30_reports.yml

target_default: 30_reports

include:
  - 26_mixtures.yml
  
packages:
  - knitr
  - rmarkdown
  - toxEval
  - openxlsx
  - dplyr
  - tidyr
  - ggplot2
  - yaml
  - RColorBrewer
  
sources:
  - 30_reports/src/render.R
  - 30_reports/src/create_tables.R
  - 30_reports/src/create_figures.R
  
targets:
  30_reports:
    depends:
      #- reports/fig2.html
      #- reports/fig3.html
      - reports/method_comparison.html
      #- figure/ToxCast_class.png
      #- figure/Benchmark_class.png
      #- figure/Conc_class.png
      #- figure/ToxCast_bio.png
      
  fig2.md:
    depends: 
      - chemicalSummary
      - site_info
    knitr: 
      input: 30_reports/fig2.Rmd
    cleanup_level: purge
    
  reports/fig2.html:
    command: render_html("fig2.md", target_name)
    cleanup_level: purge
    
  fig3.md:
    depends: 
      - chemicalSummary
      - site_info
    knitr: 
      input: 30_reports/fig3.Rmd
    cleanup_level: purge
    
  reports/fig3.html:
    command: render_html("fig3.md", target_name)
    cleanup_level: purge
    
  method_comparison.md:
    depends:
      - glyphosate_clean
      - pesticides_clean
      - neonics_clean
    knitr:
      input: 30_reports/method_comparison.Rmd
    cleanup_level: purge
    
  reports/method_comparison.html:
    command: render_html("method_comparison.md", target_name)
 
  cbValues:
    command: get_colors(chemicalSummary_conc)

  figure/ToxCast_class.png:
    command: plot_class_summaries(target_name, chemicalSummary, I("Chemical Class"), I("ToxCast"))

  figure/Benchmark_class.png:
    command: plot_class_summaries(target_name, chemicalSummary_bench, I("Chemical Class"), I("Benchmarks"))

  figure/Conc_class.png:
    command: plot_class_summaries(target_name, chemicalSummary_conc, I("Chemical Class"), I("Concentration"))

  figure/ToxCast_bio.png:
    command: plot_class_summaries(target_name, chemicalSummary, I("Biological"), I("ToxCast"))

  figure/facet_class.png:
     command: plot_facet_class(target_name, chemicalSummary, chemicalSummary_bench, chemicalSummary_conc)

  landuse_fig:
    command: plot_landuse(I("figure/landuse.png"), sites)
    
  stacK_fig:
    command: plot_stacks(I("figure/stack.png"), sites, chemicalSummary, site_info)