remake.yml

packages:
  - rotl
  - ape
  - rfishbase
  - brms
  - parallel
  - Hmisc
  - LoLinR
  - extrafont
  - fontcm
  - noaaErddap
  - ncdf4
  - plyr
  - zoo
  - tools
  - raster
  - envPred
  - knitr
  - rmarkdown

sources:
  - R/analyses.R
  - R/figures.R
  - R/tables.R

targets:
  all:
    depends:
      - noaaErddapLayersExist
      - output/tables/table1.csv
      - output/tables/table2.csv
      - output/tables/tableS1.csv
      - output/figures/fig1.pdf
      - output/figures/fig2.pdf
      - output/figures/fig3.pdf

  # data crunching
  noaaErddapLayersExist:
    command: checkIfNoaaErddapLayersExist()

  # phylogenetic Actinopterygii tree
  # downloaded on 01 / Dec / 2017
  tree:
    command: downloadAndProcessTree()

  otlSubs:
    command: readFile('data/otlSppSubstitutions.csv')

  spawningModeTab:
    command: readFile('data/spawningMode.csv')

  phyloTreeAndData:
    command: cleanAndExtractPhyloTreeAndMatchedData(tree = tree, otlSubs = otlSubs, filePath = 'data/fishEggsMSData.csv')

  coordinates:
    command: makeCoordinatesTable(phyloTreeAndData)

  chlTable:
    command: matchNcdfDataFrameStyle(I('chlorophyll'), coordinates)

  sstTable:
    command: matchNcdfDataFrameStyle(I('sst'), coordinates)

  predictabilityTable:
    command: makeEnvironmentalPredictabilityTable(chlTable, sstTable)

  abioticData:
    command: produceAbioticData(chlTable, sstTable, predictabilityTable)

  filteredData:
    command: filterDataForAnalysis(phyloTreeAndData, abioticData)

  # data analysis  
  allModels:
    command: runAllModels(filteredData)

  spawningCheckModel:
    command: runSpawningCheckModel(filteredData, spawningModeTab)

  comparisonTab:
    command: looComparison(allModels)

  # tables
  table1:
    command: makeTable1(filteredData)

  output/tables/table1.csv:
    command: writeTable1(dest = target_name, table1)

  table2:
    command: makeTable2(allModels)

  output/tables/table2.csv:
    command: writeTable2(dest = target_name, table2)

  tableS1:
    command: makeTableS1(spawningCheckModel)

  output/tables/tableS1.csv:
    command: writeTableS1(dest = target_name, tableS1)

  # figures
  output/figures/fig1.pdf:
    command: makeFig1(dest = target_name, data = filteredData)

  output/figures/fig2.pdf:
    command: makeFig2(dest = target_name, filteredData = filteredData, allModels = allModels)

  output/figures/fig3.pdf:
    command: makeFig3(dest = target_name, filteredData = filteredData, allModels = allModels)