10_load_data.yml

target_default: 10_load_data

packages:
  - readxl
  - dplyr
  - httr
  - googlesheets
  - yaml
  - dataRetrieval
  - tidyr
  - readr
  - toxEval
  
## All R files that are used must be listed here:
sources:
  - 10_load_data/src/get_neonic_data.R
  - 10_load_data/src/get_NWIS.R
  - 10_load_data/src/get_tracking.R
  - 10_load_data/src/get_schedules.R
  - 10_load_data/src/get_AOPs.R
  - 10_load_data/src/process_raw_bench.R
  - 10_load_data/src/get_chem_info.R
  - 10_load_data/src/fix_classes.R

targets:
  10_load_data:
    depends: 
      - sites
      - tracking
      - neonic
      - pesticides
      - glyphosate
      - NWIS
      - owc
      - 10_load_data/benchmarks.csv
      - classes
      - schedules
      - schedule_pCodes
      - benchmarks
      - benchmarks_hbs
      - exclusions
      - AOP
      - chem_crosswalk
      
  tracking:
    command: get_tracking_data('10_load_data/cfg/tracking_config.yaml')

  sites:
    command: get_sites(tracking,"10_load_data/raw/GLRISPSites2016.rds")
  
  AOP:
    command: get_AOPs("10_load_data/raw/AOP_crosswalk.csv")
  
  #neonic:
  #  command: >-
  #    get_neonic_data("10_load_data/raw/GLRI_Neonic_to_NWIS_011317.csv", 
  #                    "10_load_data/raw/neonicMDLs.csv",
  #                    sites,
  #                    tracking)
    
  pCodesExclude:
    command: get_pCode_exclude("10_load_data/pCodes_Exclude.txt")

  chem_crosswalk:
    command: get_chem_info('10_load_data/raw/pesticides_s2437_analyte_info.csv')
  
  classes: 
    command: get_csv("10_load_data/chemical_classes.csv")
    
  classes_fixed:
    command: fix_classes(classes)
    
  schedules:
    command: c(I("2437"), I("4433"))
    
  schedule_pCodes:
    command: get_schedules(schedules)
    
  NWIS:
    command: get_NWIS(tracking)
    
  pesticides:
    command: filter_pesticides(NWIS, schedule_pCodes, pCodesExclude)
    
  neonic: 
    command: filter_neonics(NWIS)
    
  glyphosate:
    command: filter_glyphosate(NWIS)
    
  owc:
    command: filter_owc(NWIS, schedule_pCodes)
    
  10_load_data/benchmarks.csv:
    command: process_benchmarks(in_file = '10_load_data/raw/20180305_EPA_ALBenchmarks.csv', out_file = target_name)
    
  10_load_data/hbs_levels.csv:
    command: process_hsbls(in_pesticides = '10_load_data/raw/20180312_hbsl_data_pesticides.csv', in_degradates = '10_load_data/raw/20180312_hbsl_data_pesticide_degradates.csv', out_file = target_name)
  
  benchmarks:
    command: get_csv("10_load_data/benchmarks.csv")
    
  benchmarks_hbs:
    command: get_csv("10_load_data/hbs_levels.csv")
    
  pCodeInfo:
    command: get_pCode(NWIS)
    
  exclusions:
    command: get_csv("10_load_data/exclusions.csv")