directories.R

###########################################################
# SET DIRECTORIES
#
# Set and get directories in one place in the name of consistency
# and ease. Creates any directories that do not currently exist.
#
# OUTPUTS:
#	- A list of relevant directories (within o$pth) which can
#   be referenced throughout in the pipeline
#
###########################################################

# ---------------------------------------------------------
# Define paths for project inputs and outputs
# ---------------------------------------------------------
prepare_dirs = function(o) {
  
  # Initiate list with reference to main code directory
  #
  # NOTE: We should already be in this code directory
  pth = list(code = getwd())
  
  # ---- Input and configuration directories ----
  
  # Parent path of all input files
  pth$input  = file.path(pth$code, "input")
  pth$config = file.path(pth$code, "config")
  
  # Paths to VIMC and Gapminder inputs
  pth$vimc      = file.path(pth$input, "vimc")
  pth$gapminder = file.path(pth$input, "gapminder")
  
  # Parent path of all external model output files
  pth$extern   = file.path(pth$code,   "extern")
  pth$template = file.path(pth$extern, "template")
  
  # ---- Output directories ----
  
  # Parent path of all output files
  pth$output = file.path(pth$code, "output")
  
  # Path to cached data tables
  pth$tables = file.path(pth$output, "0_tables")
  
  # Path to static model assumptions and results
  pth$static   = file.path(pth$output, "1_static")
  pth$static_d = file.path(pth$static, "disease")
  pth$static_v = file.path(pth$static, "vaccine")
  pth$static_t = file.path(pth$static, "vaccine_type")
  
  # Path to imputation and impact function files
  pth$impute = file.path(pth$output, "2_impute")
  pth$impact = file.path(pth$output, "3_impact")
  
  # Path to figures and other output results
  pth$history = file.path(pth$output, "4_history")
  pth$infer   = file.path(pth$output, "5_infer")
  
  # Path to relative risk and impact factor files
  # pth$uncertainty = file.path(pth$output, "6_uncertainty")
  
  # Path to all figures
  pth$figures = file.path(pth$output, "6_figures")
  
  # Append paths to o list
  o = set_dirs(o, pth)
    
  return(o)
}

# ---------------------------------------------------------
# Make all output directories and append to o list
# ---------------------------------------------------------
set_dirs = function(o, pth) {
  
  # Iterate through dirs
  for (pth_name in names(pth)) {
    this_pth = pth[[pth_name]]
    
    # If it does not already exist, create it
    if (!dir.exists(this_pth)) {
      dir.create(this_pth, recursive = TRUE)
    }
    
    # Add a file separator to end of dir path
    pth[[pth_name]] = paste0(this_pth, file_sep())
  }
  
  # Append to o list
  o$pth = pth
  
  return(o)
}