remake.yml

packages:
  - readr
  - rstan
  - dplyr
  - cowplot
  - ggplot2
  - bookdown
  - rmarkdown
  

sources:
  - 'R'

plot_options:
  2col_square:
    width: 6.6
    height: 6.6
    
  1col_portrait:
    width: 3.46
    height: 6.6
    
targets:
  all:
    depends:
      - resprout_model
      - figures/mortality_partial_plots.pdf
      - figures/count_partial_plots.pdf
      - figures/tribe_effects.pdf
      - figures/spp_effects.pdf
      - manuscript/supplementary.pdf
 
  #------------- Load data --------------------------- 
  resprout_data:
    command: load_data("raw_data/data.csv")
    cleanup_level: purge

  #------------- Run stan models ---------------------------
  resprout_model:
    command: run_stan_model(resprout_data)
    cleanup_level: purge
  
  #------------- make figures ---------------------------
  figures/mortality_partial_plots.pdf:
    command: plot_partial_mortality(resprout_model)
    plot: 2col_square

  figures/count_partial_plots.pdf:
    command: plot_partial_count(resprout_model)
    plot: 2col_square

  figures/tribe_effects.pdf:
    command: plot_tribe_effects(resprout_model)
    plot: 1col_portrait

  figures/spp_effects.pdf:
    command: plot_spp_effects(resprout_model)
    plot: 1col_portrait

  #------------- supplemental material ---------------------------
  manuscript/supplementary.pdf:
    command: render("manuscript/supplementary.Rmd")