2_process_data.yml

target_default: 2_process_data

packages:
  - dplyr
  
include:
  - 1_get_raw_data.yml
  
sources:
  - 2_process_data/src/process_data.R
  
targets:
  2_process_data:
    depends:
      - processed_sample_merge
      - processed_sample
      - processed_5507
      - processed_5433
  
  processed_sample_merge: 
    command: process_sample_merge(raw_sample, raw_site)
    # merges samples with site metadata, uses pah::get_compound_info to also merge
    # with compound-specific metadata (e.g., molecular weight)
    
  processed_sample:
    command: process_nondetects(processed_sample_merge, detect.decision = I("zero"),
                               code.column = I("LAB_QUAL"), detect.code = I("U"), 
                               detect.limit.column = I("DETECT_LIMIT"))
    # turns values BDL into zeros
    
  processed_5507:
    command: process_mke(raw = raw_5507)
    # turns values BDL into zeros
    
  processed_5433:
    command: process_5433(raw = raw_5433)
    # turns values BDl into zeros