var bibbase_data = {"data":"\n\n
\n <script src=\"https://bibbase.org/show?bib=https%3A%2F%2Fraw.githubusercontent.com%2Fropensci%2Fnlrx%2Fmaster%2Fvignettes%2Farticles%2Fnlrx_papers.bib&jsonp=1&jsonp=1\"></script>\n
\n \n <?php\n $contents = file_get_contents(\"https://bibbase.org/show?bib=https%3A%2F%2Fraw.githubusercontent.com%2Fropensci%2Fnlrx%2Fmaster%2Fvignettes%2Farticles%2Fnlrx_papers.bib&jsonp=1\");\n print_r($contents);\n ?>\n
\n \n <iframe src=\"https://bibbase.org/show?bib=https%3A%2F%2Fraw.githubusercontent.com%2Fropensci%2Fnlrx%2Fmaster%2Fvignettes%2Farticles%2Fnlrx_papers.bib&jsonp=1\"></iframe>\n
\n \n For more details see the documention.\n
\nTo the site owner:
\n\nAction required! Mendeley is changing its\n API. In order to keep using Mendeley with BibBase past April\n 14th, you need to:\n
\n \n \n Fix it now\n
\n@Article{Ahmad2023,\n author = {Ahmad, Riris Andono and Imron, Muhammad Ali and Ramadona, Aditya Lia and Lathifah, Nurul and Azzahra, Faradhina and Widyastuti, Kirana and Fuad, Anis},\n journal = {Frontiers in Ecology and Evolution},\n title = {Modeling social interaction and metapopulation mobility of the COVID-19 pandemic in main cities of highly populated Java Island, Indonesia: An agent-based modeling approach},\n year = {2023},\n issn = {2296-701X},\n volume = {10},\n abstract = {<sec>IntroductionCoronavirus transmission is strongly influenced by human mobilities and interactions within and between different geographical regions. Human mobility within and between cities is motivated by several factors, including employment, cultural-driven, holidays, and daily routines.</sec><sec>MethodWe developed a sustained metapopulation (SAMPAN) model, an agent-based model (ABM) for simulating the effect of individual mobility and interaction behavior on the spreading of COVID-19 viruses across main cities on Java Island, Indonesia. The model considers social classes and social mixing affecting the mobility and interaction behavior within a sub-population of a city in the early pandemic. Travelers’ behavior represents the mobility among cities from central cities to other cities and commuting behavior from the surrounding area of each city.</sec><sec>ResultsLocal sensitivity analysis using one factor at a time was performed to test the SAMPAN model, and we have identified critical parameters for the model. While validation was carried out for the Jakarta area, we are confident in implementing the model for a larger area with the concept of metapopulation dynamics. We included the area of Bogor, Depok, Bekasi, Bandung, Semarang, Surakarta, Yogyakarta, Surabaya, and Malang cities which have important roles in the COVID-19 pandemic spreading on this island.</sec><sec>DiscussionOur SAMPAN model can simulate various waves during the first year of the pandemic caused by various phenomena of large social mobilities and interactions, particularly during religious occasions and long holidays.</sec>},\n doi = {10.3389/fevo.2022.958651},\n url = {https://www.frontiersin.org/articles/10.3389/fevo.2022.958651},\n}\n\n\n
@InProceedings{Wilsdorf2022,\n author = {Wilsdorf, Pia and Uhrmacher, Adelinde M.},\n booktitle = {2022 Winter Simulation Conference (WSC)},\n title = {Creating PROV-DM Graphs from Model Databases},\n year = {2022},\n pages = {2118-2129},\n doi = {10.1109/WSC57314.2022.10015331},\n}\n\n\n
@Article{Dudenhoeffer2022,\n author = {Dudenhöffer, Jan-Hendrik and Luecke, Noah and Crawford, Kerri},\n journal = {Nature Ecology & Evolution},\n title = {Changes in precipitation patterns can destabilize plant species coexistence via changes in plant–soil feedback},\n year = {2022},\n month = {05},\n pages = {1-9},\n volume = {6},\n doi = {10.1038/s41559-022-01700-7},\n}\n\n\n
@Article{Shin2022,\n author = {Hyesop Shin},\n journal = {MethodsX},\n title = {Quantifying the health effects of exposure to non-exhaust road emissions using agent-based modelling (ABM)},\n year = {2022},\n issn = {2215-0161},\n pages = {101673},\n volume = {9},\n abstract = {This paper provides an agent-based model, entitled TRAPSim, to examine the exposure to non-exhaust emissions (NEEs) and the consequent health effects of driver and pedestrians groups in Seoul. To make the model reproducible and replicable, TRAPSim uses the ODD protocol to demonstrate the details of the agents and parameters, as well as provide the codes alongside the descriptions to avoid possible ambiguity. The model’s main parameters are thoroughly tested through sensitivity experiments and are calibrated with the city’s air pollution monitoring networks. This paper also provides the instructions to the model, possible artefacts, and the configurations to submit the model on the HPC cluster.•An ODD protocol is used to document the agent-based model TRAPSim.•Sensitivity experiments and calibration are explained.•The step-by-step codes and annotations are attached in the protocol and HPC sections.},\n doi = {https://doi.org/10.1016/j.mex.2022.101673},\n keywords = {Agent-based modelling, Traffic simulation, Air pollution, Exposure, NetLogo},\n url = {https://www.sciencedirect.com/science/article/pii/S2215016122000577},\n}\n\n\n
@Article{Daly2022,\n author = {Aisling J. Daly and Lander {De Visscher} and Jan M. Baetens and Bernard {De Baets}},\n journal = {Environmental Modelling & Software},\n title = {Quo vadis, agent-based modelling tools?},\n year = {2022},\n issn = {1364-8152},\n pages = {105514},\n volume = {157},\n abstract = {Agent-based models (ABMs) are an increasingly popular choice for simulating large systems of interacting components, and have been applied across a wide variety of natural and environmental systems. However, ABMs can be incredibly disparate and often opaque in their formulation, implementation, and analysis. This can impede critical assessment and re-implementation, and jeopardize the reproducibility and conclusions of ABM studies. In this review, we survey recent work towards standardization in ABM methodology in several aspects: model description and documentation, model implementation, and model analysis and inference. Based on a critical review of the literature, focused on ABMs of environmental and natural systems, we describe a recurrent trade-off between flexibility and standardization in ABM methodology. We find that standard protocols for model documentation are beginning to establish, although their uptake by the ABM community is inhibited by their sometimes excessive level of detail. We highlight how implementation options now exist at all points along a spectrum from ad hoc, ‘from scratch’ implementations, to specific software offering ‘off-the-shelf’ ABM implementations. We outline how the main focal points of ABM analysis (behavioural and inferential analysis) are facing similar issues with similar approaches. While this active development of ABM analysis techniques brings additional methods to our analysis toolbox, it does not contribute to the development of a standardized framework, since the performance and design of these methods tends to be highly problem-specific. We therefore recommend that agent-based modellers should consider multiple approaches simultaneously when analysing their model. Well-documented software packages, and critical comparative reviews of such, will be important facilitators in these advances. ABMs can additionally make better use of developments in other fields working with high-dimensional problems, such as Bayesian statistics and machine learning.},\n doi = {https://doi.org/10.1016/j.envsoft.2022.105514},\n keywords = {Agent-based models, Simulation, Model analysis, Inference, Calibration},\n url = {https://www.sciencedirect.com/science/article/pii/S1364815222002146},\n}\n\n\n
@Article{MedeirosSousa2022,\n author = {Antônio Ralph Medeiros-Sousa and Gabriel Zorello Laporta and Luis Filipe Mucci and Mauro Toledo Marrelli},\n journal = {Ecological Modelling},\n title = {Epizootic dynamics of yellow fever in forest fragments: An agent-based model to explore the influence of vector and host parameters},\n year = {2022},\n issn = {0304-3800},\n pages = {109884},\n volume = {466},\n abstract = {Yellow fever (YF) is an acute infectious hemorrhagic disease caused by the yellow fever virus (YFV) and transmitted to humans by infected mosquitoes. In Brazil and other South American countries, the disease has been restricted to the sylvatic cycle, in which the virus circulates among mosquitoes and non-human primates in forested areas. Frequent outbreaks in the Amazon basin that spread to other Brazilian ecoregions have been observed in recent years. The most recent started in 2014 and spread to forests in densely populated areas on the Brazilian Atlantic Coast, resulting in the death of hundreds of humans and thousands of monkeys. However, the underlying ecological mechanisms that support YFV amplification and the severity of an epizootic and persistence of the virus on a microgeographic scale in these forest patches are still poorly understood. Here, we developed an agent-based model that simulates the dynamics of YFV transmission in a hypothetical forest fragment. The proposed model contains individual agents representing mosquitoes, breeding sites, howler monkeys (Alouatta) and other vertebrate species living and interacting in an environment where the YFV has emerged. The model simulations aimed to investigate the isolated and interaction effects of important input parameters linked to mosquitoes, monkeys, the environment and hypothetical alternative hosts on the following outcomes: (1) maximum proportion of infected mosquitoes, (2) proportion of dead monkeys and (3) YFV persistence in the environment. Local and global sensitivity analyses were used to assess the influence of different sets of input parameter values on the outputs. The model simulations indicated that mosquito abundance had the greatest influence on the outputs and made a major contribution to monkey mortality. Additionally, most of the variation in the outputs was due to complex and indirect effects of the different input parameters. These results suggest that mosquito density is one of the main factors responsible for YFV amplification during epizootics and reinforce the hypothesis that the severity and persistence of an outbreak depend on a complex web of interactions between different factors associated with vectors, hosts and the environment.},\n doi = {https://doi.org/10.1016/j.ecolmodel.2022.109884},\n keywords = {Yellow fever, Agent-based model, Mosquitoes, ,},\n url = {https://www.sciencedirect.com/science/article/pii/S0304380022000126},\n}\n\n\n
@Article{Reiner2022,\n author = {Reiner, Dominik and Spangenberg, Matthias C. and Grimm, Volker and Groeneveld, Jürgen and Wiegand, Kerstin},\n journal = {Environmental Toxicology and Chemistry},\n title = {Chronic and Acute Effects of Imidacloprid on a Simulated BEEHAVE Honeybee Colony},\n year = {2022},\n number = {9},\n pages = {2318-2327},\n volume = {41},\n abstract = {Abstract Honeybees (Apis mellifera) are important pollinators for wild plants as well as for crops, but honeybee performance is threatened by several stressors including varroa mites, gaps in foraging supply, and pesticides. The consequences of bee colony longtime exposure to multiple stressors are not well understood. The vast number of possible stressor combinations and necessary study duration require research comprising field, laboratory, and simulation experiments. We simulated long-term exposure of a honeybee colony to the insecticide imidacloprid and to varroa mites carrying the deformed wing virus in landscapes with different temporal gaps in resource availability as single stressors and in combinations. Furthermore, we put a strong emphasis on chronic lethal, acute sublethal, and acute lethal effects of imidacloprid on honeybees. We have chosen conservative published values to parameterize our model (e.g., highest reported imidacloprid contamination). As expected, combinations of stressors had a stronger negative effect on bee performance than each single stressor alone, and effect sizes were larger after 3 years of exposure than after the first year. Imidacloprid-caused reduction in bee performance was almost exclusively due to chronic lethal effects because the thresholds for acute effects were rarely met in simulations. In addition, honeybee colony extinctions were observed by the last day of the first year but more pronounced on the last days of the second and third simulation year. In conclusion, our study highlights the need for more long-term studies on chronic lethal effects of pesticides on honeybees. Environ Toxicol Chem 2022;41:2318–2327. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.},\n doi = {https://doi.org/10.1002/etc.5420},\n eprint = {https://setac.onlinelibrary.wiley.com/doi/pdf/10.1002/etc.5420},\n keywords = {Ecotoxicology, Insecticide, Pesticide risk assessment},\n url = {https://setac.onlinelibrary.wiley.com/doi/abs/10.1002/etc.5420},\n}\n\n\n
@Article{Ferraro2022,\n author = {Ferraro, Kristy M. and Schmitz, Oswald J. and McCary, Matthew A.},\n journal = {Ecography},\n title = {Effects of ungulate density and sociality on landscape heterogeneity: a mechanistic modeling approach},\n year = {2022},\n number = {2},\n volume = {2022},\n abstract = {Animals can be important vectors of nutrient transfer within and across landscapes, with important implications for ecosystem productivity and composition. While it is presumed large ungulates are agents of nutrient dispersal via movement and activity, research analyzing their net effects on landscapes remains scarce. We present an individual-based model that investigates how caribou affect the distribution of nutrients on a landscape through consumption only, as well through the cumulative effects of consumption and nutrient deposition (i.e. fecal waste and carcass deposition). We explored these dynamics in simulations that altered the context of environments, either initially containing heterogeneous or homogeneous nutrient distributions, animal densities and sociality of caribou behavior. In the consumption-only simulations, caribou density and sociality created different patterns of heterogeneity at both the landscape and local scale depending on the initial landscape conditions. In these simulations, caribou populations crashed at high densities because the lack of animal deposition resulted in low resources across the landscape. This was not the case when considering the cumulative effects of consumption and deposition, indicating the return of nutrients from animals may be important for population stability. Additionally, in simulations considering the cumulative effects of caribou, increasing caribou density increased landscape heterogeneity irrespective of the initial condition (i.e. heterogeneous and homogeneous landscapes), and maintained or increased local heterogeneity in heterogeneous and homogenous landscape, respectively. Importantly, in all simulations the net impact of caribou at the individual patch level was extremely variable, suggesting that animal inputs are highly varied throughout the landscape. Our results indicate the movement of large ungulates such as caribou can increase the heterogeneity of available nutrients within a landscape and provide an important feedback for population stability. Thus, the loss of large ungulates from natural ecosystems via anthropogenic activity is likely to result in less heterogeneous natural landscapes.},\n doi = {https://doi.org/10.1111/ecog.06039},\n eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/ecog.06039},\n keywords = {caribou, ecosystems, individual-based modeling, population dynamics, ungulates, zoogeochemistry},\n url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ecog.06039},\n}\n\n\n
@Inbook{Reinhardt2022,\nauthor="Reinhardt, Oliver\nand Warnke, Tom\nand Uhrmacher, Adelinde M.",\ntitle="Agent-Based Modelling and Simulation with Domain-Specific Languages",\nbookTitle="Towards Bayesian Model-Based Demography: Agency, Complexity and Uncertainty in Migration Studies",\nyear="2022",\npublisher="Springer International Publishing",\naddress="Cham",\npages="113--134",\nabstract="Conducting simulation studies within a model-based framework is a complex process, in which many different concerns must be considered. Central tasks include the specification of the simulation model, the execution of simulation runs, the conduction of systematic simulation experiments, and the management and documentation of the model's context. In this chapter, we look into how these concerns can be separated and handled by applying domain-specific languages (DSLs), that is, languages that are tailored to specific tasks in a specific application domain. We demonstrate and discuss the features of the approach by using the modelling language ML3, the experiment specification language SESSL, and PROV, a graph-based standard to describe the provenance information underlying the multi-stage process of model development.",\nisbn="978-3-030-83039-7",\ndoi="10.1007/978-3-030-83039-7_7",\nurl="https://doi.org/10.1007/978-3-030-83039-7_7"\n}\n\n\n
@Article{Dahirel2021,\n author = {Dahirel, Maxime and Bertin, Aline and Haond, Marjorie and Blin, Aurélie and Lombaert, Eric and Calcagno, Vincent and Fellous, Simon and Mailleret, Ludovic and Malausa, Thibaut and Vercken, Elodie},\n journal = {Oikos},\n title = {Shifts from pulled to pushed range expansions caused by reduction of landscape connectivity},\n year = {2021},\n number = {5},\n pages = {708-724},\n volume = {130},\n abstract = {Range expansions are key processes shaping the distribution of species; their ecological and evolutionary dynamics have become especially relevant today, as human influence reshapes ecosystems worldwide. Many attempts to explain and predict range expansions assume, explicitly or implicitly, so-called ‘pulled' expansion dynamics, in which the low-density edge populations provide most of the ‘fuel' for the species advance. Some expansions, however, exhibit very different dynamics, with high-density populations behind the front ‘pushing' the expansion forward. These two types of expansions are predicted to have different effects on e.g. genetic diversity and habitat quality sensitivity. However, empirical studies are lacking due to the challenge of generating reliably pushed versus pulled expansions in the laboratory, or discriminating them in the field. We here propose that manipulating the degree of connectivity among populations may prove a more generalizable way to create pushed expansions. We demonstrate this with individual-based simulations as well as replicated experimental range expansions (using the parasitoid wasp Trichogramma brassicae as model). By analyzing expansion velocities and neutral genetic diversity, we showed that reducing connectivity led to pushed dynamics. Low connectivity alone, i.e. without density-dependent dispersal, can only lead to ‘weakly pushed' expansions, where invasion speed conforms to pushed expectations, but the decline in genetic diversity does not. In empirical expansions however, low connectivity may in some cases also lead to adjustments to the dispersal-density function, recreating ‘classical' pushed expansions. In the current context of habitat loss and fragmentation, we need to better account for this relationship between connectivity and expansion regimes to successfully predict the ecological and evolutionary consequences of range expansions.},\n doi = {https://doi.org/10.1111/oik.08278},\n eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/oik.08278},\n keywords = {biological control, biological invasions, density-dependent dispersal, individual-based model, range shifts, Trichogramma},\n url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/oik.08278},\n}\n\n\n
@Article{Wesener2021,\n author = {Wesener, Felix and Szymczak, Aleksandra and Rillig, Matthias C. and Tietjen, Britta},\n journal = {Environmental Microbiology},\n title = {Stress priming affects fungal competition - evidence from a combined experimental and modelling study},\n year = {2021},\n number = {10},\n pages = {5934-5945},\n volume = {23},\n abstract = {Summary Priming, an inducible stress defence strategy that prepares an organism for an impending stress event, is common in microbes and has been studied mostly in isolated organisms or populations. How the benefits of priming change in the microbial community context and, vice versa, whether priming influences competition between organisms, remain largely unknown. In this study, we grew different isolates of soil fungi that experienced heat stress in isolation and pairwise competition experiments and assessed colony extension rate as a measure of fitness under priming and non-priming conditions. Based on this data, we developed a cellular automaton model simulating the growth of the ascomycete Chaetomium angustispirale competing against other fungi and systematically varied fungal response traits to explain similarities and differences observed in the experimental data. We showed that competition changes the priming benefit compared with isolated growth and that it can even be reversed depending on the competitor's traits such as growth rate, primeability and stress susceptibility. With this study, we transfer insights on priming from studies in isolation to competition between species. This is an important step towards understanding the role of inducible defences in microbial community assembly and composition.},\n doi = {https://doi.org/10.1111/1462-2920.15418},\n eprint = {https://ami-journals.onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.15418},\n url = {https://ami-journals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.15418},\n}\n\n\n\n\n\n\n\n
@Article{Ghoreishi2021,\n author = {Mohammad Ghoreishi and Saman Razavi and Amin Elshorbagy},\n journal = {Hydrological Sciences Journal},\n title = {Understanding human adaptation to drought: agent-based agricultural water demand modeling in the Bow River Basin, Canada},\n year = {2021},\n number = {3},\n pages = {389-407},\n volume = {66},\n abstract = {ABSTRACTThe farmers in the Bow River Basin (BRB), Canada, have adopted water conservation strategies to reduce water needs. This reduction, however, encouraged the expansion of irrigation, which may rebound agricultural water demands. This paradox requires an understanding of human adaptation to drought by mapping individual farmers’ water conservation decisions to the dynamics of the basin-wide water demand. We develop an agent-based agricultural water demand (ABAD) model, simulating farmers’ behavior in adopting new on-farm irrigation systems and/or changing crop patterns in response to drought conditions in the BRB. ABAD demonstrates (1) how farmers’ attitude toward profits, risk aversion, environmental protection, social interaction, and irrigation expansion explains the dynamics of the water demand and (2) how the conservation program may paradoxically lead to the rebound phenomenon. ABAD, subject to its conceptualization limitations, can be used for exploration and scenario analysis of future agricultural water demand in response to water conservation programs in the BRB.},\n doi = {10.1080/02626667.2021.1873344},\n eprint = {https://doi.org/10.1080/02626667.2021.1873344},\n publisher = {Taylor & Francis},\n url = {https://doi.org/10.1080/02626667.2021.1873344},\n}\n\n\n
@Article{DOrazio2021,\n author = {Marco D'Orazio and Gabriele Bernardini and Enrico Quagliarini},\n journal = {Safety Science},\n title = {Sustainable and resilient strategies for touristic cities against COVID-19: An agent-based approach},\n year = {2021},\n issn = {0925-7535},\n pages = {105399},\n volume = {142},\n abstract = {Touristic cities will suffer from COVID-19 emergency because of its economic impact on their communities. The first emergency phases involved a wide closure of such areas to support “social distancing” measures (i.e. travels limitation; lockdown of (over)crowd-prone activities). In the “second phase”, individual’s risk-mitigation strategies (facial masks) could be properly linked to “social distancing” to ensure re-opening touristic cities to visitors. Simulation tools could support the effectiveness evaluation of risk-mitigation measures to look for an economic and social optimum for activities restarting. This work modifies an existing Agent-Based Model to estimate the virus spreading in touristic areas, including tourists and residents’ behaviours, movement and virus effects on them according to a probabilistic approach. Consolidated proximity-based and exposure-time-based contagion spreading rules are included according to international health organizations and previous calibration through experimental data. Effects of tourists’ capacity (as “social distancing”-based measure) and other strategies (i.e. facial mask implementation) are evaluated depending on virus-related conditions (i.e. initial infector percentages). An idealized scenario representing a significant case study has been analysed to demonstrate the tool capabilities and compare the effectiveness of those solutions. Results show that “social distancing” seems to be more effective at the highest infectors’ rates, although represents an extreme measure with important economic effects. This measure loses its full effectiveness (on the community) as the infectors’ rate decreases and individuals’ protection measures become predominant (facial masks). The model could be integrated to consider other recurring issues on tourist-related fruition and schedule of urban spaces and facilities (e.g. cultural/leisure buildings).},\n doi = {https://doi.org/10.1016/j.ssci.2021.105399},\n keywords = {COVID-19, Infectious disease, Airborne disease transmission, Simulation model, Agent-based modelling},\n url = {https://www.sciencedirect.com/science/article/pii/S0925753521002435},\n}\n\n\n
@Article{Azizi2021,\n author = {Azizi, Asma and Mubayi, Anamika and Mubayi, Anuj},\n journal = {Journal of the Indian Institute of Science},\n title = {Social Ecological Contexts and Alcohol Drinking Dynamics: An Application of the Survey Data-Driven Agent-Based Model for University Students},\n year = {2021},\n month = {08},\n volume = {101},\n doi = {10.1007/s41745-021-00252-2},\n}\n\n\n
@Article{Azizi2020,\n author = {Asma Azizi and Anamika Mubayi and Anuj Mubayi},\n journal = {arxiv.org},\n title = {The Impact of Individual's Ecological Factors on the Dynamics of Alcohol Drinking among Arizona State University Students: An Application of the Survey Data-driven Agent-based Model},\n year = {2020},\n abstract = {College-aged students are one of the most vulnerable populations to high-risk alcohol drinking behaviors that could cause them consequences such as injury or sexual assault. An important factor that may influence college students' decision on alcohol drinking behavior is socializing at certain contexts across university environment. The present study aims to identify and better understand ecological conditions driving the dynamics of distribution of alcohol use among college-aged students.\nTo this end, a pilot study is conducted to evaluate students' movement patterns to different contexts across the Arizona State University (ASU) campus, and to use its results to develop an agent-based simulation model designed for examining the role of environmental factors on development and maintenance of alcohol drinking behavior by a representative sample of ASU students. The proposed model that resembles an approximate reaction-diffusion model accounts for movement of agents to various contexts (i.e. diffusion) and alcohol drinking influences within those contexts (i.e., reaction) via a SIR-type model. Of the four most visited contexts at ASU Tempe campus -- Library, Memorial Union, Fitness Center, and Dorm -- the context with the highest visiting probability, Memorial Union, is the most influential and most sensitive context (around 16 times higher impact of alcohol related influences than the other contexts) on spreading alcohol drinking behavior.\nOur findings highlight the crucial role of socialization at local environments on the dynamics of students' alcohol use as well as on the long-term prediction of the college drinking prevalence.},\n archiveprefix = {arXiv},\n eprint = {2011.01876},\n primaryclass = {stat.AP},\n url = {https://arxiv.org/abs/2011.01876v1},\n}\n\n\n
@Article{Murphy2020,\n author = {Murphy, Kilian J. and Ciuti, Simone and Kane, Adam},\n title = {An introduction to agent-based models as an accessible surrogate to field-based research and teaching},\n journal = {Ecology and Evolution},\n year = {2020},\n volume = {n/a},\n number = {n/a},\n abstract = {Abstract There are many barriers to fieldwork including cost, time, and physical ability. Unfortunately, these barriers disproportionately affect minority communities and create a disparity in access to fieldwork in the natural sciences. Travel restrictions, concerns about our carbon footprint, and the global lockdown have extended this barrier to fieldwork across the community and led to increased anxiety about gaps in productivity, especially among graduate students and early-career researchers. In this paper, we discuss agent-based modeling as an open-source, accessible, and inclusive resource to substitute for lost fieldwork during COVID-19 and for future scenarios of travel restrictions such as climate change and economic downturn. We describe the benefits of Agent-Based models as a teaching and training resource for students across education levels. We discuss how and why educators and research scientists can implement them with examples from the literature on how agent-based models can be applied broadly across life science research. We aim to amplify awareness and adoption of this technique to broaden the diversity and size of the agent-based modeling community in ecology and evolutionary research. Finally, we discuss the challenges facing agent-based modeling and discuss how quantitative ecology can work in tandem with traditional field ecology to improve both methods.},\n doi = {https://doi.org/10.1002/ece3.6848},\n eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.6848},\n keywords = {accessible resource, agent-based model, computational tools, ecology, fieldwork, inclusive resource, NetLogo, open-source resource, quantitative methods},\n url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.6848},\n}\n\n\n
@Article{DOrazio2020,\n author = {D'Orazio, Marco and Bernardini, Gabriele and Quagliarini, Enrico},\n title = {A probabilistic model to evaluate the effectiveness of main solutions to COVID-19 spreading in university buildings according to proximity and time-based consolidated criteria},\n journal = {Research Square},\n year = {2020},\n month = nov,\n issn = {2693-5015},\n abstract = {Crowds in buildings open to the public can alter the occupants’ safety in different emergency conditions, including those related to a pandemic. In this sense, university buildings are one of the most relevant scenarios in which the COVID-19 event clearly pointed out the stakeholders’ needs toward safety issues, especially because of the possibility of day-to-day presences of the same users (i.e. students, teachers) and overcrowding causing long-lasting contacts with possible “infectors” in such closed environments. While waiting for the vaccine, as for other public buildings, policy-makers’ measures to limit (second) virus outbreaks combine individual’s strategies (facial masks), occupants’ capacity and access control to avoid lockdowns and ensure adequate conditions for occupants. Simulators could support effectiveness evaluations of such measures. To fill this gap, this work proposes a quick and probabilistic simulation model based on consolidated proximity and exposure-time-based rules for virus transmission (confirmed by international health organizations). The building occupancy is defined according to university schedule, identifying the main “attraction areas” in the building (classrooms, break-areas). Scenarios are defined in terms of occupants’ densities, mitigation strategies, virus-related aspects. The model is calibrated on experimental data and applied to a relevant university building. Results demonstrate the model capabilities. In the case study, occupants’ capacity limitation could support the adoption of surgical masks by users instead of FFPk masks (thus improving users’ comfort issues). Preliminary correlations to combine acceptable mask filters-occupants’ density are proposed to support stakeholders in organizing users’ presences in the building during the pandemic.&nbsp;},\n doi = {10.21203/rs.3.rs-82941/v1},\n refid = {rs-82941},\n url = {https://doi.org/10.21203/rs.3.rs-82941/v1},\n}\n\n\n
@Inbook{Ma2020,\n chapter = {High-Performance Pareto-Based Optimization Model for Spatial Land Use Allocation},\n pages = {185--209},\n title = {High Performance Computing for Geospatial Applications},\n publisher = {Springer International Publishing},\n year = {2020},\n author = {Ma, Xiaoya and Zhao, Xiang and Jiang, Ping and Liu, Yuangang},\n editor = {Tang, Wenwu and Wang, Shaowen},\n address = {Cham},\n isbn = {978-3-030-47998-5},\n abstract = {Spatial land use allocation is often formulated as a complex multiobjective optimization problem. As effective tools for multiobjective optimization, Pareto-based heuristic optimization algorithms, such as genetic, artificial immune system, particle swarm optimization, and ant colony optimization algorithms, have been introduced to support trade-off analysis and posterior stakeholder involvement in land use decision making. However, these algorithms are extremely time consuming, and minimizing the computational time has become one of the largest challenges in obtaining the Pareto frontier in spatial land use allocation problems. To improve the efficiency of these algorithms and better support multiobjective decision making in land use planning, high-performance Pareto-based optimization algorithms for shared-memory and distributed-memory computing platforms were developed in this study. The OpenMP and Message Passing Interface (MPI) parallel programming technologies were employed to implement the shared-memory and distributed-memory parallel models, respectively, in parallel in the Pareto-based optimization algorithm. Experiments show that both the shared-memory and message-passing parallel models can effectively accelerate multiobjective spatial land use allocation models. The shared-memory model achieves satisfying performance when the number of CPU cores used for computing is less than 8. Conversely, the message-passing model displays better scalability than the shared-memory model when the number of CPU cores used for computing is greater than 8.},\n booktitle = {High Performance Computing for Geospatial Applications},\n doi = {10.1007/978-3-030-47998-5_11},\n url = {https://doi.org/10.1007/978-3-030-47998-5_11},\n}\n\n\n
@Article{DOrazio2020a,\n author = {Marco D'Orazio and Gabriele Bernardini and Enrico Quagliarini},\n journal = {arxiv.org},\n title = {Sustainable and resilient strategies for touristic cities against COVID-19: an agent-based approach},\n year = {2020},\n abstract = {Touristic cities will suffer from COVID-19 emergency because of its economic impact on their communities. The first emergency phases involved a wide closure of such areas to support "social distancing" measures (i.e. travels limitation; lockdown of (over)crowd-prone activities). In the second phase, individual's risk-mitigation strategies (facial masks) could be properly linked to "social distancing" to ensure re-opening touristic cities to visitors. Simulation tools could support the effectiveness evaluation of risk-mitigation measures to look for an economic and social optimum for activities restarting. This work modifies an existing Agent-Based Model to estimate the virus spreading in touristic areas, including tourists and residents' behaviours, movement and virus effects on them according to a probabilistic approach. Consolidated proximity-based and exposure-time-based contagion spreading rules are included according to international health organizations and previous calibration through experimental data. Effects of tourists' capacity (as "social distancing"-based measure) and other strategies (i.e. facial mask implementation) are evaluated depending on virus-related conditions (i.e. initial infector percentages). An idealized scenario representing a significant case study has been analysed to demonstrate the tool capabilities and compare the effectiveness of those solutions. Results show that "social distancing" seems to be more effective at the highest infectors' rates, although represents an extreme measure with important economic effects. This measure loses its full effectiveness (on the community) as the infectors' rate decreases and individuals' protection measures become predominant (facial masks). The model could be integrated to consider other recurring issues on tourist-related fruition and schedule of urban spaces and facilities (e.g. cultural/leisure buildings).},\n archiveprefix = {arXiv},\n eprint = {2005.12547},\n primaryclass = {physics.soc-ph},\n url = {https://arxiv.org/abs/2005.12547},\n}\n\n\n
@Article{DOrazio2020b,\n author = {Marco D'Orazio and Gabriele Bernardini and Enrico Quagliarini},\n journal = {arxiv.org},\n title = {How to restart? An agent-based simulation model towards the definition of strategies for COVID-19 "second phase" in public buildings},\n year = {2020},\n abstract = {Restarting public buildings activities in the "second phase" of COVID-19 emergency should be supported by operational measures to avoid a second virus spreading. Buildings hosting the continuous presence of the same users and significant overcrowd conditions over space/time (e.g. large offices, universities) are critical scenarios due to the prolonged contact with infectors. Beside individual's risk-mitigation strategies performed (facial masks), stakeholders should promote additional strategies, i.e. occupants' load limitation (towards "social distancing") and access control. Simulators could support the measures effectiveness evaluation. This work provides an Agent-Based Model to estimate the virus spreading in the closed built environment. The model adopts a probabilistic approach to jointly simulate occupants' movement and virus transmission according to proximity-based and exposure-time-based rules proposed by international health organizations. Scenarios can be defined in terms of building occupancy, mitigation strategies and virus-related aspects. The model is calibrated on experimental data ("Diamond Princess" cruise) and then applied to a relevant case-study (a part of a university campus). Results demonstrate the model capabilities. Concerning the case-study, adopting facial masks seems to be a paramount strategy to reduce virus spreading in each initial condition, by maintaining an acceptable infected people's number. The building capacity limitation could support such measure by potentially moving from FFPk masks to surgical masks use by occupants (thus improving users' comfort issues). A preliminary model to combine acceptable mask filters-occupants' density combination is proposed. The model could be modified to consider other recurring scenarios in other public buildings (e.g. tourist facilities, cultural buildings).},\n archiveprefix = {arXiv},\n eprint = {2004.12927},\n primaryclass = {physics.soc-ph},\n url = {https://arxiv.org/abs/2004.12927},\n}\n\n\n
@Article{Kaaronen2020,\n author = {Kaaronen, Roope Oskari and Strelkovskii, Nikita},\n journal = {One Earth},\n title = {Cultural Evolution of Sustainable Behaviors: Pro-environmental Tipping Points in an Agent-Based Model},\n year = {2020},\n issn = {2590-3330},\n month = nov,\n number = {1},\n pages = {85--97},\n volume = {2},\n abstract = {To reach sustainability transitions, we must learn to leverage social systems into tipping points, where societies exhibit positive-feedback loops in the adoption of sustainable behavioral and cultural traits. However, much less is known about the most efficient ways to reach such transitions or how self-reinforcing systemic transformations might be instigated through policy. We employ an agent-based model to study the emergence of social tipping points through various feedback loops that have been previously identified to constitute an ecological approach to human behavior. Our model suggests that even a linear introduction of pro-environmental affordances (action opportunities) to a social system can have non-linear positive effects on the emergence of collective pro-environmental behavior patterns. We validate the model against data on the evolution of cycling and driving behaviors in Copenhagen. Our model gives further evidence and justification for policies that make pro-environmental behavior psychologically salient, easy, and the path of least resistance.\nTo reach sustainability transitions, we must learn to leverage social systems into tipping points, where societies exhibit positive-feedback loops in the adoption of sustainable behavioral and cultural traits. However, much less is known about the most efficient ways to reach such transitions or how self-reinforcing systemic transformations might be instigated through policy. We employ an agent-based model to study the emergence of social tipping points through various feedback loops that have been previously identified to constitute an ecological approach to human behavior. Our model suggests that even a linear introduction of pro-environmental affordances (action opportunities) to a social system can have non-linear positive effects on the emergence of collective pro-environmental behavior patterns. We validate the model against data on the evolution of cycling and driving behaviors in Copenhagen. Our model gives further evidence and justification for policies that make pro-environmental behavior psychologically salient, easy, and the path of least resistance.},\n comment = {doi: 10.1016/j.oneear.2020.01.003},\n doi = {10.1016/j.oneear.2020.01.003},\n groups = {[jan:]},\n publisher = {Elsevier},\n url = {https://doi.org/10.1016/j.oneear.2020.01.003},\n}\n\n\n
@Inbook{Tang2020,\n chapter = {Code Reusability and Transparency of Agent-Based Modeling: A Review from a Cyberinfrastructure Perspective},\n pages = {115--134},\n title = {High Performance Computing for Geospatial Applications},\n publisher = {Springer International Publishing},\n year = {2020},\n author = {Tang, Wenwu and Grimm, Volker and Tesfatsion, Leigh and Shook, Eric and Bennett, David and An, Li and Gong, Zhaoya and Ye, Xinyue},\n editor = {Tang, Wenwu and Wang, Shaowen},\n address = {Cham},\n isbn = {978-3-030-47998-5},\n abstract = {Agent-based models have been increasingly applied to the study of space-time dynamics in real-world systems driven by biophysical and social processes. For the sharing and communication of these models, code reusability and transparency play a pivotal role. In this chapter, we focus on code reusability and transparency of agent-based models from a cyberinfrastructure perspective. We identify challenges of code reusability and transparency in agent-based modeling and suggest how to overcome these challenges. As our findings reveal, while the understanding of and demands for code reuse and transparency are different in various domains, they are inherently related, and they contribute to each step of the agent-based modeling process. While the challenges to code development are daunting, continually evolving cyberinfrastructure-enabled computing technologies such as cloud computing, high-performance computing, and parallel computing tend to lower the computing-level learning curve and, more importantly, facilitate code reuse and transparency of agent-based models.},\n booktitle = {High Performance Computing for Geospatial Applications},\n doi = {10.1007/978-3-030-47998-5_7},\n url = {https://doi.org/10.1007/978-3-030-47998-5_7},\n}\n\n\n
@Article{Zakharova2020,\n author = {L. Zakharova and K.M. Meyer and M. Seifan},\n title = {Combining trait- and individual-based modelling to understand desert plant community dynamics},\n journal = {Ecological Modelling},\n year = {2020},\n volume = {434},\n pages = {109260},\n issn = {0304-3800},\n abstract = {Understanding the mechanisms driving community dynamics helps us to make reliable predictions about communities’ response to environmental change. Studying desert plant communities is particularly challenging because of strong intra- and interannual fluctuations in precipitation. Models rise to this challenge by providing an arena for systematic evaluation of the parameter space in virtual experiments. We applied a trait- and individual-based model to explore how community dynamics arise from the plant traits and interactions of plants with other plants and with their environment. The model is based on data from annual plant communities in the Negev Desert dominated by the True Rose of Jericho (Anastatica hierochuntica). We showed that functional traits that are involved in plant-plant interactions are equally important for community dynamics as traits promoting tolerance to abiotic stress. The sensitivity analysis of the model highlights relative growth rate, maximum biomass, the amount of time in dormancy and germination probability as the most important traits for community dynamics. The model reflects the particular importance of environmental factors such as precipitation and soil water availability based on topography for community dynamics. Our model benefits from the ability of individual-based models to capture plant-plant interactions and derive community properties from individual characteristics and from the feature of trait-based approaches to link traits to organismal functions. Our study demonstrates the advantages of the combined use of trait- and individual-based models for investigating community drivers in changing extreme environments.},\n doi = {https://doi.org/10.1016/j.ecolmodel.2020.109260},\n keywords = {Annual plants, Community dynamics, Functional trait, Individual-based model, Negev Desert},\n url = {http://www.sciencedirect.com/science/article/pii/S0304380020303306},\n}\n\n\n
@PhdThesis{Kaaronen2020a,\n author = {Kaaronen, Roope Oskari},\n title = {Steps to a Sustainable Mind : Explorations into the Ecology of Mind and Behaviour},\n school = {University of Helsinki, Faculty of Social Sciences},\n year = {2020},\n type = {Doctoral dissertation},\n abstract = {This transdisciplinary doctoral thesis presents various theoretical, methodological and empirical approaches that together form an ecological approach to the study of social sciences. The key argument follows: to understand how sustainable behaviours and cultures may emerge, and how their development can be facilitated, we must further learn how behaviours emerge as a function of the person and the material and social environment. Furthermore, in this thesis the sustainability crises are framed as sustain-ability crises. We must better equip our cultures with abilities to deal with the complexity and uncertainty of socio-ecological systems, and use these cultural skillsets to survive in and adapt to an increasingly unpredictable world.\n\nThis thesis employs a plurality of ecological social sciences and related methodologies—such as ecological psychology, ecological rationality and agent-based modelling—to enlighten the question of how the collective adoption of sustainable behaviours can be leveraged, particularly by changing the affordances in the material environment. What is common to these ecological approaches is the appreciation of ‘processes’ over ‘products’: we must understand the various processes through which sustainable forms of behaviour or decision-making emerge to truly locate leverage points in social systems. Finally, this thesis deals extensively with uncertainty in complex systems. It proposes that we can look to local and traditional knowledge in learning how to deal adaptively with uncertainty.},\n url = {https://helda.helsinki.fi/handle/10138/319046},\n}\n\n\n
@Article{Dahirel2020,\n author = {Dahirel, Maxime and Bertin, Aline and Haond, Marjorie and Blin, Aur{\\'e}lie and Lombaert, Eric and Calcagno, Vincent and Fellous, Simon and Mailleret, Ludovic and Vercken, Elodie},\n title = {Shifts from pulled to pushed range expansions caused by reductions in connectedness},\n journal = {bioRxiv},\n year = {2020},\n abstract = {While species ranges have always moved, the ecological and evolutionary dynamics of range expansions have become especially relevant today, as human influence reshapes ecosystems worldwide. As a consequence, there have been many attempts to explain and predict evolutionary and demographic dynamics observed during range expansions. However, many of these predictions are based, explicitly or implicitly, on a subset of possible range expansion types, so-called {\\textquotedblleft}pulled{\\textquotedblright} dynamics, in which the low-density front populations provide most of the {\\textquotedblleft}fuel{\\textquotedblright} for the advance. Some expansions may exhibit very different dynamics, with high-density populations behind the front {\\textquotedblleft}pushing{\\textquotedblright} the expansion forward. Studying the ecological and evolutionary consequences of pushed vs. pulled dynamics remains challenging, due to difficulties in reliably generating or identifying pushed and pulled waves in experimental or natural settings. Manipulations of the within-habitat quality to create Allee effects have successfully created pushed waves, but may only be applicable in some contexts. We here propose that manipulating, and specifically reducing the degree of structural connectivity among habitats may prove a more generalizable way to create pushed waves, through density-dependent dispersal. We demonstrate this using both individual-based simulations as well as replicated experimental range expansions (with the parasitoid wasp Trichogramma brassicae as model). Analysing expansion velocities and neutral genetic diversity, we showed that restricting connectivity did lead to pushed dynamics. Interestingly, our results suggest that reducing connectivity led to density-dependent spread (and thus pushed waves) through two different mechanisms in simulated and experimental expansions. In the current context of habitat loss and fragmentation, we need to better account for this relationship between connectedness and expansion regimes to be able to successfully predict the ecological and especially evolutionary consequences of range expansions.Competing Interest StatementThe authors have declared no competing interest.},\n doi = {10.1101/2020.05.13.092775},\n elocation-id = {2020.05.13.092775},\n eprint = {https://www.biorxiv.org/content/early/2020/05/15/2020.05.13.092775.full.pdf},\n publisher = {Cold Spring Harbor Laboratory},\n url = {https://www.biorxiv.org/content/early/2020/05/15/2020.05.13.092775},\n}\n\n\n
@Article{Kopp2020,\n author = {Thomas Kopp and Jan Salecker},\n title = {How traders influence their neighbours: Modelling social evolutionary processes and peer effects in agricultural trade networks},\n journal = {Journal of Economic Dynamics and Control},\n year = {2020},\n volume = {117},\n pages = {103944},\n issn = {0165-1889},\n abstract = {Marketing channel choices in agricultural trade networks affect the networks’ overall performance and influence rural livelihoods. This study identifies key determinants of these choices among natural rubber traders in Indonesia to evaluate four policy scenarios and their potential effects on rural incomes. Since traders’ marketing decisions are based on past interactions, resulting trade networks are formed in recursive processes and can be understood as complex adaptive systems. Due to inherent endogeneity in these systems, process-based approaches such as agent-based modelling (ABM) can be effective in understanding them. Using a self-gathered primary dataset from Jambi Province, Indonesia, we implement and parameterise an ABM to simulate the formation of the rubber trading network and analyse the effects on rural livelihoods of four hypothetical policy scenarios: improved micro-credit availability, increased access to education, better infrastructure and transportation capacity, and market information availability. The model is calibrated through a genetic algorithm which maximises the similarity between the simulated network and the actual network observed in the data. Results indicate that sellers’ decisions on a buyer are primarily determined by debt obligations and past peer-interactions. The most influential sellers have a similar level of formal education as their peers and live in close physical proximity. Results of the policy scenario analysis suggests that policies aimed at reducing sellers’ dependence on credit from buyers and increasing education are the most effective policies for improving value chains and reducing poverty in the region under consideration.},\n doi = {https://doi.org/10.1016/j.jedc.2020.103944},\n keywords = {Agent-based modelling, Complex adaptive systems, Networks, Rubber, Indonesia, Agricultural trade},\n url = {http://www.sciencedirect.com/science/article/pii/S0165188920301123},\n}\n\n\n
@Article{Widyastuti2020,\n author = {Widyastuti, Kirana and Imron, Muhammad Ali and Pradopo, Subyantoro Tri and Suryatmojo, Hatma and Sopha, Bertha Maya and Spessa, Allan and Berger, Uta},\n journal = {International Journal of Wildland Fire},\n title = {PeatFire: an agent-based model to simulate fire ignition and spreading in a tropical peatland ecosystem},\n year = {2020},\n abstract = {The increased frequency and spread of tropical peat fires over the last two decades have attracted global attention because they cause significant environmental and health impacts at local to global scales. To understand the relative importance of key factors controlling tropical peatland burning events, we developed PeatFire, an agent-based model simulating the interaction between human-induced ignitions, fire and peat characteristics. The model describes (1) above- and belowground fires, which spread independently but interact with each other; (2) above- and belowground biomass; and (3) the watertable determining peat dryness and susceptibility to fire. We applied PeatFire to a region in South Sumatra that has experienced profound natural rainforest loss due to peat fires. Sensitivity analysis of the model suggests that fire sizes depend mostly on watertable depth, peat-dry-index and number of dry days before ignition. Using pattern-oriented modelling, these factors were parameterised so that the model output matches spatiotemporal fire patterns observed in the study region in 2015. Our results emphasise the risk of a sudden shift from moderate fire occurrence to complete burning and highlight the importance of local context to peatland regulation, which should consider both biophysical and socioeconomic factors and strategies for peatland fire management.},\n groups = {jan:6},\n keywords = {Keywords: agent-based model, burnt area, degraded habitat, Indonesia, peatland, tropical peat fire, watertable depth, wildlife reserve.},\n url = {https://doi.org/10.1071/WF19213},\n}\n\n\n
@Article{Wesener2020,\n author = {Wesener, Felix and Szymczak, Aleksandra and Rillig, Matthias C. and Tietjen, Britta},\n title = {Stress priming affects fungal competition {\\textendash} evidence from a combined experimental and modeling study},\n journal = {bioRxiv},\n year = {2020},\n abstract = {Priming, an inducible stress defense strategy that prepares an organism for an impending stress event, is common in microbes and has been studied mostly in isolated organisms or populations. How the benefits of priming change in the microbial community context and, vice versa, whether priming influences competition between organisms, remains largely unknown. In this combined experimental and modeling study, we developed a cellular automaton model based on dedicated data of different isolates of soil fungi in isolation and pairwise competition experiments. With the model, we simulated growth of the ascomycete Chaetomium elatum competing against other fungi to understand which species traits influence the benefit of priming and the effect of priming on competition. We showed that competition changes the priming benefit compared to isolated growth, and that it depends not only on the primeable species itself, but also on the competitors{\\textquoteright} traits such as growth rate, primeability and stress susceptibility. In addition, we showed that priming benefits were not always reflected in the competitive outcome. With this study, we transferred insights on priming from studies in isolation to the community context. This is an important step towards understanding the role of inducible defenses in microbial community assembly and composition.},\n doi = {10.1101/2020.03.04.976357},\n elocation-id = {2020.03.04.976357},\n eprint = {https://www.biorxiv.org/content/early/2020/03/05/2020.03.04.976357.full.pdf},\n publisher = {Cold Spring Harbor Laboratory},\n url = {https://www.biorxiv.org/content/early/2020/03/05/2020.03.04.976357},\n}\n\n\n
@Article{Salecker2019,\n author = {Salecker, Jan and Sciaini, Marco and Meyer, Katrin M. and Wiegand, Kerstin},\n title = {The nlrx r package: A next-generation framework for reproducible NetLogo model analyses},\n journal = {Methods in Ecology and Evolution},\n year = {2019},\n volume = {10},\n number = {11},\n pages = {1854-1863},\n abstract = {Abstract Agent-based models find wide application in all fields of science where large-scale patterns emerge from properties of individuals. Due to increasing capacities of computing resources it was possible to improve the level of detail and structural realism of next-generation models in recent years. However, this is at the expense of increased model complexity, which requires more efficient tools for model exploration, analysis and documentation that enable reproducibility, repeatability and parallelization. NetLogo is a widely used environment for agent-based model development, but it does not provide sufficient built-in tools for extensive model exploration, such as sensitivity analyses. One tool for controlling NetLogo externally is the r-package RNetLogo. However, this package is not suited for efficient, reproducible research as it has stability and resource allocation issues, is not straightforward to be setup and used on high performance computing clusters and does not provide utilities, such as storing and exchanging metadata, in an easy way. We present the r-package nlrx, which overcomes stability and resource allocation issues by running NetLogo simulations via dynamically created XML experiment files. Class objects make setting up experiments more convenient and helper functions provide many parameter exploration approaches, such as Latin Hypercube designs, Sobol sensitivity analyses or optimization approaches. Output is automatically collected in user-friendly formats and can be post-processed with provided utility functions. nlrx enables reproducibility by storing all relevant information and simulation output of experiments in one r object which can conveniently be archived and shared. We provide a detailed description of the nlrx package functions and the overall workflow. We also present a use case scenario using a NetLogo model, for which we performed a sensitivity analysis and a genetic algorithm optimization. The nlrx package is the first framework for documentation and application of reproducible NetLogo simulation model analysis.},\n doi = {https://doi.org/10.1111/2041-210X.13286},\n eprint = {https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.13286},\n keywords = {agent-based modelling, algorithm optimization, individual-based modelling, model analysis, NetLogo, r package, reproducible workflow, sensitivity analysis},\n url = {https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13286},\n}\n\n\n
@Article{Salecker2019a,\n author = {Salecker, Jan AND Dislich, Claudia AND Wiegand, Kerstin AND Meyer, Katrin M. AND Pe´er, Guy},\n title = {EFForTS-LGraf: A landscape generator for creating smallholder-driven land-use mosaics},\n journal = {PLOS ONE},\n year = {2019},\n volume = {14},\n number = {9},\n pages = {1-24},\n month = {09},\n abstract = {Spatially-explicit simulation models are commonly used to study complex ecological and socio-economic research questions. Often these models depend on detailed input data, such as initial land-cover maps to set up model simulations. Here we present the landscape generator EFFortS-LGraf that provides artificially-generated land-use maps of agricultural landscapes shaped by small-scale farms. EFForTS-LGraf is a process-based landscape generator that explicitly incorporates the human dimension of land-use change. The model generates roads and villages that consist of smallholder farming households. These smallholders use different establishment strategies to create fields in their close vicinity. Crop types are distributed to these fields based on crop fractions and specialization levels. EFForTS-LGraf model parameters such as household area or field size frequency distributions can be derived from household surveys or geospatial data. This can be an advantage over the abstract parameters of neutral landscape generators. We tested the model using oil palm and rubber farming in Indonesia as a case study and validated the artificially-generated maps against classified satellite images. Our results show that EFForTS-LGraf is able to generate realistic land-cover maps with properties that lie within the boundaries of landscapes from classified satellite images. An applied simulation experiment on landscape-level effects of increasing household area and crop specialization revealed that larger households with higher specialization levels led to spatially more homogeneous and less scattered crop type distributions and reduced edge area proportion. Thus, EFForTS-LGraf can be applied both to generate maps as inputs for simulation modelling and as a stand-alone tool for specific landscape-scale analyses in the context of ecological-economic studies of smallholder farming systems.},\n doi = {10.1371/journal.pone.0222949},\n publisher = {Public Library of Science},\n url = {https://doi.org/10.1371/journal.pone.0222949},\n}\n\n\n