bmi_trajectory_change_lowbmi_excluded_sexageimdethnic_adjusted: 
    run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_trajectory_change_lowbmi_excluded_sexageimdethnic_adjusted.R --output-dir=output/data 
    needs: [bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive: 
        table1: output/data/sexageimdethnic_adjusted_lowbmi_excluded_bmi_trajectory_change.csv
        table2: output/data/sexageimdethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_hypertension.csv
        table3: output/data/sexageimdethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM.csv
        table4: output/data/sexageimdethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T2DM.csv

  bmi_trajectory_change_lowbmi_excluded_T1DM_redact: 
    run: r:latest analysis/bmi_trajectory/trajectory_change/redact_T1DM_traj_change.R --output-dir=output/data 
    needs: [bmi_trajectory_change_lowbmi_excluded_sexageimdethnic_adjusted,  bmi_trajectory_change_lowbmi_excluded_sexageethnic_adjusted, bmi_trajectory_change_lowbmi_excluded_sexageimd_adjusted, bmi_trajectory_change_lowbmi_excluded_sexage_adjusted, bmi_trajectory_change_lowbmi_excluded_ethnic_adjusted, bmi_trajectory_change_lowbmi_excluded_imd_adjusted, bmi_trajectory_change_lowbmi_excluded_sex_adjusted, bmi_trajectory_change_lowbmi_excluded_age_adjusted, bmi_trajectory_change_lowbmi_excluded_univariate, bmi_trajectory_change_summary_lowbmi_excluded ]
    outputs:
      moderately_sensitive: 
        table1: output/data/mean_bmi_traj_change_cancerandlowbmi_removed_T1DM_redact.csv
        table2: output/data/univariate_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv
        table3: output/data/ethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv
        table4: output/data/sex_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv
        table5: output/data/sexageimdethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv
        table6: output/data/sexageethnic_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv 
        table7: output/data/sexageimd_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv
        table8: output/data/sexage_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv
        table9: output/data/imd_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv
        table10: output/data/age_adjusted_lowbmi_excluded_bmi_trajectory_change_T1DM_redact.csv


  bmi_trajectory_change_lowbmi_excluded_complete_data_proportions: 
    run: r:latest analysis/bmi_trajectory/trajectory_change/BMI_traj_change_complete_case_counts.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive: 
        table1: output/data/complete_traj_data_proportions.csv







## box plots with filtered data (excluding extreme changes
  bmi_change_boxplots: 
    run: r:latest analysis/bmi_change_boxplots.R --output-dir=output/data 
    needs: [BMI_trajectories_demographics_correction]
    outputs:
      moderately_sensitive:
        chart1: output/covid_bmi_change_cardiac.png
        chart2: output/covid_bmi_change_depression.png
        chart3: output/covid_bmi_change_ethnicity.png
        chart4: output/covid_bmi_change_learning_diff.png
        chart5: output/covid_bmi_change_region.png
        chart6: output/covid_bmi_change_sex.png
        chart7: output/covid_bmi_change_serious_mental.png
        chart8: output/covid_bmi_change_t1dm.png
        chart9: output/covid_bmi_change_t2dm.png
        chart10: output/covid_bmi_change_imd.png
        chart11: output/covid_bmi_change_hypertension.png

## Tables of BMI change categories
  bmi_change_category_tables: 
    run: r:latest analysis/BMI_change_trajectories_table.R --output-dir=output/data 
    needs: [bmi_change_category_proportion_plots]
    outputs:
      moderately_sensitive:
        table1: output/data/postcovid_bmi_trajectories.csv
        table2: output/data/precovid_bmi_trajectories.csv

### Transition between BMI categories
  generate_bmi_category_data: 
    run: r:latest analysis/BMI_cat_change_data.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      highly_sensitive:
        table1: output/data/BMI_category_transition.feather
      
## univariate models of transition between categories
  bmi_category_transitions: 
    run: r:latest analysis/BMI_category_transitions_univariate.R --output-dir=output/data 
    needs: [generate_bmi_category_data]
    outputs:
      moderately_sensitive:
        table1: output/data/bmi_category_transitions.csv
        table2: output/data/healthy_transition_weightgain_univariate.csv
        table3: output/data/healthy_transition_weightgain_2017_univariate.csv
        table4: output/data/healthy_transition_weightgain_2019_univariate.csv
        table5: output/data/overweight_transition_weightgain_univariate.csv 
        table6: output/data/overweight_transition_weightgain_2017_univariate.csv 
        table7: output/data/overweight_transition_weightgain_2019_univariate.csv 
        table8: output/data/overweight_transition_weightloss_univariate.csv 
        table9: output/data/overweight_transition_weightloss_2017_univariate.csv 
        table10: output/data/overweight_transition_weightloss_2019_univariate.csv 
        table11: output/data/obese_transition_weightloss_univariate.csv 
        table12: output/data/obese_transition_weightloss_2017_univariate.csv 
        table13: output/data/obese_transition_weightloss_2019_univariate.csv 


## age adjusted models of transition between categories
  bmi_category_transitions_age_adjusted: 
    run: r:latest analysis/BMI_category_transitions_age_adj.R --output-dir=output/data 
    needs: [generate_bmi_category_data]
    outputs:
      moderately_sensitive:
        table1: output/data/bmi_category_transitions_round.csv
        table2: output/data/healthy_transition_weightgain_age_adj.csv
        table3: output/data/healthy_transition_weightgain_2017_age_adj.csv
        table4: output/data/healthy_transition_weightgain_2019_age_adj.csv
        table5: output/data/overweight_transition_weightgain_age_adj.csv 
        table6: output/data/overweight_transition_weightgain_2017_age_adj.csv 
        table7: output/data/overweight_transition_weightgain_2019_age_adj.csv 
        table8: output/data/overweight_transition_weightloss_age_adj.csv 
        table9: output/data/overweight_transition_weightloss_2017_age_adj.csv 
        table10: output/data/overweight_transition_weightloss_2019_age_adj.csv 
        table11: output/data/obese_transition_weightloss_age_adj.csv 
        table12: output/data/obese_transition_weightloss_2017_age_adj.csv 
        table13: output/data/obese_transition_weightloss_2019_age_adj.csv 

  bmi_category_transitions_admin:
    run: r:latest analysis/admin_round_bmi_category_transitions.R --output-dir=output/data 
    needs: [bmi_category_transitions_age_adjusted]
    outputs:
      moderately_sensitive:
        table1: output/data/bmi_category_transitions_round_2.csv


  bmi_category_transitions_counts: 
    run: r:latest analysis/BMI_category_transitions_counts.R --output-dir=output/data 
    needs: [generate_bmi_category_data]
    outputs:
      moderately_sensitive:
        table1: output/data/healthy_transition_weightgain_counts.csv
        table2: output/data/overweight_transition_weightgain_counts.csv
        table3: output/data/overweight_transition_weightloss_counts.csv
        table4: output/data/obese_transition_weightloss_counts.csv





###########################  
###########################  
## DWMP Eligible



  generate_DWMP_proportion:
    run: r:latest analysis/DWMP_proportion.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/proportion_DWMP_eligible_2019.csv
        table2: output/data/proportion_DWMP_eligible_2020.csv
        table3: output/data/proportion_DWMP_eligible_2021.csv

  generate_DWMP_hypertension_proportion:
    run: r:latest analysis/DWMP_proportion_hypertension.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/proportion_DWMP_hypertension_2019.csv
        table2: output/data/proportion_DWMP_hypertension_2020.csv
        table3: output/data/proportion_DWMP_hypertension_2021.csv

  generate_DWMP_t2dm_proportion:
    run: r:latest analysis/DWMP_proportion_t2dm.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/proportion_DWMP_T2DM_2019.csv
        table2: output/data/proportion_DWMP_T2DM_2020.csv
        table3: output/data/proportion_DWMP_T2DM_2021.csv


  generate_DWMP_t1dm_proportion:
    run: r:latest analysis/DWMP_proportion_t1dm.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/proportion_DWMP_T1DM_2019.csv
        table2: output/data/proportion_DWMP_T1DM_2020.csv
        table3: output/data/proportion_DWMP_T1DM_2021.csv

  DWMP_2017_2021_counts:
    run: r:latest analysis/DWMP_counts.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/DWMP_counts_total_pop.csv
        table2: output/data/DWMP_counts_all_eligible.csv
        table3: output/data/DWMP_counts_hypertension.csv
        table4: output/data/DWMP_counts_T1DM.csv
        table5: output/data/DWMP_counts_T2DM.csv

  DWMP_2017_2021_models:
    run: r:latest analysis/DWMP_counts_models.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/univariate_DWMP_hypertension.csv
        table2: output/data/univariate_DWMP_T2DM.csv
        table3: output/data/univariate_DWMP_T1DM.csv
        table4: output/data/age_adjusted_DWMP_hypertension.csv
        table5: output/data/age_adjusted_DWMP_T2DM.csv
        table6: output/data/age_adjusted_DWMP_T1DM.csv


## TOTAL ELIGIBLE USING ALL BMI DATA FROM LAST 5 YEARS
  DWMP_eligible_5yr_data:
    run: r:latest analysis/DWMP_eligibility/DWMP_eligible.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/DWMP_eligible_5yr_data_all.csv
        table2: output/data/DWMP_eligible_5yr_data_hypertension.csv
        table3: output/data/DWMP_eligible_5yr_data_T1DM.csv
        table4: output/data/DWMP_eligible_5yr_data_T2DM.csv
        table5: output/data/DWMP_eligible_5yr_data_years.csv

  obese_eligible_5yr_data:
    run: r:latest analysis/DWMP_eligibility/Obese_5yr.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/obese_5yr_data_all.csv
        table2: output/data/obese_5yr_data_hypertension.csv
        table3: output/data/obese_5yr_data_T1DM.csv
        table4: output/data/obese_5yr_data_T2DM.csv
        table5: output/data/obese_5yr_data_years.csv

##################################################################
### >> HAD_SBP ANALYSIS
######################################################################
# who had_bmi measured: 
  generate_had_sbp_proportion_2019:
    run: r:latest analysis/had_sbp_proportions_2019.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/proportion_had_sbp_2019.csv


  generate_had_sbp_proportion_2020:
    run: r:latest analysis/had_sbp_proportions_2020.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/proportion_had_sbp_2020.csv


  generate_had_sbp_proportion_2021:
    run: r:latest analysis/had_sbp_proportions_2021.R --output-dir=output/data 
    needs: [generate_complete_median_BMI_data]
    outputs:
      moderately_sensitive:
        table1: output/data/proportion_had_sbp_2021.csv


############################################################
## Hba1c
##############################################################

  generate_hba1c_2018_2019_data:
    run: r:latest analysis/hba1c_2018_2019.R --output-dir=output/data --output-format feather
    needs: [join_meds]
    outputs:
      highly_sensitive:
        cohort1: output/data/hba1c_2019_summary.feather
        cohort2: output/data/hba1c_2018_summary.feather
        cohort3: output/data/hba1c_2019_long.feather
        cohort4: output/data/hba1c_2018_long.feather
        cohort5: output/data/precovid_hba1c_control.feather
       
  generate_hba1c_2020_2021_data:
    run: r:latest analysis/hba1c_2020_2021.R --output-dir=output/data --output-format feather
    needs: [join_meds]
    outputs:
      highly_sensitive:
        cohort1: output/data/hba1c_2020_summary.feather
        cohort2: output/data/hba1c_2021_summary.feather
        cohort3: output/data/hba1c_2021_long.feather
        cohort4: output/data/hba1c_2020_long.feather




  T2DM_hba1c_proportions_2019:
    run: r:latest analysis/hba1c_had_proportion_2019_t2dm.R --output-dir=output/data --output-format feather
    needs: [generate_hba1c_2018_2019_data]
    outputs:
      moderately_sensitive:
        table1: output/data/T2DM_proportion_hba1c_2019.csv

  T2DM_hba1c_proportions_2020:
    run: r:latest analysis/hba1c_had_proportion_2020_t2dm.R --output-dir=output/data --output-format feather
    needs: [generate_hba1c_2018_2019_data, generate_hba1c_2020_2021_data]
    outputs:
      moderately_sensitive:
        table1: output/data/T2DM_proportion_hba1c_2020.csv

  T2DM_hba1c_proportions_2021:
    run: r:latest analysis/hba1c_had_proportion_2021_t2dm.R --output-dir=output/data --output-format feather
    needs: [generate_hba1c_2018_2019_data, generate_hba1c_2020_2021_data]
    outputs:
      moderately_sensitive:
        table1: output/data/T2DM_proportion_hba1c_2021.csv


  check_hba1c:
    run: r:latest analysis/check_hba1c.R --output-dir=output/data --output-format feather
    needs: [generate_study_population_1]
    outputs:
      moderately_sensitive:
        table1: output/data/check_hba1c.csv


  merge_tables:
    run: r:latest analysis/combine_proportions.R --output-dir=output/data --output-format feather
    needs: [generate_median_bmi_range_2019, generate_median_bmi_range_2020, generate_median_bmi_range_2021, generate_DWMP_proportion, generate_DWMP_hypertension_proportion, generate_DWMP_t2dm_proportion, generate_DWMP_t1dm_proportion, generate_had_bmi_proportion_2019, generate_had_bmi_proportion_2020, generate_had_bmi_proportion_2021, generate_obese_proportion_2019, generate_obese_proportion_2020, generate_obese_proportion_2021, generate_had_sbp_proportion_2019, generate_had_sbp_proportion_2020, generate_had_sbp_proportion_2021]
    outputs:
      moderately_sensitive:
        table1: output/data/had_bmi_all.csv
        table2: output/data/proportion_obese_all.csv
        table3: output/data/had_sbp_all.csv
        table4: output/data/DWMP_all.csv
        table5: output/data/DWMP_hypertension_all.csv
        table6: output/data/DWMP_T2DM_all.csv
        table7: output/data/DWMP_T1DM_all.csv
        table8: output/data/BMI_median_range_all.csv
        
  round_tables:
    run: r:latest analysis/admin_round_redact_table.R --output-dir=output/data --output-format feather
    needs: [bmi_change_univariate, bmi_change_category_tables, bmi_trajectory_change_summary]
    outputs:
      moderately_sensitive:
        table1: output/data/rapid_bmi_change_popcharac_round.csv
        table2: output/data/precovid_bmi_trajectories.round.csv
        table3: output/data/postcovid_bmi_trajectories.round.csv
        table4: output/data/mean_bmi_traj_change_round.csv

  round_tables_2:
    run: r:latest analysis/admin_round_2.R --output-dir=output/data --output-format feather
    needs: [BMI_trajectories_demographics_correction]
    outputs:
      moderately_sensitive:
        table1: output/data/complete_bmi_trajectory_data.csv

###########
## SENSITIVITY ANALYSIS
###########

## Prepare for MICS

  MICE_data_1:
    run: r:latest analysis/sensitivity_analyses/MICE_data_prep1.R --output-dir=output/data --output-format feather
    needs: [BMI_trajectories_demographics_correction]
    outputs:
      highly_sensitive:
        table1: output/data/imputation_data_long.csv
  
  MICE_data_2:
    run: r:latest analysis/sensitivity_analyses/MICE_data_prep2.R --output-dir=output/data --output-format feather
    needs: [MICE_data_1]
    outputs:
      highly_sensitive:
        table1: output/data/imputation_dataframe.csv
        table2: output/data/imputation_DF_for_impute.csv
        table3: output/data/imputation_sample_missing.csv


  MICE_sample_data:
    run: r:latest analysis/sensitivity_analyses/MICE_sample_pop_demog.R --output-dir=output/data --output-format feather
    needs: [MICE_data_2]
    outputs:
      moderately_sensitive:
        table1: output/data/imputation_sample_pop_demographics.csv
        table2: output/data/imputation_sample_missing_data.csv


  MICE_model_check:
    run: r:latest analysis/sensitivity_analyses/MICE_model_check.R --output-dir=output/data --output-format feather
    needs: [MICE_data_1]
    outputs:
      highly_sensitive:
        table1: output/data/imputation_dataframe_check.csv
        table2: output/data/imputation_DF_for_impute_check.csv

  MICE_models_age:
    run: r:latest analysis/sensitivity_analyses/MICE_models_age_adj.R --output-dir=output/data --output-format feather
    needs: [MICE_data_2]
    outputs:
      moderately_sensitive:
        table1: output/data/imputation_age_adj.csv

  MICE_models_sex:
    run: r:latest analysis/sensitivity_analyses/MICE_models_sex.R --output-dir=output/data --output-format feather
    needs: [MICE_data_2]
    outputs:
      moderately_sensitive:
        table1: output/data/imputation_sex_adj.csv

  MICE_models_age_sex:
    run: r:latest analysis/sensitivity_analyses/MICE_models_age_sex.R --output-dir=output/data --output-format feather
    needs: [MICE_data_2]
    outputs:
      moderately_sensitive:
        table1: output/data/imputation_age_sex_adj.csv

  MICE_data_3:
    run: r:latest analysis/sensitivity_analyses/MICE_data_prep3.R --output-dir=output/data --output-format feather
    needs: [MICE_data_2, MICE_sample_data]
    outputs:
      moderately_sensitive:
        table1: output/data/imputation_univariate.csv
        table2: output/data/imputation_sample_pop_demographic_round.csv