Creates standard diagnostic figures for Atlantis output — make_atlantis_diagnostic

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

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