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EM: Calibrating process-based marine ecosystem models: An example case using Atlantis (EM-981)
Collapse All
Expand AllEM Identity and Description
EM Identification
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EM ID
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EM-981 |
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EM Short Name
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Atlantis ecosystem biology submodel |
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EM Full Name
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Calibrating process-based marine ecosystem models: An example case using Atlantis |
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EM Source or Collection
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None |
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EM Source Document ID
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459 |
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Document Author
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Pethybridge, H. R., Weijerman, M., Perrymann, H., Audzijonyte, A., Porobic, J., McGregor, V., … & Fulton, E. |
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Document Year
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2019 |
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Document Title
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Calibrating process-based marine ecosystem models: An example case using Atlantis |
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Document Status
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Peer reviewed and published |
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Comments on Status
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Published journal manuscript |
Software and Access
| https://noaa-fisheries-integrated-toolbox.github.io/Atlantis | |
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Contact Name
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Heidi R. Pethybridge |
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Contact Address
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CSIRO Oceans and Atmosphere, GPO Box 1538, Hobart, Tasmania, 7000, Australia |
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Contact Email
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Heidi.Pethybridge@csiro.au |
EM Description
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Summary Description
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Calibration of complex, process-based ecosystem models is a timely task with modellers challenged by many parameters, multiple outputs of interest and often a scarcity of empirical data. Incorrect calibration can lead to unrealistic ecological and socio-economic predictions with the modeller’s experience and available knowledge of the modelled system largely determining the success of model calibration. Here we provide an overview of best practices when calibrating an Atlantis marine ecosystem model, a widely adopted framework that includes the parameters and processes comprised in many different ecosystem models. We highlight the importance of understanding the model structure and data sources of the modelled system. We then focus on several model outputs (biomass trajectories, age distributions, condition at age, realised diet proportions, and spatial maps) and describe diagnostic routines that can assist modellers to identify likely erroneous parameter values. We detail strategies to fine tune values of four groups of core parameters: growth, predator-prey interactions, recruitment and mortality. Additionally, we provide a pedigree routine to evaluate the uncertainty of an Atlantis ecosystem model based on data sources used. Describing best and current practices will better equip future modellers of complex, processed-based ecosystem models to provide a more reliable means of explaining and predicting the dynamics of marine ecosystems. Moreover, it promotes greater transparency between modellers and end-users, including resource managers. |
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Specific Policy or Decision Context Cited
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N/A |
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Biophysical Context
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Marine ecosystem |
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EM Scenario Drivers
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No scenarios presented |
EM Relationship to Other EMs or Applications
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Method Only, Application of Method or Model Run
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Method Only |
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New or Pre-existing EM?
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Application of existing model |
Related EMs (for example, other versions or derivations of this EM) described in ESML
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Document ID for related EM
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Doc-456 |
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EM ID for related EM
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EM-978 | EM-983 | EM-985 | EM-990 | EM-991 |
EM Modeling Approach
EM Relationship to Time
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EM Temporal Extent
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Not applicable |
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EM Time Dependence
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time-dependent |
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EM Time Reference (Future/Past)
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Not applicable |
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EM Time Continuity
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continuous |
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EM Temporal Grain Size Value
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Not applicable |
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EM Temporal Grain Size Unit
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Not applicable |
EM Spatial Extent
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Bounding Type
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Not applicable |
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Spatial Extent Name
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Not applicable |
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Spatial Extent Area (Magnitude)
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Not applicable |
Spatial Distribution of Computations
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EM Spatial Distribution
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Not applicable |
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Spatial Grain Type
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Not applicable |
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Spatial Grain Size
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Not applicable |
EM Structure and Computation Approach
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EM Computational Approach
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Analytic |
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EM Determinism
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deterministic |
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Statistical Estimation of EM
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Model Checking Procedures Used
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Model Calibration Reported?
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Yes |
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Model Goodness of Fit Reported?
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Not applicable |
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Goodness of Fit (metric| value | unit)
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None |
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Model Operational Validation Reported?
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Not applicable |
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Model Uncertainty Analysis Reported?
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Not applicable |
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Model Sensitivity Analysis Reported?
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Not applicable |
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Model Sensitivity Analysis Include Interactions?
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Not applicable |
EM Locations, Environments, Ecology
Location of EM Application
Terrestrial location (Classification hierarchy: Continent > Country > U.S. State [United States only])
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| None |
Marine location (Classification hierarchy: Realm > Region > Province > Ecoregion)
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| None |
Centroid Lat/Long (Decimal Degree)
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Centroid Latitude
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Not applicable |
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Centroid Longitude
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Not applicable |
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Centroid Datum
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Not applicable |
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Centroid Coordinates Status
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Not applicable |
Environments and Scales Modeled
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EM Environmental Sub-Class
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Aquatic Environment (sub-classes not fully specified) | Rivers and Streams | Inland Wetlands | Lakes and Ponds | Near Coastal Marine and Estuarine | Open Ocean and Seas |
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Specific Environment Type
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Multiple |
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EM Ecological Scale
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Ecological scale corresponds to the Environmental Sub-class |
Scale and taxa of organisms modeled
Scale of differentiation of organisms modeled
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EM Organismal Scale
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Not applicable |
Taxonomic level and name of organisms or groups identified
taxonomyHelp
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| None Available |
EnviroAtlas URL
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| None Available |
EM Ecosystem Goods and Services (EGS) potentially modeled, by classification system
CICES v 4.3 - Common International Classification of Ecosystem Services (Section > Division > Group > Class)
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(Environmental Subclass > Ecological End-Product (EEP) > EEP Subclass > EEP Modifier)
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EM Variable Names (and Units)
Predictor
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Intermediate
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Intermediate (Computed) Variables (and Units)
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None |
Response
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Observed Response Variables (and Units)
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None |
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Computed Response Variables (and Units)
view details (4 variables)
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