Statistical Quantification of Individual Differences (SQuID): an educational and statistical tool for understanding multilevel phenotypic data in linear mixed models

Hassen Allegue; Yimen G. Araya-Ajoy; Niels J. Dingemanse; Ned A. Dochtermann; László Z. Garamszegi; Shinichi Nakagawa; Denis Réale; Holger Schielzeth; David F. Westneat

doi:10.1111/2041-210X.12659

Statistical Quantification of Individual Differences (SQuID): an educational and statistical tool for understanding multilevel phenotypic data in linear mixed models

Hassen Allegue
, Yimen G. Araya-Ajoy
, Niels J. Dingemanse
, Ned A. Dochtermann
, László Z. Garamszegi
, Shinichi Nakagawa
, Denis Réale
, Holger Schielzeth
, David F. Westneat

Research output: Contribution to journal › Article › peer-review

46 Scopus citations

Abstract

Phenotypic variation exists in and at all levels of biological organization: variation exists among species, among-individuals within-populations, and in the case of l within-populations abile traits, within-individuals. Mixed-effects models represent ideal tools to quantify multilevel measurements of traits and are being increasingly used in evolutionary ecology. Mixed-effects models are relatively complex, and two main issues may be hampering their proper usage: (i) the relatively few educational resources available to teach new users how to implement and interpret them and (ii) the lack of tools to ensure that the statistical parameters of interest are correctly estimated. In this paper, we introduce Statistical Quantification of Individual Differences (SQuID), a simulation-based tool that can be used for research and educational purposes. SQuID creates a virtual world inhabited by subjects whose phenotypes are generated by a user-defined phenotypic equation, which allows easy translation of biological hypotheses into quantifiable parameters. Statistical Quantification of Individual Differences currently models normally distributed traits with linear predictors, but SQuID is subject to further development and will adapt to handle more complex scenarios in the future. The current framework is suitable for performing simulation studies, determining optimal sampling designs for user-specific biological problems and making simulation-based inferences to aid in the interpretation of empirical studies. Statistical Quantification of Individual Differences is also a teaching tool for biologists interested in learning, or teaching others, how to implement and interpret linear mixed-effects models when studying the processes causing phenotypic variation. Interface-based modules allow users to learn about these issues. As research on effects of sampling designs continues, new issues will be implemented in new modules, including nonlinear and non-Gaussian data.

Original language	English
Pages (from-to)	257-267
Number of pages	11
Journal	Methods in Ecology and Evolution
Volume	8
Issue number	2
DOIs	https://doi.org/10.1111/2041-210X.12659
State	Published - Feb 1 2017

Bibliographical note

Publisher Copyright:
© 2016 The Authors. Methods in Ecology and Evolution © 2016 British Ecological Society

Funding

SQuID was conceived at the Symposium \u2018Personality: Causes and Consequences of Consistent Behavioural Variation\u2019 funded by the Volkswagen Foundation (2013), and born and potty-trained during two follow-up workshop at the Max Planck Institute for Ornithology (Seewiesen) funded by the Volkswagen Foundation (2014) and the International Max Planck Research School for Organismal Biology (2015). Y.G.A.A. and N.J.D were supported by the Max Planck Society, L.Z.G. by the Plan Nacional Program (CGL2015-70639-P) and the National Research, Development and Innovation Office of Hungary (K-115970), S.N. by an Australian Future Fellowship, D.R. by a Discovery Grant of the National Sciences and Engineering Research Council of Canada, H.S. by the German Research Foundation (SCHI 1188/1-1) and D.F.W. by the National Science Foundation of the U.S.A. Authors gratefully acknowledge feedback on an earlier version of the manuscript from Jarrod Hadfield, Sandra Hamel, Julien Martin and an anonymous reviewer.

Funders	Funder number
Volkswagen Foundation
International Max Planck Research School for Organismal Biology
Max-Planck-Instituts für Ornithologie
U.S. Department of Energy Chinese Academy of Sciences Guangzhou Municipal Science and Technology Project Oak Ridge National Laboratory Extreme Science and Engineering Discovery Environment National Science Foundation National Energy Research Scientific Computing Center National Natural Science Foundation of China	1257718
Nemzeti Kutatási Fejlesztési és Innovációs Hivatal	K-115970
Fritz-Haber-Institut der Max-Planck-Gesellschaft	CGL2015-70639-P
Deutsche Forschungsgemeinschaft	SCHI 1188/1-1

Keywords

individual differences
linear mixed-effects modelling
model fitting
multilevel data
personality
phenotypic equation
phenotypic plasticity
reaction norm
repeatability
variance components

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Ecological Modeling

Access to Document

10.1111/2041-210X.12659

Cite this

Allegue, H., Araya-Ajoy, Y. G., Dingemanse, N. J., Dochtermann, N. A., Garamszegi, L. Z., Nakagawa, S., Réale, D., Schielzeth, H., & Westneat, D. F. (2017). Statistical Quantification of Individual Differences (SQuID): an educational and statistical tool for understanding multilevel phenotypic data in linear mixed models. Methods in Ecology and Evolution, 8(2), 257-267. https://doi.org/10.1111/2041-210X.12659

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title = "Statistical Quantification of Individual Differences (SQuID): an educational and statistical tool for understanding multilevel phenotypic data in linear mixed models",

abstract = "Phenotypic variation exists in and at all levels of biological organization: variation exists among species, among-individuals within-populations, and in the case of l within-populations abile traits, within-individuals. Mixed-effects models represent ideal tools to quantify multilevel measurements of traits and are being increasingly used in evolutionary ecology. Mixed-effects models are relatively complex, and two main issues may be hampering their proper usage: (i) the relatively few educational resources available to teach new users how to implement and interpret them and (ii) the lack of tools to ensure that the statistical parameters of interest are correctly estimated. In this paper, we introduce Statistical Quantification of Individual Differences (SQuID), a simulation-based tool that can be used for research and educational purposes. SQuID creates a virtual world inhabited by subjects whose phenotypes are generated by a user-defined phenotypic equation, which allows easy translation of biological hypotheses into quantifiable parameters. Statistical Quantification of Individual Differences currently models normally distributed traits with linear predictors, but SQuID is subject to further development and will adapt to handle more complex scenarios in the future. The current framework is suitable for performing simulation studies, determining optimal sampling designs for user-specific biological problems and making simulation-based inferences to aid in the interpretation of empirical studies. Statistical Quantification of Individual Differences is also a teaching tool for biologists interested in learning, or teaching others, how to implement and interpret linear mixed-effects models when studying the processes causing phenotypic variation. Interface-based modules allow users to learn about these issues. As research on effects of sampling designs continues, new issues will be implemented in new modules, including nonlinear and non-Gaussian data.",

keywords = "individual differences, linear mixed-effects modelling, model fitting, multilevel data, personality, phenotypic equation, phenotypic plasticity, reaction norm, repeatability, variance components",

author = "Hassen Allegue and Araya-Ajoy, \{Yimen G.\} and Dingemanse, \{Niels J.\} and Dochtermann, \{Ned A.\} and Garamszegi, \{L{\'a}szl{\'o} Z.\} and Shinichi Nakagawa and Denis R{\'e}ale and Holger Schielzeth and Westneat, \{David F.\}",

note = "Publisher Copyright: {\textcopyright} 2016 The Authors. Methods in Ecology and Evolution {\textcopyright} 2016 British Ecological Society",

year = "2017",

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doi = "10.1111/2041-210X.12659",

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Allegue, H, Araya-Ajoy, YG, Dingemanse, NJ, Dochtermann, NA, Garamszegi, LZ, Nakagawa, S, Réale, D, Schielzeth, H & Westneat, DF 2017, 'Statistical Quantification of Individual Differences (SQuID): an educational and statistical tool for understanding multilevel phenotypic data in linear mixed models', Methods in Ecology and Evolution, vol. 8, no. 2, pp. 257-267. https://doi.org/10.1111/2041-210X.12659

Statistical Quantification of Individual Differences (SQuID): an educational and statistical tool for understanding multilevel phenotypic data in linear mixed models. / Allegue, Hassen; Araya-Ajoy, Yimen G.; Dingemanse, Niels J. et al.
In: Methods in Ecology and Evolution, Vol. 8, No. 2, 01.02.2017, p. 257-267.

Research output: Contribution to journal › Article › peer-review

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AU - Araya-Ajoy, Yimen G.

AU - Dingemanse, Niels J.

AU - Dochtermann, Ned A.

AU - Garamszegi, László Z.

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AU - Réale, Denis

AU - Schielzeth, Holger

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Statistical Quantification of Individual Differences (SQuID): an educational and statistical tool for understanding multilevel phenotypic data in linear mixed models

Abstract

Bibliographical note

Funding

Keywords

ASJC Scopus subject areas

Access to Document

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Cite this