Environmental Modelling & Software

Antosz and colleagues' review of the role of theory in agent-based modelling (ABM) makes important recommendations for modelling practitioners. However, macro-micro-macro frameworks are not necessarily as reliant on existing theory as the review suggests. Adopting a critical realist perspective to ABM design would help to deliver the recommendations, within which macro-micro-macro frameworks can play an important enabling role.

Internal feedback of nutrients may impede timely improvement in lake water quality. We describe a parsimonious, mechanistic framework for modeling lag times to recovery of phosphorus-enriched lakes, given decreases in external loading. The approach assumes first-order kinetics in a two-compartment system taking account of phosphorus storage in and loading from benthic sediments. Bayesian parameter modeling, published sediment phosphorus release rates, and a prior dynamic calibration for one lake are used to derive estimates of key parameters...

An operational urban air quality modelling system ENFUSER is presented with an evaluation against measured data. ENFUSER combines several dispersion modelling approaches, uses data assimilation, and continuously extracts information from online, global open-access sources. The modelling area is described with a combination of geographic datasets. These GIS datasets are globally available with open access, and therefore the model can be applied worldwide. Urban scale dispersion is addressed with a combination of Gaussian puff and Gaussian plume modelling, and long-range transport of pollutants is accounted for via a separate regional model...

Complex simulation models are a valuable tool to inform nutrient management decisions aimed at reducing hypoxia in the northern Gulf of Mexico, yet simulated hypoxia response to reduced nutrients varies greatly between models. We compared two biogeochemical models driven by the same hydrodynamics, the Coastal Generalized Ecosystem Model (CGEM) and Gulf of Mexico Dissolved Oxygen Model (GoMDOM), to investigate how they differ in simulating hypoxia and their response to reduced nutrients. Different phytoplankton nutrient kinetics produced 2-3 times more hypoxic area and volume on the western shelf in CGEM compared to GoMDOM...

We developed statistical models to generate runoff time-series at National Hydrography Dataset Plus Version 2 (NHDPlusV2) catchment scale for the Continental United States (CONUS). The models use Normalized Difference Vegetation Index (NDVI) based Curve Number (CN) to generate initial runoff time-series which then is corrected using statistical models to improve accuracy. We used the North American Land Data Assimilation System 2 (NLDAS-2) catchment scale runoff time-series as the reference data for model training and validation...

Data portals and services have increased coastal water quality data availability and accessibility. However, tools to process this data are limited - geospatial frameworks at the land-sea interface are either adapted from open- water frameworks or extended from watershed frameworks. This study explores use of a geospatial framework based on hexagons from a Discrete Global Grid System (DGGS) in a coastal area. Two DGGS implementations are explored, dggridR and H3. The geospatial frameworks are compared based on their ability to aggregate data to scales from existing frameworks, integrate data across frameworks, and connect flows across the land-sea interface...

Marine Ecosystem Models (MEMs) provide a deeper understanding of marine ecosystem dynamics. The United Nations Decade of Ocean Science for Sustainable Development has highlighted the need to deploy these complex mechanistic spatial-temporal models to engage policy makers and society into dialogues towards sustainably managed oceans. From our shared perspective, MEMs remain underutilized because they still lack formal validation, calibration, and uncertainty quantifications that undermines their credibility and uptake in policy arenas...

In the majority of EU Member States, agricultural land is expected to decrease not only due to land-use changes in favour of urban expansion and afforestation but also to land abandonment processes. The knowledge on location and extent of agricultural land abandonment is relevant for estimating local external effects and adapting policy interventions. Currently, multi-level land-use models are able to capture determined processes of demand-driven redevelopment. However, land abandonment is much more difficult to capture because of its more ambiguous definition and the lack of data on its spatial distribution...

This paper presents SHERPA-City, a web application to assess the potential of traffic measures to abate NO2 air pollution in cities. The application is developed by the Joint Research Centre. It is freely available (https://integrated-assessment.jrc.ec.europa.eu) and allows the user to perform a fast screening of possible NO2 abatement measures addressing traffic in European cities. SHERPA-City results depend on the quality of the default input data. It is therefore important to stress that the SHERPA-City default traffic flows, emission factors, fleet composition, road network topology, NO2 pollution from other sources and meteorological data are based on EU-wide datasets that may not always represent perfectly a particular local situation...

System-of-systems approaches for integrated assessments have become prevalent in recent years. Such approaches integrate a variety of models from different disciplines and modeling paradigms to represent a socio-environmental (or social-ecological) system aiming to holistically inform policy and decision-making processes. Central to the system-of-systems approaches is the representation of systems in a multi-tier framework with nested scales. Current modeling paradigms, however, have disciplinary-specific lineage, leading to inconsistencies in the conceptualization and integration of socio-environmental systems...

Being able to replicate research results is the hallmark of science. Replication of research findings using computational models should, in principle, be possible. In this manuscript, we assess code sharing and model documentation practices of 7,500 publications about individual-based and agent-based models. The code availability increased over the years, up to 18% in 2018. Model documentation does not include all the elements that could improve the transparency of the models, such as mathematical equations, flow charts, and pseudocode...

Despite the plethora of methods available for uncertainty quantification, their use has been limited in the practice of water quality (WQ) modeling. In this paper, a decision support tool (DST) that yields a continuous time series of WQ loads from sparse data using streamflows as predictor variables is presented. The DST estimates uncertainty by analyzing residual errors using a relevance vector machine. To highlight the importance of uncertainty quantification, two applications enabled within the DST are discussed...

Optical remotely sensed data are typically discontinuous, with missing values due to cloud cover. Consequently, gap-filling solutions are needed for accurate crop phenology characterization. The here presented Decomposition and Analysis of Time Series software (DATimeS) expands established time series interpolation methods with a diversity of advanced machine learning fitting algorithms (e.g., Gaussian Process Regression: GPR) particularly effective for the reconstruction of multiple-seasons vegetation temporal patterns...

The Piscine Stream Community Estimation System (PiSCES) provides users with a hypothesized fish community for any stream reach in the conterminous United States using information obtained from Nature Serve, the US Geological Survey (USGS), StreamCat, and the Peterson Field Guide to Freshwater Fishes of North America for over 1000 native and non-native freshwater fish species. PiSCES can filter HUC8-based fish assemblages based on species-specific occurrence models; create a community abundance/biomass distribution by relating relative abundance to mean body weight of each species; and allow users to query its database to see ancillary characteristics of each species (e...

Model structure uncertainty is seldom calculated because of the difficulty and time required to perform such analyses. Here we explore how a coastal model using the Monod versus Droop formulations and a 6 km × 6 km versus 2 km 2 × km computational grid size predict primary production and hypoxic area in the Gulf of Mexico. Results from these models were compared to each other and to observations, and sensitivity analyses were performed. The different models fit the observations almost equally well. The 6k-model calculated higher rates of production and settling, and especially a larger hypoxic area, in comparison to the 2k-model...

Input data acquisition and preprocessing is time-consuming and difficult to handle and can have major implications on environmental modeling results. US EPA's Hydrological Micro Services Precipitation Comparison and Analysis Tool (HMS-PCAT) provides a publicly available tool to accomplish this critical task. We present HMS-PCAT's software design and its use in gathering, preprocessing, and evaluating precipitation data through web services. This tool simplifies catchment and point-based data retrieval by automating temporal and spatial aggregations...

Modelling is key to adapting agriculture to climate change (CC), facilitating evaluation of the impacts and efficacy of adaptation measures, and the design of optimal strategies. Although there are many challenges to modelling agricultural CC adaptation, it is unclear whether these are novel or, whether adaptation merely adds new motivations to old challenges. Here, qualitative analysis of modellers' views revealed three categories of challenge: Content, Use, and Capacity. Triangulation of findings with reviews of agricultural modelling and Climate Change Risk Assessment was then used to highlight challenges specific to modelling adaptation...

The current influx of climate related information required scientists to communicate their findings to decision makers in governments, disaster preparedness organizations, and the general public. The Soil and Water Assessment Tool (SWAT) is a powerful modelling tool that allows scientists to simulate many of the physical processes involved in the water cycle. This article presents the design, methods and development efforts to overcome some of the limitations of the previously developed SWAT visualization software programs by creating a set of modular web applications that can be duplicated, customized, and run...

Time series models of malaria cases can be applied to forecast epidemics and support proactive interventions. Mosquito life history and parasite development are sensitive to environmental factors such as temperature and precipitation, and these variables are often used as predictors in malaria models. However, malaria-environment relationships can vary with ecological and social context. We used a genetic algorithm to optimize a spatiotemporal malaria model by aggregating locations into clusters with similar environmental sensitivities...

One major challenge in applying crop simulation models at the regional or global scale is the lack of available global gridded soil profile data. We developed a 10-km resolution global soil profile dataset, at 2 m depth, compatible with DSSAT using SoilGrids1km. Several soil physical and chemical properties required by DSSAT were directly extracted from SoilGrids1km. Pedo-transfer functions were used to derive soil hydraulic properties. Other soil parameters not available from SoilGrids1km were estimated from HarvestChoice HC27 generic soil profiles...