compare_spatial_vars: Creates post-processing output for Atlantis

In sgaichas/atlantisdiagnostics: Process Atlantis model output and implements model performance diagnostics

Creates post-processing output for Atlantis

Description

Creates post-processing output for Atlantis

Usage

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

sgaichas/atlantisdiagnostics documentation built on June 13, 2025, 6:11 a.m.