19 research outputs found
jamiemkass/ENMeval: ENMeval v2.0.0
No full textThis is an archive of the R package ENMeval 2.0.0, which includes the vignette. The package can be found on Github here: https://github.com/jamiemkass/ENMeval. It will also soon be uploaded to CRAN, where it can be found here: https://CRAN.R-project.org/package=ENMeval. The reference for the published paper describing this package, which was just accepted to Methods in Ecology and Evolution, is here:
Kass, J. M., Muscarella, R., Galante, P. J., Bohl, C., Pinilla-Buitrago, G. E., Boria, R. A., Soley‐Guardia, M., & Anderson, R. P. (2021). ENMeval 2.0: redesigned for customizable and reproducible modeling of species’ niches and distributions. Methods in Ecology and Evolution
Data from: A new null model approach to quantify performance and significance for ecological niche models of species distributions
No full textAim: Ecological niche modelling requires robust estimation of model performance and significance, but common evaluation approaches often yield biased estimates. Null models provide a solution but are rarely used in this field. We implemented an important modification to existing null-model tests, evaluating null models with the same withheld records that were used to evaluate the real model. We built and evaluated models across a range of modelling scenarios and for various performance measures using the algorithm Maxent and the monk parakeet (Myiopsitta monachus).
Location: Native range in Southern America and global invasions predominantly in North/Central America and Europe
Methods: We tested the ability of models built under 15 scenarios (five sets of calibration records and three settings that varied the level of model complexity) to predict spatially independent evaluation data in the invaded range (in effect, testing the models under spatial transfer). We quantified performance with measures of discriminatory ability and overfitting based on AUC and the omission error rate. We estimated null distributions of these measures and calculated effect size and significance. We determined how these estimates varied across modelling scenarios, comparing with two tests existing in the literature.
Results: Performance varied starkly across modelling scenarios. As expected, the measures of overfitting agreed with each other and provided different information than that of discriminatory ability. However, high performance per se did not show strong association with high effect size and significance.
Main Conclusions: Ecological niche models should be assessed with measures of effect size and significance based on appropriate null distributions, in contrast to several approaches existing in the literature. The proposed approach using independent evaluation data, implemented with our accompanying code, allows such estimates for either the same or a different region/time period, and it merits use and continued development
Data from: A new null model approach to quantify performance and significance for ecological niche models of species distributions
No full textAim: Ecological niche modelling requires robust estimation of model performance and significance, but common evaluation approaches often yield biased estimates. Null models provide a solution but are rarely used in this field. We implemented an important modification to existing null-model tests, evaluating null models with the same withheld records that were used to evaluate the real model. We built and evaluated models across a range of modelling scenarios and for various performance measures using the algorithm Maxent and the monk parakeet (Myiopsitta monachus).
Location: Native range in Southern America and global invasions predominantly in North/Central America and Europe
Methods: We tested the ability of models built under 15 scenarios (five sets of calibration records and three settings that varied the level of model complexity) to predict spatially independent evaluation data in the invaded range (in effect, testing the models under spatial transfer). We quantified performance with measures of discriminatory ability and overfitting based on AUC and the omission error rate. We estimated null distributions of these measures and calculated effect size and significance. We determined how these estimates varied across modelling scenarios, comparing with two tests existing in the literature.
Results: Performance varied starkly across modelling scenarios. As expected, the measures of overfitting agreed with each other and provided different information than that of discriminatory ability. However, high performance per se did not show strong association with high effect size and significance.
Main Conclusions: Ecological niche models should be assessed with measures of effect size and significance based on appropriate null distributions, in contrast to several approaches existing in the literature. The proposed approach using independent evaluation data, implemented with our accompanying code, allows such estimates for either the same or a different region/time period, and it merits use and continued development
A new null model approach to quantify performance and significance for ecological niche models of species distributions
No full text
Author Correction: An automated deep learning pipeline for EMVI classification and response prediction of rectal cancer using baseline MRI
No full textCorrection to: npj Precision Oncologyhttps://doi.org/10.1038/s41698-024-00516-x, published online 22 January 2024 “In this article, the name of the author Monique Maas was misspelled as Monique Mass. The original article has been corrected.”</p
Sharing the cost of river basin adaptation portfolios to climate change: Insights from social justice and cooperative game theory
No full text[EN] The adaptation of water resource systems to the potential impacts of climate change requires
mixed portfolios of supply and demand adaptation measures. The issue is not only to select efficient, robust, and flexible adaptation portfolios but also to find equitable strategies of cost allocation among the stakeholders. Our work addresses such cost allocation problems by applying two different theoretical approaches: social justice and cooperative game theory in a real case study. First of all, a cost-effective portfolio of adaptation measures at the basin scale is selected using a least-cost optimization model. Cost allocation solutions are then defined based on economic rationality concepts from cooperative game theory (the Core). Second, interviews are conducted to characterize stakeholders perceptions of social justice principles associated with the definition of alternatives cost allocation rules. The comparison of the cost allocation scenarios leads to contrasted insights in order to inform the decision-making process at the river basin scale and potentially reap the efficiency gains from cooperation in the design of river basin adaptation portfolios.The study has been partially supported by the IMPADAPT project (CGL2013-48424-C2-1-R) from the Spanish ministry MINECO (Ministerio de Economia y Competitividad) with European FEDER funds. The first author is supported by a grant from the University Lecturer Training Program (FPU12/03803) of the Ministry of Education, Culture and Sports of Spain. The second author is financially supported by BRGM's research program 30 (environmental and risk economics). Readers interested in the data can request those by e-mail to Corentin Girard, [email protected], CDP.; Rinaudo, J.; Pulido-Velazquez, M. (2016). Sharing the cost of river basin adaptation portfolios to climate change: Insights from social justice and cooperative game theory. 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Global Environmental Change, 34, 132-146. doi:10.1016/j.gloenvcha.2015.07.002Girard, C., Rinaudo, J.-D., & Pulido-Velazquez, M. (2015). Index-Based Cost-Effectiveness Analysis vs. Least-Cost River Basin Optimization Model: Comparison in the Selection of a Programme of Measures at the River Basin Scale. Water Resources Management, 29(11), 4129-4155. doi:10.1007/s11269-015-1049-0Graham, S., Barnett, J., Fincher, R., Mortreux, C., & Hurlimann, A. (2014). Towards fair local outcomes in adaptation to sea-level rise. Climatic Change, 130(3), 411-424. doi:10.1007/s10584-014-1171-7Hallegatte, S. (2009). Strategies to adapt to an uncertain climate change. Global Environmental Change, 19(2), 240-247. doi:10.1016/j.gloenvcha.2008.12.003Harou, J. J., Pulido-Velazquez, M., Rosenberg, D. E., Medellín-Azuara, J., Lund, J. R., & Howitt, R. E. (2009). Hydro-economic models: Concepts, design, applications, and future prospects. 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Database of Embodied Quantity Outputs: Lowering Material Impacts Through Engineering
No full textCurrent studies and performance labels focus mainly on the operational energy demand of buildings due to heating, cooling, ventilation, lighting, and hot water, but they rarely account for embodied impacts. Performing a life cycle assessment (LCA) on an entire building structure, let alone a building, requires time and data, both of which are often lacking for practitioners in the construction industry. Limited knowledge on the embodied carbon equivalent of building structures led to the benchmarking effort of the database of embodied quantity outputs (DEQO), developed by the first author over the last 6 years in close collaboration with industry and academia. DEQO col- lects material quantities for existing buildings in a robust way directly from industry. This paper presents the lessons learned from this da- tabase to define the next steps for structural engineers to lower the environmental impacts related to the material quantities in their projects. To create confidence and comparability in the results, recommendations are given such as implementing uncertainty analysis into practice to avoid inaccurate comparisons with a false sense of precision.SX
ENMeval 2.0: Redesigned for customizable and reproducible modeling of species’ niches and distributions
No full text１．Quantitative evaluations to optimize complexity have become standard for avoiding overfitting of ecological niche models (ENMs) that estimate species’ potential geographic distributions. ENMeval was the first R package to make such evaluations (often termed model tuning) widely accessible for the Maxent algorithm. It also provided multiple methods for partitioning occurrence data and reported various performance metrics.
２．Requests by users, recent developments in the field, and needs for software compatibility led to a major redesign and expansion. We additionally conducted a literature review to investigate trends in ENMeval use (2015–2019).
３．ENMeval 2.0 has a new object-oriented structure for adding other algorithms, enables customizing algorithmic settings and performance metrics, generates extensive metadata, implements a null-model approach to quantify significance and effect sizes, and includes features to increase the breadth of analyses and visualizations. In our literature review, we found insufficient reporting of model performance and parameterization, heavy reliance on model selection with AICc and low utilization of spatial cross-validation; we explain how ENMeval 2.0 can help address these issues.
４．This redesigned and expanded version can promote progress in the field and improve the information available for decision-making
The Legacy of Iconoclasm: religious war and the relic landscape of Tours, Blois and Vendôme, 1550-1750
No full textThis study explores the process of physically rebuilding, renewing and reinventing the relic landscape in the regions around Tours, Blois and Vendôme following the widespread iconoclastic damage of the French religious wars. The author takes a long-term perspective exploring developments over two hundred years, from the mid-sixteenth through to the mid-eighteenth centuries. The book explores what the physical renewal of the landscape can tell us about evolving beliefs and practices concerning relics during the Catholic Reformation and what reconstruction activities reveal about the meaning and experience of relic veneration. It pays particular attention to how the relic landscape evolved through relic translations and how communities that oversaw relic shrines remembered the iconoclastic acts of the religious wars through liturgical and ritual commemorations, memorials, artistic renderings, oral traditions and written accounts.Publisher PD
