Add JOSS paper

Author: danielvartan

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+@article{baker2016,
+  title = {1,500 scientists lift the lid on reproducibility},
+  author = {Baker, Monya},
+  date = {2016-05-01},
+  journaltitle = {Nature},
+  volume = {533},
+  number = {7604},
+  pages = {452--454},
+  publisher = {Nature Publishing Group},
+  issn = {1476-4687},
+  doi = {10.1038/533452a},
+  url = {https://www.nature.com/articles/533452a},
+  urldate = {2024-06-09},
+  abstract = {Survey sheds light on the "crisis" rocking research.},
+  langid = {english},
+  keywords = {reproducibility,science},
+}
+
+@article{barba2022,
+  title = {Defining the role of open source software in research reproducibility},
+  author = {Barba, Lorena A.},
+  date = {2022-08},
+  journaltitle = {Computer},
+  volume = {55},
+  number = {8},
+  pages = {40--48},
+  issn = {1558-0814},
+  doi = {10.1109/MC.2022.3177133},
+  url = {https://ieeexplore.ieee.org/document/9847328},
+  urldate = {2025-04-15},
+  abstract = {I explain the success of open source software (OSS) from the perspectives of connectivism and the language-action framework. Reproducibility engenders trust, which we build via conversations, and OSS practices help us to learn how to be more effective learning together, contributing to the same goal.},
+  keywords = {information sharing,open source software,oral communication,reproducibility of results,research and development},
+}
+
+@article{barker2022,
+  title = {Introducing the {{FAIR Principles}} for research software},
+  author = {Barker, Michelle and Chue Hong, Neil P. and Katz, Daniel S. and Lamprecht, Anna-Lena and Martinez-Ortiz, Carlos and Psomopoulos, Fotis and Harrow, Jennifer and Castro, Leyla Jael and Gruenpeter, Morane and Martinez, Paula Andrea and Honeyman, Tom},
+  date = {2022-10-14},
+  journaltitle = {Scientific Data},
+  shortjournal = {Sci Data},
+  volume = {9},
+  number = {1},
+  pages = {622},
+  publisher = {Nature Publishing Group},
+  issn = {2052-4463},
+  doi = {10.1038/s41597-022-01710-x},
+  url = {https://www.nature.com/articles/s41597-022-01710-x},
+  urldate = {2025-04-15},
+  abstract = {Research software is a fundamental and vital part of research, yet significant challenges to discoverability, productivity, quality, reproducibility, and sustainability exist. Improving the practice of scholarship is a common goal of the open science, open source, and FAIR (Findable, Accessible, Interoperable and Reusable) communities and research software is now being understood as a type of digital object to which FAIR should be applied. This emergence reflects a maturation of the research community to better understand the crucial role of FAIR research software in maximising research value. The FAIR for Research Software (FAIR4RS) Working Group has adapted the FAIR Guiding Principles to create the FAIR Principles for Research Software (FAIR4RS Principles). The contents and context of the FAIR4RS Principles are summarised here to provide the basis for discussion of their adoption. Examples of implementation by organisations are provided to share information on how to maximise the value of research outputs, and to encourage others to amplify the importance and impact of this work.},
+  langid = {english},
+  keywords = {fair principles,reproducibility,research management,science},
+}
+
+@dataset{carvalho2023a,
+  title = {Global syndemic: {{The}} impact of anthropogenic climate change on the health and nutrition of children under five years old attended by {{Brazil}}'s public health system ({{SUS}})},
+  author = {family=Carvalho, given=Aline Martins, prefix=de, useprefix=false and Klapka, Cecilia Stanzani and Magalhães, Arthur Ramalho and Barbosa, Brena Barreto and Vartanian, Daniel and Pereira, Estela Barici},
+  date = {2023},
+  doi = {10.17605/OSF.IO/8W36C},
+  abstract = {This research project investigates the impact of anthropogenic climate change on the health and nutrition of children under five years old attended by Brazil's public health system (SUS). By analyzing datasets on climate change, health records, and nutritional surveys, combined with the application of complex system techniques, this research seeks to uncover hidden patterns and correlations that could inform policies for mitigating the adverse effects of climate change on children's health and well-being.},
+  keywords = {complexity science,global syndemic,health sciences,interdisciplinary fields,nutrition,public health}
+}
+
+@article{fick2017a,
+  title = {{{WorldClim}} 2: {{New}} 1-km spatial resolution climate surfaces for global land areas},
+  shorttitle = {{{WorldClim}} 2},
+  author = {Fick, Stephen E. and Hijmans, Robert J.},
+  date = {2017},
+  journaltitle = {International Journal of Climatology},
+  volume = {37},
+  number = {12},
+  pages = {4302--4315},
+  issn = {1097-0088},
+  doi = {10.1002/joc.5086},
+  url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/joc.5086},
+  urldate = {2024-06-11},
+  abstract = {We created a new dataset of spatially interpolated monthly climate data for global land areas at a very high spatial resolution (approximately 1 km2). We included monthly temperature (minimum, maximum and average), precipitation, solar radiation, vapour pressure and wind speed, aggregated across a target temporal range of 1970–2000, using data from between 9000 and 60 000 weather stations. Weather station data were interpolated using thin-plate splines with covariates including elevation, distance to the coast and three satellite-derived covariates: maximum and minimum land surface temperature as well as cloud cover, obtained with the MODIS satellite platform. Interpolation was done for 23 regions of varying size depending on station density. Satellite data improved prediction accuracy for temperature variables 5–15\% (0.07–0.17 °C), particularly for areas with a low station density, although prediction error remained high in such regions for all climate variables. Contributions of satellite covariates were mostly negligible for the other variables, although their importance varied by region. In contrast to the common approach to use a single model formulation for the entire world, we constructed the final product by selecting the best performing model for each region and variable. Global cross-validation correlations were ≥ 0.99 for temperature and humidity, 0.86 for precipitation and 0.76 for wind speed. The fact that most of our climate surface estimates were only marginally improved by use of satellite covariates highlights the importance having a dense, high-quality network of climate station data.},
+  langid = {english},
+  keywords = {climate,climate modeling,data interpolation,databases,environmental sciences,exact sciences,geography,interdisciplinary fields,meteorology,modeling,open data,open science,probability and statistics,worldclim},
+}
+
+@article{grimm2006a,
+  title = {A standard protocol for describing individual-based and agent-based models},
+  author = {Grimm, Volker and Berger, Uta and Bastiansen, Finn and Eliassen, Sigrunn and Ginot, Vincent and Giske, Jarl and Goss-Custard, John and Grand, Tamara and Heinz, Simone K. and Huse, Geir and Huth, Andreas and Jepsen, Jane U. and Jørgensen, Christian and Mooij, Wolf M. and Müller, Birgit and Pe'er, Guy and Piou, Cyril and Railsback, Steven F. and Robbins, Andrew M. and Robbins, Martha M. and Rossmanith, Eva and Rüger, Nadja and Strand, Espen and Souissi, Sami and Stillman, Richard A. and Vabø, Rune and Visser, Ute and DeAngelis, Donald L.},
+  date = {2006-09-15},
+  journaltitle = {Ecological Modelling},
+  shortjournal = {Ecological Modelling},
+  volume = {198},
+  number = {1},
+  pages = {115--126},
+  issn = {0304-3800},
+  doi = {10.1016/j.ecolmodel.2006.04.023},
+  url = {https://www.sciencedirect.com/science/article/pii/S0304380006002043},
+  urldate = {2024-05-17},
+  abstract = {Simulation models that describe autonomous individual organisms (individual based models, IBM) or agents (agent-based models, ABM) have become a widely used tool, not only in ecology, but also in many other disciplines dealing with complex systems made up of autonomous entities. However, there is no standard protocol for describing such simulation models, which can make them difficult to understand and to duplicate. This paper presents a proposed standard protocol, ODD, for describing IBMs and ABMs, developed and tested by 28 modellers who cover a wide range of fields within ecology. This protocol consists of three blocks (Overview, Design concepts, and Details), which are subdivided into seven elements: Purpose, State variables and scales, Process overview and scheduling, Design concepts, Initialization, Input, and Submodels. We explain which aspects of a model should be described in each element, and we present an example to illustrate the protocol in use. In addition, 19 examples are available in an Online Appendix. We consider ODD as a first step for establishing a more detailed common format of the description of IBMs and ABMs. Once initiated, the protocol will hopefully evolve as it becomes used by a sufficiently large proportion of modellers.},
+  langid = {english},
+  keywords = {agent-based modeling,complexity science,interdisciplinary fields,odd protocol,open science,protocols,standards},
+}
+
+@article{grimm2020,
+  title = {The {{ODD}} protocol for describing agent-based and other simulation models: a second update to improve clarity, replication, and structural realism},
+  shorttitle = {The {{ODD}} protocol for describing agent-based and other simulation models},
+  author = {Grimm, Volker and Railsback, Steven F. and Vincenot, Christian E. and Berger, Uta and Gallagher, Cara and DeAngelis, Donald L. and Edmonds, Bruce and Ge, Jiaqi and Giske, Jarl and Groeneveld, Jürgen and Johnston, Alice S. A. and Milles, Alexander and Nabe-Nielsen, Jacob and Polhill, J. Gareth and Radchuk, Viktoriia and Rohwäder, Marie-Sophie and Stillman, Richard A. and Thiele, Jan C. and Ayllón, Daniel},
+  date = {2020},
+  journaltitle = {Journal of Artificial Societies and Social Simulation},
+  shortjournal = {JASSS},
+  volume = {23},
+  number = {2},
+  pages = {7},
+  issn = {1460-7425},
+  doi = {10.18564/jasss.4259},
+  url = {https://jasss.soc.surrey.ac.uk/23/2/7.html},
+  langid = {english},
+  keywords = {agent-based modeling,complexity science,interdisciplinary fields,modeling,odd protocol,open science,standards},
+}
+
+@article{hjorth2020,
+  title = {{{LevelSpace}}: {{A NetLogo}} extension for multi-level agent-based modeling},
+  shorttitle = {{{LevelSpace}}},
+  author = {Hjorth, Arthur and Head, Bryan and Brady, Corey and Wilensky, Uri},
+  date = {2020},
+  journaltitle = {Journal of Artificial Societies and Social Simulation},
+  shortjournal = {JASSS},
+  volume = {23},
+  number = {1},
+  pages = {4},
+  issn = {1460-7425},
+  doi = {10.18564/jasss.4130},
+  abstract = {Multi-Level Agent-Based Modeling (ML-ABM) has been receiving increasing attention in recent years. In this paper we present LevelSpace, an extension that allows modelers to easily build ML-ABMs in the popular and widely used NetLogo language. We present the LevelSpace framework and its associated programming primitives. Based on three common use-cases of ML-ABM – coupling of heterogenous models, dynamic adaptation of detail, and cross-level interaction - we show how easy it is to build ML-ABMs with LevelSpace. We argue that it is important to have a unified conceptual language for describing LevelSpace models, and present six dimensions along which models can differ, and discuss how these can be combined into a variety of ML-ABM types in LevelSpace. Finally, we argue that future work should explore the relationships between these six dimensions, and how different configurations of them might be more or less appropriate for particular modeling tasks.},
+  langid = {english},
+  keywords = {agent-based modeling,complexity science,computer science,exact sciences,interdisciplinary fields,netlogo,netlogo extensions},
+}
+
+@article{oneill2017,
+  title = {The roads ahead: {{Narratives}} for shared socioeconomic pathways describing world futures in the 21st century},
+  shorttitle = {The roads ahead},
+  author = {O'Neill, Brian C. and Kriegler, Elmar and Ebi, Kristie L. and Kemp-Benedict, Eric and Riahi, Keywan and Rothman, Dale S. and family=Ruijven, given=Bas J., prefix=van, useprefix=true and family=Vuuren, given=Detlef P., prefix=van, useprefix=true and Birkmann, Joern and Kok, Kasper and Levy, Marc and Solecki, William},
+  date = {2017},
+  journaltitle = {Global Environmental Change},
+  shortjournal = {Global Environmental Change},
+  volume = {42},
+  pages = {169--180},
+  issn = {0959-3780},
+  doi = {10.1016/j.gloenvcha.2015.01.004},
+  url = {https://www.sciencedirect.com/science/article/pii/S0959378015000060},
+  urldate = {2025-04-11},
+  abstract = {Long-term scenarios play an important role in research on global environmental change. The climate change research community is developing new scenarios integrating future changes in climate and society to investigate climate impacts as well as options for mitigation and adaptation. One component of these new scenarios is a set of alternative futures of societal development known as the shared socioeconomic pathways (SSPs). The conceptual framework for the design and use of the SSPs calls for the development of global pathways describing the future evolution of key aspects of society that would together imply a range of challenges for mitigating and adapting to climate change. Here we present one component of these pathways: the SSP narratives, a set of five qualitative descriptions of future changes in demographics, human development, economy and lifestyle, policies and institutions, technology, and environment and natural resources. We describe the methods used to develop the narratives as well as how these pathways are hypothesized to produce particular combinations of challenges to mitigation and adaptation. Development of the narratives drew on expert opinion to (1) identify key determinants of these challenges that were essential to incorporate in the narratives and (2) combine these elements in the narratives in a manner consistent with scholarship on their inter-relationships. The narratives are intended as a description of plausible future conditions at the level of large world regions that can serve as a basis for integrated scenarios of emissions and land use, as well as climate impact, adaptation and vulnerability analyses.},
+  keywords = {adaptation,climate change,environmental sciences,interdisciplinary fields,mitigation,narratives,scenarios,shared socioeconomic pathways},
+}
+
+@article{peng2011,
+  title = {Reproducible research in computational science},
+  author = {Peng, Roger D.},
+  date = {2011-12-02},
+  journaltitle = {Science},
+  volume = {334},
+  number = {6060},
+  pages = {1226--1227},
+  publisher = {American Association for the Advancement of Science},
+  doi = {10.1126/science.1213847},
+  url = {https://www.science.org/doi/10.1126/science.1213847},
+  urldate = {2024-06-18},
+  abstract = {Computational science has led to exciting new developments, but the nature of the work has exposed limitations in our ability to evaluate published findings. Reproducibility has the potential to serve as a minimum standard for judging scientific claims when full independent replication of a study is not possible.},
+  keywords = {computational science,computer science,modeling,replicability,reproducibility},
+}
+
+@article{ram2019,
+  title = {A community of practice around peer review for long-term research software sustainability},
+  author = {Ram, Karthik and Boettiger, Carl and Chamberlain, Scott and Ross, Noam and Salmon, Maëlle and Butland, Stefanie},
+  date = {2019-03},
+  journaltitle = {Computing in Science \& Engineering},
+  volume = {21},
+  number = {2},
+  pages = {59--65},
+  issn = {1558-366X},
+  doi = {10.1109/MCSE.2018.2882753},
+  url = {https://ieeexplore.ieee.org/document/8554180},
+  urldate = {2025-04-15},
+  abstract = {Scientific open source projects are responsible for enabling many of the major advances in modern science including recent breakthroughs such as the Laser Interferometer Gravitational-Wave Observatory project recognized in the 2017 Nobel Prize for physics. However, much of this software ecosystem is developed ad hoc with no regard for sustainable software development practices. This problem is further compounded by the fact that researchers who develop software have little in the way of resources or academic recognition for their efforts. The rOpenSci Project, founded in 2011 with the explicit mission of developing software to support reproducible science, has in recent years undertaken an effort to improve the long tail of scientific software. In this paper, we describe our software peer-review system, which brings together the best of traditional academic review with new ideas from industry code review.},
+  langid = {english},
+  keywords = {computer science,open science,r (programming language),ropensci,science,software reviews,sustainable development},
+}