remake.yml

packages:
  - bibtex
  - metafor
  - grid
  - gridExtra
  - lme4
  - ggplot2
  - tinytex

sources:
  - R

targets:
  all:
    depends:
      - ms/ms.pdf

  ms/ms.pdf:
    command: pdflatex("ms/ms.tex")
    depends:
      - figures_main
      - ms/ms-suppinfo.pdf
      - ms/refs-main.bib
      
  ms/ms-suppinfo.pdf:
    command: pdflatex("ms/ms-suppinfo.tex")
    # Don't clean because we need info for cross references
    depends:
      - figures_suppmat
      - ms/refs-suppmat.bib

  ms/ms-suppinfo.tex:
    depends:
      - R/model.R
      - GCi
      - GIi
      - Snapshot
      - read_bib
    knitr: TRUE
    
  figures_main:
    depends:
      - output/Fig1.pdf
      - output/Fig2.pdf
      - output/Fig3.pdf
      - output/Fig4.pdf

  figures_suppmat:
    depends:
      - output/FigA1.pdf
      - output/FigA2.pdf
      - output/FigA3.pdf
      - output/FigA4.pdf
      - output/FigA5.pdf
      - output/FigA6a.pdf
      - output/FigA6b.pdf
      - output/FigA6c.pdf
      - output/FigA7.pdf
      - output/FigA8.pdf
      - output/FigA9.pdf
      - output/GraphicalAbstract.pdf

# ------- References --------------------------

  paper_bib:
    command: read.bib("references/paper.bib")

  meta_bib:
    command: read.bib("references/metaanalyses.bib")

  combined_bib:
    command: merge_bib_files(meta_bib, paper_bib)

  ms/refs-main.bib:
    command: write.bib(combined_bib, file = target_name)

  suppmat_bib:
    command: merge_bib_files(combined_bib, read_bib)

  ms/refs-suppmat.bib:
    command: write.bib(suppmat_bib, file = target_name)

  read_bib:
    command: read.bib("references/read.bib")

# ------- data formatting --------------------
  # Data for top 19 traits
  AllData:
    command: clean_raw_data("data/CompileData.csv")

  CleanData:
    command: standardise_data(AllData)

  # Data for top 5 traits
  CompleteData:
    command: build_complete_data(CleanData)

  CompleteData_inter:
    command: Build_intersp_complete_data(CleanData)

  IdealData:
    command: build_ideal_data(CompleteData)

  CoordTable:
    command: build_map_data(CleanData)

  IdealData_rgr:
    command: subset_growth(IdealData, I("RGR"))

  IdealData_agr:
    command: subset_growth(IdealData, I("AbGR"))

  CompleteData_rgr:
    command: subset_growth(CompleteData_inter, I("RGR"))

  CompleteData_agr:
    command: subset_growth(CompleteData_inter, I("AbGR"))

  GCi:
    command: list_by_trait(CompleteData_inter)

  GIi:
    command: list_by_trait(IdealData)

  GIrgr:
    command: list_by_trait(IdealData_rgr)

  GIagr:
    command: list_by_trait(IdealData_agr)

  GCrgr:
    command: list_by_trait(CompleteData_rgr)

  GCagr:
    command: list_by_trait(CompleteData_agr)
  
  ## List of article recorded with the snapshot of literature  
  Snapshot:
    command: snapshot_websci("data/ref.traits/WebSci_all.csv")

  ## Create restricted Dataset: coefficient of correlation are averaged by study
  ## and by trait
  RCi1:
    command:
      - EffectSizeSum(CompleteData_rgr)

  RCi:
    command:
      - list_by_trait(RCi1)

  RIi1:
    command:
      - EffectSizeSum(IdealData_rgr)

  RIi:
    command:
      - list_by_trait(RIi1)

  ## Export compiled data
  output/data.csv:
    command: write.csv(CleanData, target_name, row.names = FALSE)

# ------- plots --------------------

  output/Fig1.pdf:
    command: figure_1(CleanData)
    plot:
      height: 3
      width:  4

  output/Fig2.pdf:
    command: figure_2(CompleteData_inter)
    plot:
      height: 9
      width:  4

  output/Fig3.pdf:
    command: figure_3(GIrgr,GCrgr )
    plot:
      height: 5
      width:  4


  output/Fig4.pdf:
    command: figure_4(GCi)
    plot:
      height: 5
      width:  4

## Figures appendix

  downloads/baad.rds:
    command: download_baad(target_name)
    packages: downloader
    cleanup_level: never

  baad:
    command: readRDS("downloads/baad.rds")

  output/FigA1.pdf: # allometry
    command: figure_A1(baad)
    plot:
      height: 3
      width:  9

  output/FigA2.pdf:  #map
    command: figure_A2(CoordTable)
    plot:
      height: 3
      width:  6

  output/FigA3.pdf:
    command: figure_A3(GCi)
    plot:
      height: 6
      width:  6

  output/FigA4.pdf:
    command: figure_A4(GIi, GIrgr, GIagr)
    plot:
      height: 6
      width:  5

  output/FigA5.pdf:
    command: figure_A5(RIi, RCi)
    plot:
      height: 6
      width:  5

  output/FigA6a.pdf:
    command: figure_A6(GCi, I("SLA"), I("WD"), I(c("a", "b")))
    plot: TRUE

  output/FigA6b.pdf:
    command: figure_A6(GCi, I("Aarea"), I("Seedmass"), I(c("c", "d")))
    plot: TRUE

  output/FigA6c.pdf:
    command: figure_A6.2(GCi, I("Hmax"), I("e"))
    plot: TRUE

  output/FigA7.pdf:
    command: figure_A7(GCi)
    plot: TRUE

  output/FigA8.pdf:
    command: figure_A8(GCi)
    plot: TRUE

  output/FigA9.pdf:
    command: figure_A9(GCi)
    plot: TRUE

  output/GraphicalAbstract.pdf:
    command: figure_graphical_abstract(GIi, GIrgr, GIagr)
    plot:
      height: 3
      width:  4