5_compare_data.yml

target_default: 5_compare_data

packages:
  - dplyr
  - tidyr
  - ggplot2
  - dataRetrieval
  - readxl
  
include:
  - 4_summarize_data.yml

sources:
  - 5_compare_data/src/compare_data.R
  
targets:
  5_compare_data:
    depends:
      - all_studies
      - battelle_5507_recovery
      - 5_compare_data/doc/spike_comparison.pdf
      - glri_battelle_5433
      - glri_battelle_5433_comparison
  
  all_studies:
    command: merge_studies(sample_dat = samples, comparison_dat = processed_5507)
    
  battelle_5507_recovery: 
    command: merge_recovery(sample_dat = samples, comparison_dat = processed_5507, sample_rec_sur = pct_rec_surrogates, mke_rec_sur = pct_rec_surrogates_5507, sample_rec_mspikes = pct_rec_mspikes, mke_rec_mspikes = pct_rec_mspikes_5507)
  
  5_compare_data/doc/spike_comparison.pdf: 
    command: plot_spikes(recovery_dat = battelle_5507_recovery, plot_location = target_name)
  
  5_compare_data/doc/surrogate_comparison.pdf: 
    command: plot_surrogates(recovery_dat = battelle_5507_recovery, plot_location = target_name)
    
  glri_battelle_5433:
    command: merge_glri_5433(dat_glri = samples, dat_5433 = raw_5433)
    # this merges the 69 sites with 6 PAH compounds in common between the battelle and 
    # NWQL lab data for the GLRI study
    
  glri_battelle_5433_comparison:
    command: compare_nwql_battelle(merged_dat = glri_battelle_5433, samples_dat = samples)
    # This makes several comparison plots and stores them in 'doc'
    
  glri_battelle_5433_spikes_comp:
    command: compare_spikes(battelle = pct_rec_mspikes, mspikes_5433 = pct_rec_mspikes_5433)