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Constrained Ordination Analysis with Enrichment of Bell-Shaped Response Functions.


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.

SUBMITTER: Zhang Y 

PROVIDER: S-EPMC4839756 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Constrained Ordination Analysis with Enrichment of Bell-Shaped Response Functions.

Zhang Yingjie Y   Thas Olivier O  

PloS one 20160421 4


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-s  ...[more]

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