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生态位：使用闪亮仪表盘和R包增强生态位建模、生态位重叠和连通性分析。

EcoNicheS: enhancing ecological niche modeling, niche overlap and connectivity analysis using the shiny dashboard and R package.

作者信息

Sunny Armando, Marmolejo Clere, Vidal-López Rodrigo, Falconi-Briones Fredy A, Cuervo-Robayo Ángela P, Bolom-Huet René

机构信息

Centro de Investigación en Ciencias Biológicas Aplicadas, Facultad de Ciencias, Universidad Autónoma del Estado de México, Toluca, Estado de México, Mexico.

Centro de Innovación Digital "Mandra" Laboratorio Nacional de Enseñanza e Innovación aplicando Cómputo de Alto Rendimiento (EICAR), CONAHCyT, Universidad Autónoma del Estado de México, Toluca, Estado de México, Mexico.

出版信息

PeerJ. 2025 Mar 28;13:e19136. doi: 10.7717/peerj.19136. eCollection 2025.

DOI:10.7717/peerj.19136
PMID:40166046
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11956771/
Abstract

EcoNicheS (https://github.com/armandosunny/EcoNicheS) is a comprehensive R package built on a Shiny dashboard that offers an intuitive and streamlined workflow for creating ecological niche models (ENMs) and landscape connectivity models. It incorporates tools for niche modeling, overlap analysis, and connectivity modeling, leveraging robust algorithms from the biomod2 suite. EcoNicheS is designed to simplify the technical complexities of ENMs, bridging the gap between advanced modeling techniques and user accessibility. The package offers an interactive interface for streamlined data input, model parameterization, and result visualization. Its comprehensive toolset includes occurrence data processing, pseudoabsence point generation, urbanization filters, and ecological connectivity modeling, distinguishing it from other platforms. EcoNicheS integrates innovative workflows with dynamic output visualizations while emphasizing reproducibility and comparability across statistical methods. Its practical applications span diverse research fields, including biogeography, epidemiology, evolutionary studies, climate change impacts, landscape connectivity, and biodiversity conservation. This versatility makes EcoNicheS a valuable resource for advancing in ecological and conservation science.

摘要

EcoNicheS（https://github.com/armandosunny/EcoNicheS）是一个基于Shiny仪表盘构建的综合R包，它为创建生态位模型（ENM）和景观连通性模型提供了直观且简化的工作流程。它整合了生态位建模、重叠分析和连通性建模工具，利用了来自biomod2套件的强大算法。EcoNicheS旨在简化生态位模型的技术复杂性，弥合先进建模技术与用户可及性之间的差距。该软件包提供了一个交互式界面，用于简化数据输入、模型参数化和结果可视化。其全面的工具集包括出现数据处理、伪缺失点生成、城市化过滤器和生态连通性建模，使其有别于其他平台。EcoNicheS将创新的工作流程与动态输出可视化相结合，同时强调跨统计方法的可重复性和可比性。它的实际应用涵盖了不同的研究领域，包括生物地理学、流行病学、进化研究、气候变化影响、景观连通性和生物多样性保护。这种多功能性使EcoNicheS成为推进生态与保护科学的宝贵资源。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7bb6/11956771/43d178126e88/peerj-13-19136-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7bb6/11956771/1c159e642356/peerj-13-19136-g001.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7bb6/11956771/72a35ec180db/peerj-13-19136-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7bb6/11956771/b035a62eaaf8/peerj-13-19136-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7bb6/11956771/e4adf574b37b/peerj-13-19136-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7bb6/11956771/befa7d97b2b0/peerj-13-19136-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7bb6/11956771/43d178126e88/peerj-13-19136-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7bb6/11956771/1c159e642356/peerj-13-19136-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7bb6/11956771/075a057ad9ad/peerj-13-19136-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7bb6/11956771/72a35ec180db/peerj-13-19136-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7bb6/11956771/b035a62eaaf8/peerj-13-19136-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7bb6/11956771/e4adf574b37b/peerj-13-19136-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7bb6/11956771/befa7d97b2b0/peerj-13-19136-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7bb6/11956771/43d178126e88/peerj-13-19136-g007.jpg

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本文引用的文献

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Biomod2 modeling for predicting the potential ecological distribution of three Fritillaria species under climate change.基于 Biomod2 模型预测气候变化下三种贝母属植物潜在生态分布。
Sci Rep. 2023 Nov 1;13(1):18801. doi: 10.1038/s41598-023-45887-6.
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Modelling the effects of climate and land-cover changes on the potential distribution and landscape connectivity of three earth snakes (Genus Conopsis, Günther 1858) in central Mexico.建立模型以研究气候和土地覆盖变化对中美洲三种地球蛇（Genus Conopsis， Günther 1858）潜在分布和景观连通性的影响。
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Ecological Niche Modelling Approaches: Challenges and Applications in Vector-Borne Diseases.
生态位建模方法：在媒介传播疾病中的挑战与应用
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Complex genetic patterns and distribution limits mediated by native congeners of the worldwide invasive red-eared slider turtle.全球入侵性红耳龟的本地同属物种介导的复杂遗传模式和分布限制
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Development of interactive biological web applications with R/Shiny.用 R/Shiny 开发交互式生物网络应用程序。
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