TY  - JOUR
A1  - Grimm, Volker
A1  - Berger, Uta
A1  - Bastiansen, Finn
A1  - Eliassen, Sigrunn
A1  - Ginot, Vincent
A1  - Giske, Jarl
A1  - Goss-Custard, John
A1  - Grand, Tamara
A1  - Heinz, Simone K.
A1  - Huse, Geir
A1  - Huth, Andreas
A1  - Jepsen, Jane U.
A1  - Jorgensen, Christian
A1  - Mooij, Wolf M.
A1  - Mueller, Birgit
A1  - Piou, Cyril
A1  - Railsback, Steven Floyd
A1  - Robbins, Andrew M.
A1  - Robbins, Martha M.
A1  - Rossmanith, Eva
A1  - Rueger, Nadja
A1  - Strand, Espen
A1  - Souissi, Sami
A1  - Stillman, Richard A.
A1  - Vabo, Rune
A1  - Visser, Ute
A1  - DeAngelis, Donald L.
T1  - A standard protocol for describing individual-based and agent-based models
JF  - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog
N2  - Simulation models that describe autonomous individual organisms (individual based models, IBM) or agents (agent-based models, ABM) have become a widely used tool, not only in ecology, but also in many other disciplines dealing with complex systems made up of autonomous entities. However, there is no standard protocol for describing such simulation models, which can make them difficult to understand and to duplicate. This paper presents a proposed standard protocol, ODD, for describing IBMs and ABMs, developed and tested by 28 modellers who cover a wide range of fields within ecology. This protocol consists of three blocks (Overview, Design concepts, and Details), which are subdivided into seven elements: Purpose, State variables and scales, Process overview and scheduling, Design concepts, Initialization, Input, and Submodels. We explain which aspects of a model should be described in each element, and we present an example to illustrate the protocol in use. In addition, 19 examples are available in an Online Appendix. We consider ODD as a first step for establishing a more detailed common format of the description of IBMs and ABMs. Once initiated, the protocol will hopefully evolve as it becomes used by a sufficiently large proportion of modellers. (c) 2006 Elsevier B.V. All rights reserved.
KW  - individual-based model
KW  - agent-based model
KW  - model description
KW  - scientific communication
KW  - standardization
Y1  - 2006
U6  - https://doi.org/10.1016/j.ecolmodel.2006.04.023
SN  - 0304-3800
VL  - 198
SP  - 115
EP  - 126
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Wang, Ming
A1  - White, Neil
A1  - Grimm, Volker
A1  - Hofman, Helen
A1  - Doley, David
A1  - Thorp, Grant
A1  - Cribb, Bronwen
A1  - Wherritt, Ella
A1  - Han, Liqi
A1  - Wilkie, John
A1  - Hanan, Jim
T1  - Pattern-oriented modelling as a novel way to verify and validate functional-structural plant models
BT  - a demonstration with the annual growth module of avocado
JF  - Annals of botany
N2  - Background and Aims Functional-structural plant (FSP) models have been widely used to understand the complex interactions between plant architecture and underlying developmental mechanisms. However, to obtain evidence that a model captures these mechanisms correctly, a clear distinction must be made between model outputs used for calibration and thus verification, and outputs used for validation. In pattern-oriented modelling (POM), multiple verification patterns are used as filters for rejecting unrealistic model structures and parameter combinations, while a second, independent set of patterns is used for validation. Key Results After calibration, our model simultaneously reproduced multiple observed architectural patterns. The model then successfully predicted, without further calibration, the validation patterns. The model supports the hypothesis that carbon allocation can be modelled as being dependent on current organ biomass and sink strength of each organ type, and also predicted the observed developmental timing of the leaf sink-source transition stage.
KW  - Pattern-oriented modelling
KW  - agent-based model
KW  - individual-based model
KW  - functional-structural plant model
KW  - model analysis
KW  - model verification
KW  - model validation
KW  - ODD (Overview, Design concepts, Details) protocol
KW  - Persea americana
KW  - plant architecture
KW  - carbon allocation
KW  - L-systems
Y1  - 2018
U6  - https://doi.org/10.1093/aob/mcx187
SN  - 0305-7364
SN  - 1095-8290
VL  - 121
IS  - 5
SP  - 941
EP  - 959
PB  - Oxford Univ. Press
CY  - Oxford
ER  -