process_atl_output: 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

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

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