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一个用于调整和评估物种分布模型的R软件包。

: An R package to tune and evaluate species distribution models.

作者信息

Vignali Sergio, Barras Arnaud G, Arlettaz Raphaël, Braunisch Veronika

机构信息

Division of Conservation Biology Institute of Ecology and Evolution University of Bern Bern Switzerland.

Forest Research Institute of Baden-Wuerttemberg Freiburg Germany.

出版信息

Ecol Evol. 2020 Sep 30;10(20):11488-11506. doi: 10.1002/ece3.6786. eCollection 2020 Oct.

Abstract

Balancing model complexity is a key challenge of modern computational ecology, particularly so since the spread of machine learning algorithms. Species distribution models are often implemented using a wide variety of machine learning algorithms that can be fine-tuned to achieve the best model prediction while avoiding overfitting. We have released , a new R package that aims to facilitate training, tuning, and evaluation of species distribution models in a unified framework. The main innovations of this package are its functions to perform data-driven variable selection, and a novel genetic algorithm to tune model hyperparameters. Real-time and interactive charts are displayed during the execution of several functions to help users understand the effect of removing a variable or varying model hyperparameters on model performance. supports three different metrics to evaluate model performance: the area under the receiver operating characteristic curve, the true skill statistic, and Akaike's information criterion corrected for small sample sizes. It implements four statistical methods: artificial neural networks, boosted regression trees, maximum entropy modeling, and random forest. Moreover, it includes functions to display the outputs and create a final report. therefore represents a new, unified and user-friendly framework for the still-growing field of species distribution modeling.

摘要

平衡模型复杂性是现代计算生态学的一项关键挑战,尤其是自机器学习算法普及以来。物种分布模型通常使用各种各样的机器学习算法来实现,这些算法可以进行微调以实现最佳模型预测,同时避免过度拟合。我们发布了一个新的R包,旨在在统一框架中促进物种分布模型的训练、调优和评估。该包的主要创新之处在于其执行数据驱动变量选择的功能,以及一种用于调整模型超参数的新型遗传算法。在执行几个函数期间会显示实时交互式图表,以帮助用户了解删除一个变量或改变模型超参数对模型性能的影响。支持三种不同的指标来评估模型性能:受试者工作特征曲线下的面积、真实技能统计量以及针对小样本量校正的赤池信息准则。它实现了四种统计方法:人工神经网络、提升回归树、最大熵建模和随机森林。此外,它还包括显示输出和创建最终报告的功能。因此,对于仍在不断发展的物种分布建模领域来说,它代表了一个新的、统一且用户友好的框架。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6f93/7593178/d55e4947c941/ECE3-10-11488-g001.jpg

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