Fitting Linear Mixed-Effects Models Using lme4
TLDR
In this article, a model is described in an lmer call by a formula, in this case including both fixed-and random-effects terms, and the formula and data together determine a numerical representation of the model from which the profiled deviance or the profeatured REML criterion can be evaluated as a function of some of model parameters.Abstract:
Maximum likelihood or restricted maximum likelihood (REML) estimates of the parameters in linear mixed-effects models can be determined using the lmer function in the lme4 package for R. As for most model-fitting functions in R, the model is described in an lmer call by a formula, in this case including both fixed- and random-effects terms. The formula and data together determine a numerical representation of the model from which the profiled deviance or the profiled REML criterion can be evaluated as a function of some of the model parameters. The appropriate criterion is optimized, using one of the constrained optimization functions in R, to provide the parameter estimates. We describe the structure of the model, the steps in evaluating the profiled deviance or REML criterion, and the structure of classes or types that represents such a model. Sufficient detail is included to allow specialization of these structures by users who wish to write functions to fit specialized linear mixed models, such as models incorporating pedigrees or smoothing splines, that are not easily expressible in the formula language used by lmer.read more
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Journal ArticleDOI
Circadian regulation of sunflower heliotropism, floral orientation, and pollinator visits
Hagop S. Atamian,Nicky M. Creux,Evan A. Brown,Austin G. Garner,Benjamin K. Blackman,Benjamin K. Blackman,Stacey L. Harmer +6 more
TL;DR: It is shown that circadian regulation of directional growth pathways accounts for both phenomena and leads to increased vegetative biomass and enhanced pollinator visits to flowers, and this warmth attracts pollinators.
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Reliability from α to ω: A tutorial.
William Revelle,David M. Condon +1 more
TL;DR: This work considers multiple measures of reliability, ranging from the worst to average, and why model-based estimates should be reported, for a single test administration, and addresses the utility of test-retest and alternate form reliabilities.
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Near-island biological hotspots in barren ocean basins
Jamison M. Gove,Margaret A. McManus,Anna B. Neuheimer,Jeffrey J. Polovina,Jeffrey C. Drazen,Craig R. Smith,Mark A. Merrifield,Mark A. Merrifield,Alan M. Friedlander,Julia S. Ehses,Charles W. Young,Amanda Dillon,Gareth J. Williams,Gareth J. Williams +13 more
TL;DR: It is shown that IME is a near-ubiquitous feature among a majority (91%) of coral reef ecosystems surveyed, creating near-island ‘hotspots' of phytoplankton biomass throughout the upper water column.
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Agriculturally dominated landscapes reduce bee phylogenetic diversity and pollination services
Heather Grab,Michael G. Branstetter,Nolan Amon,Nolan Amon,Katherine R. Urban-Mead,Mia G. Park,Jason Gibbs,Eleanor J. Blitzer,Katja Poveda,Greg Loeb,Bryan N. Danforth +10 more
TL;DR: This study links landscape–mediated changes in the phylogenetic structure of natural communities to the disruption of ecosystem services, which may fail to protect ecosystem functions and the full diversity of life from which they are derived.
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Effect of an intravitreal antisense oligonucleotide on vision in Leber congenital amaurosis due to a photoreceptor cilium defect
Artur V. Cideciyan,Samuel G. Jacobson,Arlene V. Drack,Allen C. Ho,Jason Charng,Alexandra V. Garafalo,Alejandro J. Roman,Alexander Sumaroka,Ian C. Han,Maria D. Hochstedler,Wanda L. Pfeifer,Elliott H. Sohn,Magali Taiel,Michael R. Schwartz,Patricia Biasutto,Wilma de Wit,Michael E. Cheetham,Peter Adamson,David M. Rodman,Gerard Platenburg,Maria D. Tome,Irina Balikova,Fanny Nerinckx,Julie De Zaeytijd,Caroline Van Cauwenbergh,Bart P. Leroy,Stephen R. Russell +26 more
TL;DR: RNA antisense oligonucleotide therapy to restore normal splicing of a ciliopathy gene shows promising safety and efficacy results in a clinical trial to treat a form of childhood blindness.
References
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Journal Article
R: A language and environment for statistical computing.
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Book
Bayesian Data Analysis
TL;DR: Detailed notes on Bayesian Computation Basics of Markov Chain Simulation, Regression Models, and Asymptotic Theorems are provided.
Book
Mixed-Effects Models in S and S-PLUS
TL;DR: Linear Mixed-Effects and Nonlinear Mixed-effects (NLME) models have been studied in the literature as mentioned in this paper, where the structure of grouped data has been used for fitting LME models.
Book
Data Analysis Using Regression and Multilevel/Hierarchical Models
Andrew Gelman,Yu-Sung Su +1 more
TL;DR: Data Analysis Using Regression and Multilevel/Hierarchical Models is a comprehensive manual for the applied researcher who wants to perform data analysis using linear and nonlinear regression and multilevel models.