| 1. |
- Ayllón, Daniel, et al.
(författare)
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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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Ingår i: Environmental Modelling & Software. - : Elsevier BV. - 1364-8152 .- 1873-6726. ; 136
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Tidskriftsartikel (refereegranskat)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. |
- Bakx, Tristan R.M., et al.
(författare)
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Farmland birds occupying forest clear-cuts respond to both local and landscape features
- 2020
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Ingår i: Forest Ecology and Management. - : Elsevier BV. - 0378-1127. ; 478
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Tidskriftsartikel (refereegranskat)abstract
- Agricultural landscapes have changed fast in Europe, which has led to steep declines in farmland biodiversity. While this has differentially impacted “farmland species”, some of these seem to be able to use alternative man-made open habitats in forests, such as forest clear-cuts and powerline rights-of-way. We investigated the use of clear-cuts by two historically declining farmland birds, the Yellowhammer (Emberiza citrinella) and the Red-backed Shrike (Lanius collurio), to determine both local and landscape habitat characteristics of clear-cuts used for breeding. Among 101 clear-cuts visited in Scania, southern Sweden, 27% were occupied by Yellowhammers and 12% by Red-backed Shrikes. Yellowhammer occurrence in clear-cuts was positively related to local spruce cover (the planted tree species). There was also an interaction between clear-cut size and the proportion of farmland in the landscape, such that the positive effect of the proportion of farmland nearby was stronger for larger clear-cuts. Red-backed Shrike occurrence was positively related to clear-cut size and the local presence of piles of forest residues (tops and branches). The relation between occurrence and the proportion of clear-cuts in the landscape was positive for small clear-cuts and negative for larger ones. Yellowhammers and Red-backed shrikes are affected by both the local habitat structure in the clearcut and on the composition of the surrounding landscape, most likely because they use the clear-cut for nesting and the surroundings as complementary feeding habitat. To what extent clear-cuts as complementary breeding habitat to farmland may contribute to the conservation of Yellowhammers and Red-backed shrikes, as well as other farmland birds, is a promising path for future investigations.
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| 3. |
- Berger, Uta, et al.
(författare)
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Towards reusable building blocks for agent-based modelling and theory development
- 2024
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Ingår i: Environmental Modelling & Software. - 1364-8152 .- 1873-6726. ; 175
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Tidskriftsartikel (refereegranskat)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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| 4. |
- Mumme, Steffen, et al.
(författare)
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Wherever I may roam—Human activity alters movements of red deer (Cervus elaphus) and elk (Cervus canadensis) across two continents
- 2023
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Ingår i: Global Change Biology. - Chichester : Wiley-Blackwell Publishing Inc.. - 1354-1013 .- 1365-2486. ; 29:20, s. 5788-5801
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Tidskriftsartikel (refereegranskat)abstract
- Human activity and associated landscape modifications alter the movements of animals with consequences for populations and ecosystems worldwide. Species performing long-distance movements are thought to be particularly sensitive to human impact. Despite the increasing anthropogenic pressure, it remains challenging to understand and predict animals' responses to human activity. Here we address this knowledge gap using 1206 Global Positioning System movement trajectories of 815 individuals from 14 red deer (Cervus elaphus) and 14 elk (Cervus canadensis) populations spanning wide environmental gradients, namely the latitudinal range from the Alps to Scandinavia in Europe, and the Greater Yellowstone Ecosystem in North America. We measured individual-level movements relative to the environmental context, or movement expression, using the standardized metric Intensity of Use, reflecting both the directionality and extent of movements. We expected movement expression to be affected by resource (Normalized Difference Vegetation Index, NDVI) predictability and topography, but those factors to be superseded by human impact. Red deer and elk movement expression varied along a continuum, from highly segmented trajectories over relatively small areas (high intensity of use), to directed transitions through restricted corridors (low intensity of use). Human activity (Human Footprint Index, HFI) was the strongest driver of movement expression, with a steep increase in Intensity of Use as HFI increased, but only until a threshold was reached. After exceeding this level of impact, the Intensity of Use remained unchanged. These results indicate the overall sensitivity of Cervus movement expression to human activity and suggest a limitation of plastic responses under high human pressure, despite the species also occurring in human-dominated landscapes. Our work represents the first comparison of metric-based movement expression across widely distributed populations of a deer genus, contributing to the understanding and prediction of animals' responses to human activity. Global Change Biology© 2023 The Authors. Global Change Biology published by John Wiley & Sons Ltd.
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| 5. |
- Vigiak, Olga, et al.
(författare)
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A disaggregating approach to describe overland flow occurrence within a catchment
- 2006
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Ingår i: Journal of Hydrology. - : Elsevier. - 0022-1694 .- 1879-2707. ; 323:1-4, s. 22-40
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Tidskriftsartikel (refereegranskat)abstract
- A parametrically parsimonious, data-based model was built on observations at hillslope and catchment scale to simulate the distribution of overland flow within a small East African Highlands catchment (Kwalei, Tanzania). A rainfall-flow Data Based Mechanistic model identified catchment effective rainfall and separated the discharge quick flow, interpreted as the combination of overland flow plus reinfiltration along the slopes, and the slow flow, interpreted as ground water displacement. Observations of overland flow occurrence along the slopes were used to derive probability distribution functions (pdfs) of overland flow in relation to effective rainfall for two pre-defined hydrologic response units (HRUs): perennial (HRU_1) versus other crops (HRU_2). At low effective rainfall, overland flow was more frequent in HRU_2, while at high effective rainfall overland flow in the two HRUs was similar. The pdfs were employed to disaggregate the quick flow into HRU overland flow depth. Reinfiltration was accounted for by assuming that only the overland flow generated in the lower part of the field would drain downslope. Effective reinfiltration length was about 4 m. Comparison of model simulations versus Gerlach trough measurements indicated that rainfall intensity was not accounted for sufficiently. The use of smaller time steps or, alternatively, of a rainfall intensity threshold could improve model performance. However, given the high variability of overland flow observed along the slopes and the limited dataset, model simulations were considered satisfactory. Though the model needs further testing on other datasets, the disaggregating approach represents an inductive alternative to the use of infiltration equations to model overland flow within a catchment. (c) 2005 Elsevier B.V. All rights reserved.
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