Zhang Yingjie, Thas Olivier
Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, Ghent 9000, Belgium.
National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, University of Wollongong, Northfields Ave, Wollongong NSW 2522, Australia.
PLoS One. 2016 Apr 21;11(4):e0154079. doi: 10.1371/journal.pone.0154079. eCollection 2016.
Constrained ordination methods aims at finding an environmental gradient along which the species abundances are maximally separated. The species response functions, which describe the expected abundance as a function of the environmental score, are according to the ecological fundamental niche theory only meaningful if they are bell-shaped. Many classical model-based ordination methods, however, use quadratic regression models without imposing the bell-shape and thus allowing for meaningless U-shaped response functions. The analysis output (e.g. a biplot) may therefore be potentially misleading and the conclusions are prone to errors. In this paper we present a log-likelihood ratio criterion with a penalisation term to enforce more bell-shaped response shapes. We report the results of a simulation study and apply our method to metagenomics data from microbial ecology.
约束排序方法旨在找到一个环境梯度，沿着该梯度物种丰度能得到最大程度的分离。物种响应函数描述了预期丰度作为环境得分的函数，根据生态基础生态位理论，只有当它们呈钟形时才有意义。然而，许多基于经典模型的排序方法使用二次回归模型，而不强制其呈钟形，因此允许出现无意义的U形响应函数。分析输出（例如双标图）可能因此具有潜在的误导性，结论也容易出错。在本文中，我们提出了一种带有惩罚项的对数似然比准则，以强制得到更呈钟形的响应形状。我们报告了一项模拟研究的结果，并将我们的方法应用于微生物生态学的宏基因组学数据。
