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Atlantis Ecosystem Model Container

Source: R/atlantis.R
Atlantis.Rd

An S7 class that serves as a comprehensive container for all components of an Atlantis ecosystem model, including input parameters, spatial geometry, and simulation outputs. This class provides a structured way to organize and access the various data types produced by Atlantis model runs.

Usage

Atlantis(
  geometry = NULL,
  run = NULL,
  initial = NULL,
  biology = NULL,
  group = NULL,
  physics = NULL,
  forcing = NULL,
  fisheries = NULL,
  harvest = NULL,
  main_output = NULL,
  biomass_all = NULL,
  biomass_box = NULL,
  biomass_age = NULL,
  biomass_age_annual = NULL,
  diet = NULL,
  diet_detailed = NULL,
  yoy = NULL,
  file_paths = NULL,
  version = character(0)
)

Arguments

geometry

[sf object]
Spatial geometry from geometry (Box Geometry Model) file defining the model domain as polygons with depth layers and connectivity.

run

[list]
Run configuration parameters from .prm file including simulation settings, timesteps, and output specifications.

initial

[list]
Initial conditions from .nc file specifying starting biomass, numbers, and other state variables for each functional group.

biology

[list]
Biology parameters from .prm file including growth rates, mortality, recruitment, and physiological parameters for each functional group.

group

[data.frame]
Functional group definitions specifying species codes, names, group types (vertebrate/invertebrate), and model structure.

physics

[list]
Physical oceanographic parameters including mixing, transport, and hydrodynamic processes.

forcing

[list]
Environmental forcing data including temperature, salinity, and other physical drivers that vary through time.

fisheries

[list]
Fisheries configuration and catch time series data for commercial and recreational fishing activities.

harvest

[list]
Harvest policies and management scenarios including fishing mortality rates and selectivity patterns.

main_output

[data.frame]
Primary model outputs including biomass and abundance time series for all functional groups aggregated across space.

biomass_all

[array]
Complete biomass snapshots at specific time points showing spatial distribution across all boxes and depth layers.

biomass_box

[array]
Biomass snapshots aggregated by box (spatial polygon) for each functional group and time point.

biomass_age

[array]
Age-structured biomass snapshots showing cohort dynamics for vertebrate functional groups.

biomass_age_annual

[array]
Annual summaries of age-structured biomass data for long-term trend analysis.

diet

[matrix]
Diet composition matrix showing predator-prey relationships and consumption rates between functional groups.

diet_detailed

[array]
Detailed diet matrices with temporal, spatial, and size-based resolution of predation interactions.

yoy

[array]
Snapshot of biomass of recruits per year.

file_paths

[dataframe]
Data frame listing path to input and output files.

version

[character]
Atlantis version used.

Model Components

The Atlantis class contains the following major component types:

Input Files:

  • Spatial geometry and configuration

  • Biological and physical parameters

  • Initial conditions and forcing data

Output Files:

  • Time series biomass and abundance data

  • Spatial distribution snapshots

  • Predation and diet composition matrices

References

Output list avaialbe here https://atlantis-ecosystem-model.github.io/AtlantisWiki/user_guides/markdown_output/AtlantisUserGuide_PartI_CLEAN.html#simulation-outputs