G5 Doctoral dissertation (article)
On modeling multivariate abundance data with generalized linear latent variable models (2020)
Niku, J. (2020). On modeling multivariate abundance data with generalized linear latent variable models [Doctoral dissertation]. Jyväskylän yliopisto. JYU Dissertations, 192. http://urn.fi/URN:ISBN:978-951-39-8062-7
JYU authors or editors
Publication details
All authors or editors: Niku, Jenni
eISBN: 978-951-39-8062-7
Journal or series: JYU Dissertations
eISSN: 2489-9003
Publication year: 2020
Number in series: 192
Publisher: Jyväskylän yliopisto
Place of Publication: Jyväskylä
Publication country: Finland
Publication language: English
Persistent website address: http://urn.fi/URN:ISBN:978-951-39-8062-7
Publication open access: Openly available
Publication channel open access: Open Access channel
Abstract
The multivariate abundance data consist typically of multiple, correlated species encountered at a set of sites, together with records of additional covariates. When analysing such data, model-based approaches have been shown to outperform classical algorithmic-based dimension reduction methods. In this thesis we consider generalized linear latent variable models, which offer a general framework for the analysis of multivariate abundance data. In order to make the models more attractive among practitioners, new computationally efficient algorithms for the parameter estimation are developed by applying closed form approximation methods, the variational approximation method and the Laplace approximation method, for the marginal likelihood and by utilizing automatic differentiation tools when implementing the algorithms. The accuracy and computational efficiency of the methods are investigated and compared to existing methods through extensive simulation studies. The developed algorithms and additional tools implemented for model diagnosis, visualization and statistical inference are collected in R package gllvm. Several examples are provided to illustrate the use of the generalized linear latent variable models in ordination and when studying the between-species correlations and the effects of environmental variables, trait variables and their interactions on ecological communities.
Keywords: statistical models; multivariable methods; linear models; approximation; ecology; biotic communities; biodiversity
Free keywords: Community analysis; ecological data; fourth-corner models; generalized linear models; joint modeling; Laplace approximation; latent variables; multivariate analysis; ordination; species interactions; variational approximation
Contributing organizations
Ministry reporting: Yes
Reporting Year: 2020