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
Citations
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Mindfulness Meditation and Cognitive Behavioral Therapy Intervention Reduces Pain Severity and Sensitivity in Opioid-Treated Chronic Low Back Pain: Pilot Findings from a Randomized Controlled Trial.
Aleksandra Zgierska,Cindy A. Burzinski,Jennifer Cox,John Kloke,Aaron J. Stegner,Dane B. Cook,Janice Singles,Shilagh Mirgain,Christopher L. Coe,Miroslav Backonja +9 more
TL;DR: Meditation-CBT intervention reduced pain severity and sensitivity to experimental thermal pain stimuli in patients with opioid-treated chronic low back pain in a 26-week pilot randomized controlled trial.
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Influenza A variants with reduced susceptibility to baloxavir isolated from Japanese patients are fit and transmit through respiratory droplets.
Masaki Imai,Makoto Yamashita,Yuko Sakai-Tagawa,Kiyoko Iwatsuki-Horimoto,Maki Kiso,Jurika Murakami,Atsuhiro Yasuhara,Kosuke Takada,Mutsumi Ito,Noriko Nakajima,Kenta Takahashi,Tiago J. S. Lopes,Tiago J. S. Lopes,Jayeeta Dutta,Zenab Khan,Divya Kriti,Harm van Bakel,Akifumi Tokita,Haruhisa Hagiwara,Naomi Izumida,Haruo Kuroki,Tamon Nishino,Noriyuki Wada,Michiko Koga,Eisuke Adachi,Daisuke Jubishi,Hideki Hasegawa,Yoshihiro Kawaoka,Yoshihiro Kawaoka +28 more
TL;DR: It is reported that resistant viruses isolated from Japanese patients have normal replicative abilities and pathogenicity in animal models and thus might spread in humans.
Journal ArticleDOI
Seasonal abundance and survival of North America's migratory avifauna determined by weather radar.
Adriaan M. Dokter,Andrew Farnsworth,Daniel Fink,Viviana Ruiz-Gutierrez,Wesley M. Hochachka,Frank A. La Sorte,Orin J. Robinson,Kenneth V. Rosenberg,Kenneth V. Rosenberg,Steve Kelling +9 more
TL;DR: It is shown that, relative to biomass leaving in autumn, proportionally more biomass returned in spring across the southern United States than across the northern United States, providing a picture of survival rates for species with different life-history and migratory strategies.
Journal ArticleDOI
High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat.
Pang Yunlong,Liu Chunxia,Danfeng Wang,Paul St. Amand,Amy Bernardo,Amy Bernardo,Li Wenhui,Fang He,Fang He,Linzhi Li,Liming Wang,Xiufang Yuan,Lei Dong,Yu Su,Huirui Zhang,Meng Zhao,Yunlong Liang,Hongze Jia,Xitong Shen,Yue Lu,Hongming Jiang,Yuye Wu,Anfei Li,Honggang Wang,Lingrang Kong,Guihua Bai,Shubing Liu +26 more
TL;DR: Results from this study demonstrated that significantly increasing GWAS population size and marker density greatly improves detection and identification of candidate genes underlying a QTL, solidifying the foundation of large-scale QTL fine mapping, candidate gene validation, and developing functional markers for genomics-based breeding in wheat.
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Variability of Bacterial Communities in the Moth Heliothis virescens Indicates Transient Association with the Host
Heike Staudacher,Martin Kaltenpoth,J.A.J. Breeuwer,Steph B. J. Menken,David G. Heckel,Astrid T. Groot +5 more
TL;DR: In larvae, bacterial communities differed depending on the food plant on which they had been reared, although the within-group variation between biological replicates was high, and the high variability in bacterial communities suggests a loose and temporary association of the identified bacteria with H. virescens.
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.