Creates post-processing output for Atlantis

process_atl_output(
  param.dir,
  atl.dir,
  out.dir = file.path(atl.dir, "Post_Processed/Data/"),
  run.prefix,
  param.ls,
  agg.scale = "day",
  large.file = F,
  system,
  process.all = F,
  plot.all = F,
  plot.benthic = F,
  plot.overall.biomass = F,
  plot.biomass.timeseries = F,
  plot.length.age = F,
  plot.biomass.box = F,
  plot.c.mum = F,
  plot.sn.rn = F,
  plot.recruits = F,
  plot.numbers.timeseries = F,
  plot.physics = F,
  plot.growth.cons = F,
  plot.cohort = F,
  plot.diet = F,
  plot.consumption = F,
  plot.spatial.biomass = F,
  plot.spatial.biomass.seasonal = F,
  plot.catch = F,
  plot.catch.fleet = F,
  plot.spatial.catch = F,
  plot.mortality = F,
  plot.weight = F,
  plot.spatial.overlap = F
)

Arguments

param.dir: string. Path to location of atlantis parameter files
atl.dir: string. path to location of atlantis output files
out.dir: string. path to desired location of post-processed output
run.prefix: string. Prefix for atlantis run output (specified in runcommand.bat)
param.ls: list generated from get_atl_paramfiles()
agg.scale: Scale to aggregate dietcheck biomass from (either 'raw','month', or 'year' )
large.file: Boolean.
system: String. "Windows" or "Linux"
process.all: Boolean. Global option to process all components
plot.all: Boolean. Global flag for plotting everything
plot.benthic: logical. Benthic plots show timeseries of all benthic and epibenthic groups for one box
plot.overall.biomass: logical. Plots showing the total biomass across all functional groups as stacked barplots
plot.biomass.timeseries: logical. Plots showing biomass-related timeseries on various aggregations and reference points
plot.length.age: logical. Plots relating to the length-age relationship of age-structured groups
plot.biomass.box: logical. Plots relating to biomass but grouped by box
plot.c.mum: logical. Plots and tables related to tuning C and mum parameters
plot.sn.rn: logical. Plots relating to SN and RN timeseries
plot.recruits: logical. Plots of recruitment and SSB timeseries
plot.numbers.timeseries: logical. Plots showing timeseries of numbers (as opposed to biomass)
plot.physics: logical. Plots of physical statevariables as well as fluxes
plot.growth.cons: logical. Plots relating to growth and consumption
plot.cohort: logical. Plots showing timeseries of each cohort across age-structured groups
plot.diet: logical. Plots showing predation of and consumption by each functional group
plot.consumption: Boolean. Plots showing consumption
plot.spatial.biomass: logical. Plots showing the spatial (box/level) structure of groups' biomass
plot.spatial.biomass.seasonal: logical. Plots showing the spatial (box/level) structure of groups' biomass
plot.catch: logical. Plots annual catch(mt) age based catch (numbers) and age based %ages
plot.catch.fleet: Boolean
plot.spatial.catch: logical. Plots showing the spatial (box/level) structure of groups' catch
plot.mortality: logical. Plots Mortality (F, M1, M2) from two output sources (Mort, SpecificMort)
plot.weight: logical. Plots the maximum size of fish in each size class over the domain
plot.spatial.overlap: Boolean

Value

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

Author: Ryan Morse, modified by Joseph Caracappa