26_mixtures.yml

target_default: 26_mixtures

packages:
  - dplyr
  
include:
  - 25_rank_data.yml
  
## All R files that are used must be listed here:
sources:
  - 26_mixtures/src/get_mixtures.R
  
targets:
  26_mixtures:
    depends: 
      - EARsum_endpoint
      
  EARsum_endpoint:
    command: sum_endpoints(chemicalSummary_deg_meto, filter_cutoffs = TRUE)
    
  EARsum_endpoint_nofilter:
    command: sum_endpoints(chemicalSummary_deg_meto, filter_cutoffs = FALSE)
    
  contributing_chems:
    command: calc_contr_chems(EARsum_endpoint)
    
  top_mixes:
    command: calc_top_mixtures(contributing_chems)
    
  top_mixes_all:
    command: calc_top_mixtures(contributing_chems, max_only = FALSE)
    
  mixtures_summary_all:
    command: summarize_mixtures(top_mixtures = top_mixes_all)
    
  mixtures_summary:
    command: summarize_mixtures(top_mixtures = top_mixes)
    
  mixtures_n_summary_all:
    command: summarize_by_n(top_mixtures = top_mixes_all)
    
  mixtures_n_summary:
    command: summarize_by_n(top_mixtures = top_mixes)
    
  figure/mixtures_summary_all.png:
    command: plot_mix_summary(
      out_file = target_name,
      n_summary = mixtures_n_summary_all, 
      mix_summary = mixtures_summary_all, 
      top_mixtures = top_mixes_all, 
      ear_sum = EARsum_endpoint)
      
  figure/mixtures_summary_limited.png:
    command: plot_mix_summary(
      out_file = target_name,
      n_summary = mixtures_n_summary, 
      mix_summary = mixtures_summary, 
      top_mixtures = top_mixes, 
      ear_sum = EARsum_endpoint)

  chem_mix_metrics:
    command: calc_chem_mix_metrics(top_mixtures = top_mixes, summed_EARs = EARsum_endpoint, target_name)
  
  chem_mix_metrics_all:
    command: calc_chem_mix_metrics(top_mixtures = top_mixes_all, summed_EARs = EARsum_endpoint, target_name)
   
  26_mixtures/out/chem_mix_metrics_all.csv:
    command: write.csv(chem_mix_metrics_all, target_name, row.names = FALSE)
  
  site_mix_metrics:
    command: calc_site_mix_metrics(top_mixtures = top_mixes, chemicalSummary_conc)

  site_mix_metrics_all:
    command: calc_site_mix_metrics(top_mixtures = top_mixes_all, chemicalSummary_conc)