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
More filters
Journal ArticleDOI
Bat detective—Deep learning tools for bat acoustic signal detection
Oisin Mac Aodha,Rory Gibb,Kate E. Barlow,Ella Browning,Ella Browning,Michael Firman,Robin Freeman,Briana Harder,Libby Kinsey,Gary R. Mead,Stuart E. Newson,Ivan Pandourski,Stuart Parsons,Jon Russ,Abigel Szodoray-Paradi,Farkas Szodoray-Paradi,Elena Tilova,Mark Girolami,Gabriel J. Brostow,Kate E. Jones,Kate E. Jones +20 more
TL;DR: In this article, a convolutional neural network based open-source pipeline was developed for detecting ultrasonic, full-spectrum, search-phase calls produced by echolocating bats.
Journal ArticleDOI
Subjective Confidence Predicts Information Seeking in Decision Making.
TL;DR: Conditions in a perceptual decision task were created that were matched in accuracy but differed in subjective evaluation of accuracy by orthogonally varying the strength versus variability of evidence, providing clear support for the hypothesis that subjective confidence predicts information seeking in decision making.
Journal ArticleDOI
Patterns and drivers of recent disturbances across the temperate forest biome
Andreas Sommerfeld,Cornelius Senf,Cornelius Senf,Brian Buma,Anthony W. D'Amato,Tiphaine Després,Tiphaine Després,Ignacio Díaz-Hormazábal,Shawn Fraver,Lee E. Frelich,Alvaro G. Gutiérrez,Sarah J. Hart,Brian J. Harvey,Hong S. He,Tomáš Hlásny,Andrés Holz,Thomas Kitzberger,Dominik Kulakowski,David B. Lindenmayer,Akira Mori,Jörg Müller,Jörg Müller,Juan Paritsis,George L. W. Perry,Scott L. Stephens,Miroslav Svoboda,Monica G. Turner,Thomas T. Veblen,Rupert Seidl +28 more
TL;DR: It is shown that disturbance patterns across the temperate biome vary with agents and tree traits, yet large disturbances are consistently linked to warmer and drier than average conditions.
Journal ArticleDOI
Evidence of evolutionary homogenization of bird communities in urban environments across Europe
Federico Morelli,Yanina Benedetti,Juan Diego Ibáñez-Álamo,Jukka Jokimäki,Raivo Mänd,Piotr Tryjanowski,Anders Pape Møller +6 more
TL;DR: In this article, the effects of urbanization on the evolutionary distinctiveness of bird communities in rural and urban environments in six different European cities from different ecoregions were investigated.
Journal ArticleDOI
Excess forest mortality is consistently linked to drought across Europe.
TL;DR: Analysis of high-resolution annual satellite-based canopy mortality maps from 1987 to 2016 shows that excess forest mortality is significantly related to drought across continental Europe, and suggests that a future increase in drought could trigger widespread tree mortality in Europe.
References
More filters
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.