make_atlantis_diagnostic_figures: Creates standard diagnostic figures for Atlantis output

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

Creates standard diagnostic figures for Atlantis output

Description

Used after the post processing routine process_atl_output. Creates the full set of diagnostic and summary figures and tables from atlantis model run.

Usage

make_atlantis_diagnostic_figures(
  out.dir,
  fig.dir,
  atl.dir,
  param.dir,
  run.prefix,
  run.name,
  param.ls,
  benthic.box,
  benthic.level = 4,
  plot.all,
  plot.benthic,
  plot.overall.biomass,
  plot.biomass.timeseries,
  plot.length.age,
  plot.biomass.box,
  plot.c.mum,
  plot.sn.rn,
  plot.recruits,
  plot.numbers.timeseries,
  plot.physics,
  plot.growth.cons,
  plot.cohort,
  plot.diet,
  plot.consumption,
  plot.spatial.biomass,
  plot.spatial.biomass.seasonal,
  plot.catch,
  plot.spatial.catch,
  plot.weight,
  plot.mortality
)

Arguments

out.dir	string. Path where desired output data should be saved
fig.dir	string. Path where desired output figures should be saved
atl.dir	string. Path where atlantis model output is located
param.dir	string. Path where atlantis parameter files are located
run.prefix	sring. Prefix specified in Atlantis.bat file that begins each output file
run.name	string. Prefered name to use for output file names
param.ls	list. Output from get_atl_paramfiles
benthic.box	numeric. Box ID for benthic plots
benthic.level	numeric. Level for benthic plots (default is 4 for NEUS model)
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.spatial.catch	logical. Plots showing the spatial (box/level) structure of groups' catch
plot.weight	logical. Plots the maximum size of fish in each size class over the domain
plot.mortality	logical. Plots Mortality (F, M1, M2) from two output sources (Mort, SpecificMort)

Value

A series of figures and tables based on output grouping flags

Author: Ryan Morse, modified by J. Caracappa

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