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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Endophyte traits relevant to stress tolerance, resource use and habitat of origin predict effects on host plants
TL;DR: Overall, survival was higher for plants grown with more stress-tolerant fungi, and aboveground biomass was enhanced by fungi from warmer and drier habitats, while plant growth and physiology were also dependent on fungal resource use indicators; however, specific predictors were dependent on water availability.
Journal ArticleDOI
Quantification of uncertainties in conifer sap flow measured with the thermal dissipation method
Richard L. Peters,Richard L. Peters,Patrick Fonti,David Frank,David Frank,Rafael Poyatos,Christoforos Pappas,Ansgar Kahmen,Vinicio Carraro,Angela Luisa Prendin,Angela Luisa Prendin,Loïc Schneider,Jennifer L. Baltzer,Greg A. Baron‐Gafford,Lars Dietrich,Ingo Heinrich,R. L. Minor,Oliver Sonnentag,Ashley M. Matheny,Maxwell G. Wightman,Kathy Steppe +20 more
TL;DR: The presented ensemble of calibration curves and proposed dampening correction, together with the systematic quantification of data-processing uncertainties, provide crucial steps in improving whole-tree water-use estimates across spatial and temporal scales.
Journal ArticleDOI
Fixation durations in scene viewing: Modeling the effects of local image features, oculomotor parameters, and task
TL;DR: A LMM-based framework of analysis, applied to the control of fixation durations in scenes, suggests important constraints for models of scene perception and search, and for visual attention in general.
Journal ArticleDOI
Estimating aboveground net biomass change for tropical and subtropical forests : refinement of IPCC default rates using forest plot data
Daniela Requena Suarez,Danaë M. A. Rozendaal,Veronique De Sy,Oliver L. Phillips,Esteban Álvarez-Dávila,Kristina J. Anderson-Teixeira,Kristina J. Anderson-Teixeira,Alejandro Araujo-Murakami,Luzmila Arroyo,Timothy R. Baker,Frans Bongers,Roel Jacobus Wilhelmus Brienen,Sarah Carter,Susan C. Cook-Patton,Ted R. Feldpausch,Bronson W. Griscom,Nancy L. Harris,Bruno Hérault,Eurídice N. Honorio Coronado,Sara M. Leavitt,Simon L. Lewis,Simon L. Lewis,Beatriz Schwantes Marimon,Abel Monteagudo Mendoza,Justin Kassi N'dja,Anny Estelle N'Guessan,Lourens Poorter,Lan Qie,Ervan Rutishauser,Plinio Sist,Bonaventure Sonké,Martin J. P. Sullivan,Emilio Vilanova,Emilio Vilanova,Maria M. H. Wang,Christopher Martius,Martin Herold +36 more
TL;DR: This study provides a rigorous and traceable refinement of the IPCC 2006 default rates in tropical and subtropical ecological zones, and identifies which areas require more research on ∆AGB.
Journal ArticleDOI
How much is enough? Effects of technical and biological replication on metabarcoding dietary analysis.
Vanessa A. Mata,Hugo Rebelo,Hugo Rebelo,Hugo Rebelo,Francisco Amorim,Gary F. McCracken,Simon N. Jarman,Simon N. Jarman,Simon N. Jarman,Pedro Beja,Pedro Beja +10 more
TL;DR: It is found that diet diversity estimates increased steadily with the number of pellets analysed per individual, with seven pellets required to detect ~80% of prey species, and most variation in diet composition was associated with differences among individual bats, followed by pellets per individual and PCRs per pellet.
References
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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.
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