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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Weather whiplash in agricultural regions drives deterioration of water quality
Terrance D. Loecke,Amy J. Burgin,Diego A. Riveros-Iregui,Adam S. Ward,Steven A. Thomas,Caroline A. Davis,Martin A. St. Clair +6 more
TL;DR: In this paper, the authors show that changing precipitation patterns, resulting from climate change, interact with agricultural land use to deteriorate water quality, and that increased weather whiplash will, in part, increase the frequency of riverine N exceeding drinking water standards.
Journal ArticleDOI
Autism genes converge on asynchronous development of shared neuron classes
Bruna S. Paulsen,Silvia Velasco,Amanda J. Kedaigle,Martina Pigoni,Giorgia Quadrato,Anthony J. Deo,Xian Adiconis,Ana Uzquiano,Rafaela Sartore,Sung Min Yang,Sean Simmons,P Symvoulidis,Kwanho Kim,Kalliopi Tsafou,Archana Podury,Catherine Abbate,Ashley Tucewicz,Samantha N Smith,Alexandre Albanese,Lindy E. Barrett,Neville E. Sanjana,Xi Shi,Kwang-Ho Chung,Kasper Lage,Edward S. Boyden,Aviv Regev,Joshua Z. Levin,Paola Arlotta +27 more
TL;DR: In this paper , the authors used organoid models of the human cerebral cortex to identify cell-type-specific developmental abnormalities that result from haploinsufficiency in three ASD risk genes, SUV420H1 (also known as KMT5B), ARID1B, and CHD8, in multiple cell lines from different donors.
Journal ArticleDOI
Multi-Spectral Imaging from an Unmanned Aerial Vehicle Enables the Assessment of Seasonal Leaf Area Dynamics of Sorghum Breeding Lines.
Andries Potgieter,Barbara George-Jaeggli,Barbara George-Jaeggli,Scott Chapman,Scott Chapman,Kenneth Laws,Luz A. Suárez Cadavid,Jemima Wixted,James E. M. Watson,Mark D. B. Eldridge,David Jordan,Graeme Hammer +11 more
TL;DR: These methods to monitor dynamics of green and senesced leaf area are suitable for out-scaling to enhance phenotyping of additional crop canopy characteristics and likely crop yield responses among genotypes across large fields and multiple dates.
Journal ArticleDOI
Simulating ideal assistive devices to reduce the metabolic cost of walking with heavy loads
TL;DR: Musculoskeletal simulation is used to predict how hypothetical devices affect muscle activity and metabolic cost when walking with heavy loads and may help experimentalists decide which joint motions to target when building devices and can provide intuition for how devices may interact with the musculOSkeletal system.
Journal ArticleDOI
Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance.
Anastasiya Kazachenka,Tessa M. Bertozzi,Marcela K. Sjoberg-Herrera,Nic Walker,Joseph Gardner,Richard Gunning,Elena Pahita,Sarah Adams,David J. Adams,Anne C. Ferguson-Smith +9 more
TL;DR: A systematic genome-wide screen identifies multiple C57BL/6J murine IAPs with Avy epigenetic properties, indicating reconstruction of metastable epigenetic states and challenging the generalizability of non-genetic inheritance at these regions.
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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