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Constrained ordination analysis with enrichment of bell-shaped response functions

Yingjie Zhang (UGent) and Olivier Thas (UGent)
(2016) PLOS ONE. 11(4).
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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.
Keywords
CANONICAL CORRESPONDENCE-ANALYSIS, GENERALIZED LINEAR-MODELS, SPECIES DISTRIBUTION, GAUSSIAN ORDINATION, GRADIENT ANALYSIS, ECOLOGICAL THEORY, BETA-FUNCTION, VEGETATION, SKEWNESS

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Citation

Please use this url to cite or link to this publication:

MLA
Zhang, Yingjie, and Olivier Thas. “Constrained Ordination Analysis with Enrichment of Bell-shaped Response Functions.” PLOS ONE 11.4 (2016): n. pag. Print.
APA
Zhang, Yingjie, & Thas, O. (2016). Constrained ordination analysis with enrichment of bell-shaped response functions. PLOS ONE, 11(4).
Chicago author-date
Zhang, Yingjie, and Olivier Thas. 2016. “Constrained Ordination Analysis with Enrichment of Bell-shaped Response Functions.” Plos One 11 (4).
Chicago author-date (all authors)
Zhang, Yingjie, and Olivier Thas. 2016. “Constrained Ordination Analysis with Enrichment of Bell-shaped Response Functions.” Plos One 11 (4).
Vancouver
1.
Zhang Y, Thas O. Constrained ordination analysis with enrichment of bell-shaped response functions. PLOS ONE. 2016;11(4).
IEEE
[1]
Y. Zhang and O. Thas, “Constrained ordination analysis with enrichment of bell-shaped response functions,” PLOS ONE, vol. 11, no. 4, 2016.
@article{7222376,
  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.}},
  articleno    = {{e0154079}},
  author       = {{Zhang, Yingjie and Thas, Olivier}},
  issn         = {{1932-6203}},
  journal      = {{PLOS ONE}},
  keywords     = {{CANONICAL CORRESPONDENCE-ANALYSIS,GENERALIZED LINEAR-MODELS,SPECIES DISTRIBUTION,GAUSSIAN ORDINATION,GRADIENT ANALYSIS,ECOLOGICAL THEORY,BETA-FUNCTION,VEGETATION,SKEWNESS}},
  language     = {{eng}},
  number       = {{4}},
  pages        = {{21}},
  title        = {{Constrained ordination analysis with enrichment of bell-shaped response functions}},
  volume       = {{11}},
  year         = {{2016}},
}

Web of Science
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