remake.yml

## All R files that are used must be listed here:
packages:
  - data.table
  - LaF
  - bit64
  - stringr
  - stringi
  - PBSmapping
  - devtools

sources:
  - R/
  - man-roxygen/
  - pkgBuild/R/makeData.R
  - pkgBuild/R/update_spp.key.R
  - pkgBuild/R/update_rawData.R
  - pkgBuild/R/update_cleanData.R
  - pkgBuild/R/createSppKey.R  

## Most of a remakefile will be targets.  They can be listed in any
## order; whatever makes most sense.  Files can be split up and
## included into the main file if you need to impose more structure.
targets:
  ## 'all' is a special target that will be used as the default
  ## target by 'remake'.  It doesn't actually make anything but
  ## "depends" on other targets.
  all:
    depends:
      - clean_data
    command: 
      - document()

  # ======================
  # = Update Species Key =
  # ======================
  spp:
    depends:
      - data/spp.key.RData
      - helper_scripts
    command:
      - update_spp.key()
  
  inst/extdata/taxonomy/spp.key.csv:
    depends:
      - raw_data
      # - data/taxInfo.RData
      # - data/spp.corr1.RData
      # - data/getSppData.RData
      # - data/getTaxData.RData
      # - data/getCmmnData.RData
    command: 
      - update_spp.key(check_raw=TRUE)

  data/spp.key.RData:
    command: update_spp.key("inst/extdata/taxonomy/spp.key.csv")
  
  # ============================
  # = Scripts that affect data =
  # ============================
  raw_scripts:
    depends:
      - R/read.trawl.R
      - helper_scripts
  clean_scripts:
    depends:
      - R/clean.names.R
      - R/clean.format.R
      - R/clean.columns.R
      - R/clean.tax.R
      - R/clean.trimRow.R
      - helper_scripts
  helper_scripts:
    depends:
      - R/helperFile.R
      - R/helperMisc.R
      - R/helperStat.R
  
  # ===========================
  # = Update Raw .RData Files =
  # ===========================
  raw_data:
    depends:
      - data/raw.ai.RData
      - data/raw.ebs.RData
      - data/raw.gmex.RData
      - data/raw.goa.RData
      - data/raw.neus.RData
      - data/raw.newf.RData
      - data/raw.sa.RData
      - data/raw.sgulf.RData
      - data/raw.shelf.RData
      - data/raw.wcann.RData
      - data/raw.wctri.RData
      - raw_scripts
    command: 
      - document()
  data/raw.ai.RData:
    command: update_rawData("inst/extdata/ai.zip")
    depends:
      - raw_scripts
  data/raw.ebs.RData:
    command: update_rawData("inst/extdata/ebs.zip")
    depends:
      - raw_scripts
  data/raw.gmex.RData:
    command: update_rawData("inst/extdata/gmex.zip")
    depends:
      - raw_scripts
  data/raw.goa.RData:
    command: update_rawData("inst/extdata/goa.zip")
    depends:
      - raw_scripts
  neus_raw_files:
    command: c("inst/extdata/neus/neus-bigelow_fall_calibration.csv", "inst/extdata/neus/neus-bigelow_spring_calibration.csv", "inst/extdata/neus/neus-neusStrata.csv", "inst/extdata/neus/neus-station.RData", "inst/extdata/neus/neus-SurvDat.RData", "inst/extdata/neus/neus-SVSPP.RData")
  data/raw.neus.RData:
    command: update_rawData(neus_raw_files)
    depends:
      - raw_scripts
  data/raw.newf.RData:
    command: update_rawData("inst/extdata/newf.zip")
    depends:
      - raw_scripts
  data/raw.sa.RData:
    command: update_rawData("inst/extdata/sa.zip")
    depends:
      - raw_scripts
  data/raw.sgulf.RData:
    command: update_rawData("inst/extdata/sgulf.zip")
    depends:
      - raw_scripts
  data/raw.shelf.RData:
    command: update_rawData("inst/extdata/shelf.zip")
    depends:
      - raw_scripts
  data/raw.wcann.RData:
    command: update_rawData("inst/extdata/wcann.zip")
    depends:
      - raw_scripts
  data/raw.wctri.RData:
    command: update_rawData("inst/extdata/wctri.zip")
    depends:
      - raw_scripts
  
  
  # =============================
  # = Update Clean .RData Files =
  # =============================     
  clean_data:
    depends:
      - data/clean.ai.RData
      - data/clean.ebs.RData
      - data/clean.gmex.RData
      - data/clean.goa.RData
      - data/clean.neus.RData
      - data/clean.newf.RData
      - data/clean.sa.RData
      - data/clean.sgulf.RData
      - data/clean.shelf.RData
      - data/clean.wcann.RData
      - data/clean.wctri.RData
  data/clean.ai.RData:
    command: update_cleanData("data/raw.ai.RData")
    depends: 
      - clean_scripts
      - spp
      - data/spp.key.RData
  data/clean.ebs.RData:
    command: update_cleanData("data/raw.ebs.RData")
    depends: 
      - clean_scripts
      - spp
      - data/spp.key.RData
  data/clean.gmex.RData:
    command: update_cleanData("data/raw.gmex.RData")
    depends: 
      - clean_scripts
      - spp
      - data/spp.key.RData
  data/clean.goa.RData:
    command: update_cleanData("data/raw.goa.RData")
    depends: 
      - clean_scripts
      - spp
      - data/spp.key.RData
  data/clean.neus.RData:
    command: update_cleanData("data/raw.neus.RData")
    depends: 
      - clean_scripts
      - spp
      - data/spp.key.RData
  data/clean.newf.RData:
    command: update_cleanData("data/raw.newf.RData")
    depends: 
      - clean_scripts
      - spp
      - data/spp.key.RData
  data/clean.sa.RData:
    command: update_cleanData("data/raw.sa.RData")
    depends: 
      - clean_scripts
      - spp
      - data/spp.key.RData
  data/clean.sgulf.RData:
    command: update_cleanData("data/raw.sgulf.RData")
    depends: 
      - clean_scripts
      - spp
      - data/spp.key.RData
  data/clean.shelf.RData:
    command: update_cleanData("data/raw.shelf.RData")
    depends: 
      - clean_scripts
      - spp
      - data/spp.key.RData
  data/clean.wcann.RData:
    command: update_cleanData("data/raw.wcann.RData")
    depends: 
      - clean_scripts
      - spp
      - data/spp.key.RData
  data/clean.wctri.RData:
    command: update_cleanData("data/raw.wctri.RData")
    depends: 
      - clean_scripts
      - spp
      - data/spp.key.RData