Constrained Ordination Analysis with Enrichment of Bell-Shaped Response Functions

Yingjie Zhang and Olivier Thas

PLOS ONE, 2016, vol. 11, issue 4, 1-21

Abstract: 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.

Date: 2016
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0154079

DOI: 10.1371/journal.pone.0154079

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