Creates post-processing output for Atlantis

compare_spatial_vars(
  param.dir,
  run.dirs,
  run.names,
  ref.data,
  init.data,
  out.dir,
  out.name,
  param.ls,
  data.type = "proportion",
  comparison.type = "difference",
  ref.years,
  speciesCodes = NULL,
  plot = T
)

Arguments

param.dir: string. Path to location of atlantis parameter files
run.dirs: character vector of paths to location of atlantis output files
run.names: character vector of run names corresponding to run.dirs
ref.data: dataframe that contains reference spatial data with format (polygon|species|var.name|statistic|ref.value)
init.data: dataframe that contains initial spatial data with format (polygon|species|var.name|statistic|init.value)
out.dir: string. path to desired location of post-processed output
out.name: string. name for output file prefix
param.ls: list generated from get_atl_paramfiles()
data.type: which type of data is being compared: 'proportion','value'
comparison.type: which type of comparison should be made: 'difference','scalar'
ref.years: numeric vector with first and last year (years from start) for comparison period
speciesCodes: character vector. List of species to make plots for. Defaul = NULL (All species)
plot: logical. do you want to generate a plot

Value

Either saves an R object or returns a list called "result"

Author: Joseph Caracappa