The ODD protocol for describing agent-based and other simulation models: A second update to improve clarity, replication, and structural realism

© 2020, University of Surrey. All rights reserved. The Overview, Design concepts and Details (ODD) protocol for describing Individual-and Agent-Based Models (ABMs) is now widely accepted and used to document such models in journal articles. As a standardized document for providing a consistent, logical and readable account of the structure and dynamics of ABMs, some research groups also find it useful as a workflow for model design. Even so, there are still limitations to ODD that obstruct its more widespread adoption. Such limitations are discussed and addressed in this paper: the limited availability of guidance on how to use ODD; the length of ODD documents; limitations of ODD for highly complex models; lack of sufficient details of many ODDs to enable reimplementation without access to the model code; and the lack of provision for sections in the document structure covering model design ratio-nale, the model’s underlying narrative, and the means by which the model’s fitness for purpose is evaluated. We document the steps we have taken to provide better guidance on: structuring complex ODDs and an ODD summary for inclusion in a journal article (with full details in supplementary material; Table 1); using ODD to point readers to relevant sections of the model code; update the document structure to include sections on model rationale and evaluation. We also further advocate the need for standard descriptions of simulation experiments and argue that ODD can in principle be used for any type of simulation model. Thereby ODD would provide a lingua franca for simulation modelling

The role of the geophysical template and environmental regimes in controlling stream-living trout populations

The importance of multiple processes and instream factors to aquatic biota has been explored extensively, but questions remain about how local spatiotemporal variability of aquatic biota is tied to environmental regimes and the geophysical template of streams. We used an individual-based trout model to explore the relative role of the geophysical template versus environmental regimes on biomass of trout (Oncorhynchus clarkii clarkii). We parameterized the model with observed data from each of the four headwater streams (their local geophysical template and environmental regime) and then ran 12 simulations where we replaced environmental regimes (stream temperature, flow, turbidity) of a given stream with values from each neighboring stream while keeping the geophysical template fixed. We also performed single-parameter sensitivity analyses on the model results from each of the four streams. Although our modeled findings show that trout biomass is most responsive to changes in the geophysical template of streams, they also reveal that biomass is restricted by available habitat during seasonal low flow, which is a product of both the stream's geophysical template and flow regime. Our modeled results suggest that differences in the geophysical template among streams render trout more or less sensitive to environmental change, emphasizing the importance of local fish-habitat relationships in streams

Environment Orientation : a structured simulation approach for agent-based complex systems

Complex systems are collections of independent agents interacting with each other and with their environment to produce emergent behaviour. Agent-based computer simulation is one of the main ways of studying complex systems. A naive approach to such simulation can fare poorly, due to large communication overhead, and due to the scope for deadlock between the interacting agents sharing a computational platform. Agent interaction can instead be considered entirely from the point of view of the environment(s) within which the agents interact. Structuring a simulation using such Environment Orientation leads to a simulation that reduces communication overhead, that is effectively deadlock-free, and yet still behaves in the manner required. Additionally the Environment Orientation architecture eases the development of more sophisticated large-scale simulations, with multiple kinds of complex agents, situated in and interacting with multiple kinds of environments. We describe the Environment Orientation simulation architecture. We report on a number of experiments that demonstrate the effectiveness of the Environment Orientation approach: a simple flocking system, a flocking system with multiple sensory environments, and a flocking system in an external environment

Communicating complex ecological models to non-scientist end users

Complex computer models are used to predict how ecological systems respond to changing environ- mental conditions or management actions. Communicating these complex models to non-scientists is challenging, but necessary, because decision-makers and other end users need to understand, accept, and use the models and their predictions. Despite the importance of communicating effectively with end users, there is little guidance available as to how this may be achieved. Here, we review the challenges typically encountered by modellers attempting to communicate complex models and their outputs to managers and other non-scientist end users. We discuss the implications of failing to communicate effec- tively in each case. We then suggest a general approach for communicating with non-scientist end users. We detail the specific elements to be communicated using the example of individual-based models, which are widely used in ecology. We demonstrate that despite their complexity, individual-based models have characteristics that can facilitate communication with non-scientists. The approach we propose is based on our experiences and methods used in other fields, but which until now have not been synthesised or made broadly available to ecologists. Our aim is to facilitate the process of communicating with end users of complex models and encourage more modellers to engage in it by providing a structured approach to the communication process. We argue that developing measures of the effectiveness of communication with end users will help increase the impact of complex models in ecology

Local Variability Mediates Vulnerability of Trout Populations to Land Use and Climate Change

Land use and climate change occur simultaneously around the globe. Fully understanding their separate and combined effects requires a mechanistic understanding at the local scale where their effects are ultimately realized. Here we applied an individual-based model of fish population dynamics to evaluate the role of local stream variability in modifying responses of Coastal Cutthroat Trout (Oncorhynchus clarkii clarkii) to scenarios simulating identical changes in temperature and stream flows linked to forest harvest, climate change, and their combined effects over six decades. We parameterized the model for four neighboring streams located in a forested headwater catchment in northwestern Oregon, USA with multi-year, daily measurements of stream temperature, flow, and turbidity (2007–2011), and field measurements of both instream habitat structure and three years of annual trout population estimates. Model simulations revealed that variability in habitat conditions among streams (depth, available habitat) mediated the effects of forest harvest and climate change. Net effects for most simulated trout responses were different from or less than the sum of their separate scenarios. In some cases, forest harvest countered the effects of climate change through increased summer flow. Climate change most strongly influenced trout (earlier fry emergence, reductions in biomass of older trout, increased biomass of young-of-year), but these changes did not consistently translate into reductions in biomass over time. Forest harvest, in contrast, produced fewer and less consistent responses in trout. Earlier fry emergence driven by climate change was the most consistent simulated response, whereas survival, growth, and biomass were inconsistent. Overall our findings indicate a host of local processes can strongly influence how populations respond to broad scale effects of land use and climate change

Mathematical Aspects of the Periodic Law

We review different studies of the Periodic Law and the set of chemical elements from a mathematical point of view. This discussion covers the first attempts made in the 19th century up to the present day. Mathematics employed to study the periodic system includes number theory, information theory, order theory, set theory and topology. Each theory used shows that it is possible to provide the Periodic Law with a mathematical structure. We also show that it is possible to study the chemical elements taking advantage of their phenomenological properties, and that it is not always necessary to reduce the concept of chemical elements to the quantum atomic concept to be able to find interpretations for the Periodic Law. Finally, a connection is noted between the lengths of the periods of the Periodic Law and the philosophical Pythagorean doctrine.Comment: 20 pages, PDF fil

Antiangiogenic Activity of 2-Deoxy-D-Glucose

During tumor angiogenesis, endothelial cells (ECs) are engaged in a number of energy consuming biological processes, such as proliferation, migration, and capillary formation. Since glucose uptake and metabolism are increased to meet this energy need, the effects of the glycolytic inhibitor 2-deoxy-D-glucose (2-DG) on in vitro and in vivo angiogenesis were investigated.In cell culture, 2-DG inhibited EC growth, induced cytotoxicity, blocked migration, and inhibited actively forming but not established endothelial capillaries. Surprisingly, 2-DG was a better inhibitor of these EC properties than two more efficacious glycolytic inhibitors, 2-fluorodeoxy-D-glucose and oxamate. As an alternative to a glycolytic inhibitory mechanism, we considered 2-DG's ability to interfere with endothelial N-linked glycosylation. 2-DG's effects were reversed by mannose, an N-linked glycosylation precursor, and at relevant concentrations 2-DG also inhibited synthesis of the lipid linked oligosaccharide (LLO) N-glycosylation donor in a mannose-reversible manner. Inhibition of LLO synthesis activated the unfolded protein response (UPR), which resulted in induction of GADD153/CHOP and EC apoptosis (TUNEL assay). Thus, 2-DG's effects on ECs appeared primarily due to inhibition of LLOs synthesis, not glycolysis. 2-DG was then evaluated in two mouse models, inhibiting angiogenesis in both the matrigel plug assay and the LH(BETA)T(AG) transgenic retinoblastoma model.In conclusion, 2-DG inhibits endothelial cell angiogenesis in vitro and in vivo, at concentrations below those affecting tumor cells directly, most likely by interfering with N-linked glycosylation rather than glycolysis. Our data underscore the importance of glucose metabolism on neovascularization, and demonstrate a novel approach for anti-angiogenic strategies

Emergency vaccination of rabies under limited resources – combating or containing?

BACKGROUND: Rabies is the most important viral zoonosis from a global perspective. Worldwide efforts to combat the disease by oral vaccination of reservoirs have managed to eradicate wildlife rabies in large areas of central Europe and North-America. Thus, repeated vaccination has been discontinued recently on a geographical scale. However, as rabies has not yet been eradicated globally, a serious risk of re-introduction remains. What is the best spatial design for an emergency vaccination program – particularly if resources are limited? Either, we treat a circular area around the detected case and run the risk of infected hosts leaving the limited control area, because a sufficient immunisation level has not yet been built up. Or, initially concentrate the SAME resources in order to establish a protective ring which is more distant from the infected local area, and which then holds out against the challenge of the approaching epidemic. METHODS: We developed a simulation model to contrast the two strategies for emergency vaccination. The spatial-explicit model is based on fox group home-ranges, which facilitates the simulation of rabies spread to larger areas relevant to management. We used individual-based fox groups to follow up the effects of vaccination in a detailed manner. Thus, regionally – bait distribution orientates itself to standard schemes of oral immunisation programs and locally – baits are assigned to individual foxes. RESULTS: Surprisingly, putting the controlled area ring-like around the outbreak does not outperform the circular area of the same size centred on the outbreak. Only during the very first baitings, does the ring area result in fewer breakouts. But then as rabies is eliminated within the circle area, the respective ring area fails, due to the non-controlled inner part. We attempt to take advantage of the initially fewer breakouts beyond the ring when applying a mixed strategy. Therefore, after a certain number of baitings, the area under control was increased for both strategies towards the same larger circular area. The circle-circle strategy still outperforms the ring-circle strategy and analysis of the spatial-temporal disease spread reveals why: improving control efficacy by means of a mixed strategy is impossible in the field, due to the build-up time of population immunity. CONCLUSION: For practical emergency management of a new outbreak of rabies, the ring-like application of oral vaccination is not a favourable strategy at all. Even if initial resources are substantially low and there is a serious risk of rabies cases outside the limited control area, our results suggest circular application instead of ring vaccination

Indicated Truancy Interventions: Effects on School Attendance Among Chronic Truant Students.

BACKGROUNDTruancy is a significant problem in the U.S. and in other countries around the world. Truancy has been linked to serious immediate and far-reaching consequences for youth, families, and schools and communities, leading researchers, practitioners, and policy makers to try to understand and to address the problem. Although numerous and significant steps have been taken at the local, state, and national levels to reduce truancy, the rates of truancy have at best remained stable or at worst been on the rise, depending on the indicator utilized to assess truancy rates. The costs and impact of chronic truancy are significant, with both short- and long-term implications for the truant youth as well as for the family, school, and community. Although several narrative reviews and one meta-analysis of attendance and truancy interventions have attempted to summarize the extant research, there are a number of limitations to these reviews. It is imperative that we systematically synthesize and examine the evidence base to provide a comprehensive picture of interventions that are being utilized to intervene with chronic truants, to identify interventions that are effective and ineffective, and to identify gaps and areas in which more research needs to be conducted to better inform practice and policy.OBJECTIVESThe main objective of this systematic review was to examine the effects of interventions on school attendance to inform policy, practice, and research. The questions guiding this study were: 1) Do truancy programs with a goal of increasing student attendance for truant youth affect school attendance behaviors of elementary and secondary students with chronic attendance problems?2) Are there differences in the effects of school-based, clinic/community-based, and court-based programs?3) Are some modalities (i.e., family, group, multimodal) more effective than others in increasing student attendance? SEARCH STRATEGYA systematic and comprehensive search process was employed to locate all possible studies between 1990 and 2009, with every effort made to include both published and unpublished studies to minimize publication bias. A wide range of electronic bibliographic databases and research registers was searched, websites of relevant research centers and groups were mined for possible reports, over 200 e-mails and letters were sent to programs listed in large databases of truancy programs compiled by the National Center for School Engagement and the National Dropout Prevention Center, and contact with researchers in the field of truancy and absenteeism was attempted. In addition, we examined reference lists of all previous reviews as well as citations in research reports for potential studies.SELECTION CRITERIAStudies eligible for this review were required to meet several eligibility criteria. Studies must have utilized a randomized, quasi-experimental, or single-group pre-posttest design with the aim of evaluating the effectiveness of interventions with a stated primary goal of increasing student attendance (or decreasing absenteeism) among chronic truant students. Studies must have measured an attendance outcome and reported sufficient data to calculate an effect size. Finally, studies must have been published between 1990 and 2009 in the United States, United Kingdom, Australia, or Canada. DATA COLLECTION AND ANALYSISA total of 28 studies, reported in 26 reports, met final eligibility criteria and were included in this review and meta-analysis. Of the studies that were included, 5 utilized a randomized design (RCT), 11 utilized a quasi-experimental design (QED), and 12 utilized a single group pre-posttest design (SGPP). All eligible studies were coded using a structured coding instrument, with 20% of studies coded by a second coder. Descriptive analysis was conducted to examine and describe data related to the characteristics of the included studies. Analysis of the mean effect size, the heterogeneity of effect sizes, and the relationship between effect size and methodological and substantive characteristics of the interventions was also conducted separately for the RCT/QED studies and the SGPP studies. The effect sizes were calculated using the standardized mean difference effect size statistic, correcting for small sample size using Hedges’ g (Hedges, 1992). Assuming a mixed effects model, the analog to the ANOVA and bivariate meta-regression frameworks were used to examine potential moderating variables related to study, participant, and intervention characteristics. RESULTSThe meta-analytic findings demonstrated a significant overall positive and moderate mean effect of interventions on attendance outcomes. The mean effect size for interventions examined in the included RCT studies was .57 and the mean effect size for the QED studies was .43. No significant differences were observed between the RCT and QED studies in the magnitude of the treatment effect (Qb= .28, p \u3e.05). The mean effect size of interventions examined using an SGPP design was .95. A moderate effect on attendance outcomes is encouraging; however, the overall mean effect size is masked by a large amount of heterogeneity, indicating significant variance in effect sizes between studies. Moderator analyses found no significant differences in mean effects between studies on any moderating variable tested. No differences were found between school-, court-, or community-based programs or between different modalities of programs. The duration of the intervention also did not demonstrate any association with effect size. Collaborative programs and multimodal interventions produced statistically similar effects on attendance as non-collaborative and single-modality programs, which runs counter to the prevailing beliefs and recommendations for best practices in truancy reduction found in the literature.Other significant findings from this study relate to methodological shortcomings, the absence of important variables as well as gaps in the evidence base. These findings include the lack of inclusion of minority students and a lack of reporting and statistical analysis of demographic variables, particularly race/ethnicity and socioeconomic status (SES). Given that race and SES have been linked to absenteeism, the absence of this data was surprising. The majority of studies also lacked adequate descriptions of the interventions, making replication of the intervention difficult, and failed to measure and report long-term outcomes. AUTHORS’ CONCLUSIONSOverall, the findings from this study suggest that chronic truant students benefit from interventions targeting attendance behaviors; thus it is important and worthwhile to intervene with chronic truant youth. Given the minimal differences in effects across program types and modalities, no one program type or modality stands out as being more effective than any other. Although no statistically significant differences in effects were found between types and modalities of interventions included in this review, there was a lack of available evidence to support the general belief (and popular “best-practice” recommendations) that collaborative and multimodal interventions are more effective than programs that are not collaborative and single modal interventions. Due to the small sample size and large heterogeneity between studies and within groups of studies, caution must be used when interpreting and applying the findings from this meta-analysis. Overall, the studies included in the review improved attendance by an average of 4.69 days, almost a full school week. However, although the interventions included in this study were, overall, found to be effective, the mean rates of absenteeism at posttest in most studies remained above acceptable levels. This finding indicates the need for additional work and research. Developing more effective interventions and policies as well as studying outcomes of interventions, particularly with vulnerable and at-risk populations, is crucial to combating absenteeism. The gaps and deficiencies identified in this study also affirm the need for increasing and strengthening the evidence base on which current policies and practices rest. Although additional outcome research is necessary, more of the same is not sufficient. Significant improvements in the quality of truancy intervention research are required and identified gaps need to be addressed. Recommendations to improve the quality and fill gaps in truancy intervention research are discussed here. In addition, given the significant and pervasive deficiencies in the extant research, a critical analysis of the practices, assumptions, and sociopolitical contexts underlying truancy intervention research seems warranted