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      Reproducible WiSDM: a workflow for reproducible invasive alien species risk maps under climate change scenarios using standardized open data

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          Abstract

          Introduction

          Species distribution models (SDMs) are often used to produce risk maps to guide conservation management and decision-making with regard to invasive alien species (IAS). However, gathering and harmonizing the required species occurrence and other spatial data, as well as identifying and coding a robust modeling framework for reproducible SDMs, requires expertise in both ecological data science and statistics.

          Methods

          We developed WiSDM, a semi-automated workflow to democratize the creation of open, reproducible, transparent, invasive alien species risk maps. To facilitate the production of IAS risk maps using WiSDM, we harmonized and openly published climate and land cover data to a 1 km 2 resolution with coverage for Europe. Our workflow mitigates spatial sampling bias, identifies highly correlated predictors, creates ensemble models to predict risk, and quantifies spatial autocorrelation. In addition, we present a novel application for assessing the transferability of the model by quantifying and visualizing the confidence of its predictions. All modeling steps, parameters, evaluation statistics, and other outputs are also automatically generated and are saved in a R markdown notebook file.

          Results

          Our workflow requires minimal input from the user to generate reproducible maps at 1 km 2 resolution for standard Intergovernmental Panel on Climate Change (IPCC) greenhouse gas emission representative concentration pathway (RCP) scenarios. The confidence associated with the predicted risk for each 1km 2 pixel is also mapped, enabling the intuitive visualization and understanding of how the confidence of the model varies across space and RCP scenarios.

          Discussion

          Our workflow can readily be applied by end users with a basic knowledge of R, does not require expertise in species distribution modeling, and only requires an understanding of the ecological theory underlying species distributions. The risk maps generated by our repeatable workflow can be used to support IAS risk assessment and surveillance.

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          Random Forests

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            The FAIR Guiding Principles for scientific data management and stewardship

            There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.
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              Greedy function approximation: A gradient boosting machine.

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                Author and article information

                Journal
                Frontiers in Ecology and Evolution
                Front. Ecol. Evol.
                Frontiers Media SA
                2296-701X
                February 9 2024
                February 9 2024
                : 12
                Article
                10.3389/fevo.2024.1148895
                4a458be9-e606-47fc-9242-fb8ed5d61641
                © 2024

                Free to read

                https://creativecommons.org/licenses/by/4.0/

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