11_mass_fractions.yml

target_default: 11_mass_fractions

packages:
  - pah
  
include:
  - 10_qa_summary.yml
  
targets:
  11_mass_fractions:
    depends:
      - percent_by_weight_summary
      - percent_by_weight_bysample
      - 11_mass_fractions/doc/percent_by_weight_bysample.png
      - 11_mass_fractions/doc/percent_by_weight_bysample.pdf
      - 11_mass_fractions/doc/percent_by_weight_bysample_alt.png

      
  percent_by_weight_summary:
    command: calc_mass_fractions(compound_info = samples, sample_column = I('unique_id'), conc_column = I('RESULT'), compound_column = I('PARAM_SYNONYM'), conc_unit = I('ppb'), calc_type = I('summary'))
    # this uses summary statistics of the samples (quartiles, min, max, mean) to calculate percent
    # mass fractions. Also reports source concentrations, number of PAHs summed, etc.
    
  percent_by_weight_bysample:
    command: calc_mass_fractions(compound_info = samples, sample_column = I('unique_id'), conc_column = I('RESULT'), compound_column = I('PARAM_SYNONYM'), conc_unit = I('ppb'), calc_type = I('by_sample'))
    # this calculates mass fraction for each source-sample combination. 
    # each row is a different sample, and sources are in columns.
    
  11_mass_fractions/doc/percent_by_weight_bysample.png:
    command: calc_mass_fractions(compound_info = samples, sample_column = I('unique_id'), conc_column = I('RESULT'), compound_column = I('PARAM_SYNONYM'), conc_unit = I('ppb'), calc_type = I('by_sample'), plot = TRUE, sample_order = I('norm_pah_conc'))
    plot: {width: 12, height: 5, unit: 'in', res: 600}
    # this plots the sample-specific mass fractions using a tile plot, which is colored by 
    # percent mass fraction value categories. Samples are listed from high to low PAH16 concentration(top to bottom), 
    # and sources are listed from low to high reported mean concentration (left to right)
    
  11_mass_fractions/doc/percent_by_weight_bysample.pdf:
    command: calc_mass_fractions(compound_info = samples, sample_column = I('unique_id'), conc_column = I('RESULT'), compound_column = I('PARAM_SYNONYM'), conc_unit = I('ppb'), calc_type = I('by_sample'), plot = TRUE, sample_order = I('norm_pah_conc'))
    plot: {width: 12, height: 5}
    # PDF version of above plot
    
  11_mass_fractions/doc/percent_by_weight_bysample_alt.png:
    command: calc_mass_fractions(compound_info = samples, sample_column = I('unique_id'), conc_column = I('RESULT'), compound_column = I('PARAM_SYNONYM'), conc_unit = I('ppb'), calc_type = I('by_sample'), plot = TRUE, sample_order = I('pah_conc'))
    plot: {width: 12, height: 5, unit: 'in', res: 600}
    # this plots the sample-specific mass fractions using a tile plot, which is colored by 
    # percent mass fraction value categories. Samples are listed from high to low PAH16 concentration(top to bottom), 
    # and sources are listed from low to high reported mean concentration (left to right)