remake.yml

packages:
  - rmarkdown
  - knitr
  - maps
  - parallel
  - MASS
  - quantreg
  - splines
  - bibtex

sources:
  - R

targets:
  all:
    depends:
      - manuscript
      - data

  manuscript:
    depends:
      - ms/metadata.html
      - ms/metadata.docx


  data:
    depends:
      - data_c
      - data_m
      - data_p
      - df_growth
      - output/table_plot.csv
      - output/table_stand_descrip.csv
      - output/table_stand_allo.csv
      - output/species_code.csv
      - output/status_code.csv
      - output/metadata_data_p.csv
      - output/metadata_data_m.csv
      - output/metadata_data_c.csv


  ms/metadata.md:
    knitr:
      chdir: true
      auto_figure_prefix: true
    packages:
      - whisker
    depends:
      - data
      - ms/refs.bib
      - R/ms.R

  data_c:
    command:  get_data("output/data_c.csv")

  data_m:
    command:  get_data("output/data_m.csv")

  data_p:
    command:  get_data("output/data_p.csv")

  output/data_sp_code.csv:
    command: data_sp_code(data_c)

  df_growth:
    command: get_data('output/df_growth.csv')

  output/df_growth.csv:
    command: save_data_growth(data_m, data_c)

  output/table_plot.csv:
    command: table_plot(data_p)

  output/table_stand_descrip.csv:
    command: table_stand_descrip(data_p, data_m, data_c)

  output/table_stand_allo.csv:
    command: table_stand_allo(data_p, data_m, data_c)

  ms/metadata.html:
    command: render_html("ms/metadata.md")
    quiet: true
    depends:
      - ms/metadata.Rmd

  ms/metadata.docx:
    command: render_doc("ms/metadata.md")
    quiet: true
    depends:
      - ms/metadata.Rmd