| 1. |
- Ayllón, Daniel, et al.
(author)
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Keeping modelling notebooks with TRACE : Good for you and good for environmental research and management support
- 2021
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In: Environmental Modelling & Software. - : Elsevier BV. - 1364-8152 .- 1873-6726. ; 136
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Journal article (peer-reviewed)abstract
- The acceptance and usefulness of simulation models are often limited by the efficiency, transparency, reproducibility, and reliability of the modelling process. We address these issues by suggesting that modellers (1) “trace” the iterative modelling process by keeping a modelling notebook corresponding to the laboratory notebooks used by empirical researchers, (2) use a standardized notebook structure and terminology based on the existing TRACE documentation framework, and (3) use their notebooks to compile TRACE documents that supplement publications and reports. These practices have benefits for model developers, users, and stakeholders: improved and efficient model design, analysis, testing, and application; increased model acceptance and reuse; and replicability and reproducibility of the model and the simulation experiments. Using TRACE terminology and structure in modelling notebooks facilitates production of TRACE documents. We explain the rationale of TRACE, provide example TRACE documents, and suggest strategies for keeping “TRACE Modelling Notebooks.”
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| 2. |
- Berger, Uta, et al.
(author)
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Towards reusable building blocks for agent-based modelling and theory development
- 2024
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In: Environmental Modelling & Software. - 1364-8152 .- 1873-6726. ; 175
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Journal article (peer-reviewed)abstract
- Despite the increasing use of standards for documenting and testing agent -based models (ABMs) and sharing of open access code, most ABMs are still developed from scratch. This is not only inefficient, but also leads to ad hoc and often inconsistent implementations of the same theories in computational code and delays progress in the exploration of the functioning of complex social -ecological systems (SES). We argue that reusable building blocks (RBBs) known from professional software development can mitigate these issues. An RBB is a submodel that represents a particular mechanism or process that is relevant across many ABMs in an application domain, such as plant competition in vegetation models, or reinforcement learning in a behavioural model. RBBs need to be distinguished from modules, which represent entire subsystems and include more than one mechanism and process. While linking modules faces the same challenges as integrating different models in general, RBBs are atomic enough to be more easily re -used in different contexts. We describe and provide examples from different domains for how and why building blocks are used in software development, and the benefits of doing so for the ABM community and to individual modellers. We propose a template to guide the development and publication of RBBs and provide example RBBs that use this template. Most importantly, we propose and initiate a strategy for community -based development, sharing and use of RBBs. Individual modellers can have a much greater impact in their field with an RBB than with a single paper, while the community will benefit from increased coherence, facilitating the development of theory for both the behaviour of agents and the systems they form. We invite peers to upload and share their RBBs via our website - preferably referenced by a DOI (digital object
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| 3. |
- Desprez-Loustau, Marie-Laure, et al.
(author)
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From leaf to continent : The multi-scale distribution of an invasive cryptic pathogen complex on oak
- 2018
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In: Fungal ecology. - : Elsevier BV. - 1754-5048 .- 1878-0083. ; 36, s. 39-50
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Journal article (peer-reviewed)abstract
- The spatial distribution and niche differentiation of three closely related species (Erysiphe alphitoides, Erysiphe quercicola and Erysiphe hypophylla) causing oak powdery mildew was studied at scales ranging from the European continent, where they are invasive, to a single leaf. While E. alphitoides was dominant at all scales, E. quercicola and E. hypophylla had restricted geographic, stand and leaf distributions. The large-scale distributions were likely explained by climatic factors and species environmental tolerances, with E. quercicola being more frequent in warmer climates and E. hypophylla in colder climates. The extensive sampling and molecular analyses revealed the cryptic invasion of E. quercicola in nine countries from which it had not previously been recorded. The presence of the three species was also strongly affected by host factors, such as oak species and developmental stage. Segregation patterns between Erysiphe species were observed at the leaf scale, between and within leaf surfaces, suggesting competitive effects.
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