Journal ArticleDOI
A general and simple method for obtaining R2 from generalized linear mixed-effects models
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TLDR
In this article, the authors make a case for the importance of reporting variance explained (R2) as a relevant summarizing statistic of mixed-effects models, which is rare, even though R2 is routinely reported for linear models and also generalized linear models (GLM).Abstract:
Summary
The use of both linear and generalized linear mixed-effects models (LMMs and GLMMs) has become popular not only in social and medical sciences, but also in biological sciences, especially in the field of ecology and evolution. Information criteria, such as Akaike Information Criterion (AIC), are usually presented as model comparison tools for mixed-effects models.
The presentation of ‘variance explained’ (R2) as a relevant summarizing statistic of mixed-effects models, however, is rare, even though R2 is routinely reported for linear models (LMs) and also generalized linear models (GLMs). R2 has the extremely useful property of providing an absolute value for the goodness-of-fit of a model, which cannot be given by the information criteria. As a summary statistic that describes the amount of variance explained, R2 can also be a quantity of biological interest.
One reason for the under-appreciation of R2 for mixed-effects models lies in the fact that R2 can be defined in a number of ways. Furthermore, most definitions of R2 for mixed-effects have theoretical problems (e.g. decreased or negative R2 values in larger models) and/or their use is hindered by practical difficulties (e.g. implementation).
Here, we make a case for the importance of reporting R2 for mixed-effects models. We first provide the common definitions of R2 for LMs and GLMs and discuss the key problems associated with calculating R2 for mixed-effects models. We then recommend a general and simple method for calculating two types of R2 (marginal and conditional R2) for both LMMs and GLMMs, which are less susceptible to common problems.
This method is illustrated by examples and can be widely employed by researchers in any fields of research, regardless of software packages used for fitting mixed-effects models. The proposed method has the potential to facilitate the presentation of R2 for a wide range of circumstances.read more
Citations
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Journal ArticleDOI
Climate-driven changes in functional biogeography of Arctic marine fish communities
André Frainer,Raul Primicerio,Susanne Kortsch,Magnus Aune,Andrey V. Dolgov,Maria Fossheim,Michaela Aschan +6 more
TL;DR: It is shown that increasing temperatures and reduced ice coverage are associated with the borealization of Arctic fish communities, and functional biogeography can provide important insights into the relationship between species composition, diversity, ecosystem functioning, and environmental drivers.
Journal ArticleDOI
Non-structural carbohydrates in woody plants compared among laboratories.
Audrey G. Quentin,Audrey G. Quentin,Elizabeth A. Pinkard,Michael G. Ryan,Michael G. Ryan,David T. Tissue,L. Scott Baggett,Henry D. Adams,Pascale Maillard,Jacqueline Marchand,Simon M. Landhäusser,André Lacointe,André Lacointe,Yves Gibon,William R. L. Anderegg,Shinichi Asao,Owen K. Atkin,Marc Bonhomme,Marc Bonhomme,Caroline Claye,Pak S. Chow,Anne Clément-Vidal,Noel W. Davies,L. Turin Dickman,Rita Dumbur,David S. Ellsworth,Kristen Falk,Lucía Galiano,José M. Grünzweig,Henrik Hartmann,Günter Hoch,Sharon M. Hood,Joanna E. Jones,Takayoshi Koike,Iris Kuhlmann,Francisco Lloret,Melchor Maestro,Shawn D. Mansfield,Jordi Martínez-Vilalta,Mickaël Maucourt,Mickaël Maucourt,Nate G. McDowell,Annick Moing,Bertrand Muller,Sergio G. Nebauer,Ülo Niinemets,Sara Palacio,Frida I. Piper,Eran Raveh,Andreas Richter,Gaëlle Rolland,Teresa Rosas,Brigitte Saint Joanis,Brigitte Saint Joanis,Anna Sala,Renee Smith,Frank J. Sterck,Joseph R. Stinziano,Mari Tobias,Faride Unda,Makoto Watanabe,Danielle A. Way,Danielle A. Way,Lasantha K. Weerasinghe,Lasantha K. Weerasinghe,Birgit Wild,Birgit Wild,Erin Wiley,David R. Woodruff +68 more
TL;DR: It is shown that NSC estimates for woody plant tissues cannot be compared among laboratories, and users can either adopt the reference method given in this publication, or report estimates for a portion of samples using thereference method, and report estimates to a standard reference material.
Journal ArticleDOI
Model averaging in ecology: a review of Bayesian, information-theoretic, and tactical approaches for predictive inference
Carsten F. Dormann,Justin M. Calabrese,Gurutzeta Guillera-Arroita,Eleni Matechou,Volker Bahn,Kamil A. Bartoń,Colin M. Beale,Simone Ciuti,Simone Ciuti,Jane Elith,Katharina Gerstner,Jérôme Guélat,Petr Keil,José J. Lahoz-Monfort,Laura J. Pollock,Björn Reineking,Björn Reineking,David R. Roberts,David R. Roberts,Boris Schröder,Wilfried Thuiller,David I. Warton,Brendan A. Wintle,Simon N. Wood,Rafael O. Wüest,Rafael O. Wüest,Florian Hartig,Florian Hartig +27 more
TL;DR: In this article, the authors review the mathematical foundations of model averaging along with the diversity of approaches available and stress the importance of non-parametric methods such as cross-validation for a reliable uncertainty quantification of model-averaged predictions.
Journal ArticleDOI
Biodiversity mediates top–down control in eelgrass ecosystems: a global comparative‐experimental approach
J. Emmett Duffy,J. Emmett Duffy,Pamela L. Reynolds,Christoffer Boström,James A. Coyer,Mathieu Cusson,Serena Donadi,James G. Douglass,Johan S. Eklöf,Aschwin H. Engelen,Britas Klemens Eriksson,Stein Fredriksen,Lars Gamfeldt,Camilla Gustafsson,Galice Hoarau,Masakazu Hori,Kevin A. Hovel,Katrin Iken,Jonathan S. Lefcheck,Per-Olav Moksnes,Masahiro Nakaoka,Mary I. O'Connor,Jeanine L. Olsen,J. Paul Richardson,Jennifer L. Ruesink,Erik E. Sotka,Jonas Thormar,Matthew A. Whalen,John J. Stachowicz +28 more
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Journal ArticleDOI
Explained Variance Measures for Multilevel Models
TL;DR: In multilevel models, explained variance can be reported for each level or for the total mode as mentioned in this paper, depending on the level of the model and the mode of the mode.
References
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Proceedings Article
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