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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Journal ArticleDOI
Genome-wide selection and genetic improvement during modern maize breeding.
Baobao Wang,Zechuan Lin,Xin Li,Yongping Zhao,Zhao Binbin,Guangxia Wu,Xiaojing Ma,Hai Wang,Yurong Xie,Quanquan Li,Guangshu Song,Dexin Kong,Zhigang Zheng,Hongbin Wei,Rongxin Shen,Hong Wu,Cuixia Chen,Zhaodong Meng,Tianyu Wang,Yu Li,Xinhai Li,Yanhui Chen,Jinsheng Lai,Matthew B. Hufford,Jeffrey Ross-Ibarra,Hang He,Haiyang Wang +26 more
TL;DR: This work conducted a comprehensive analysis of the genomic and phenotypic changes associated with modern maize breeding through chronological sampling of 350 elite inbred lines representing multiple eras of germplasm from both China and the United States to demonstrate the use of the breeding-era approach for identifying breeding signatures.
Journal ArticleDOI
Mixed-effects association of single cells identifies an expanded effector CD4+ T cell subset in rheumatoid arthritis.
Chamith Y. Fonseka,Deepak A. Rao,Nikola Teslovich,Ilya Korsunsky,Susan K. Hannes,Kamil Slowikowski,Michael F. Gurish,Laura T. Donlin,Laura T. Donlin,James A. Lederer,Michael E. Weinblatt,Elena Massarotti,Jonathan S. Coblyn,Simon M. Helfgott,Derrick J. Todd,Vivian P. Bykerk,Vivian P. Bykerk,Elizabeth W. Karlson,Joerg Ermann,Yvonne C. Lee,Yvonne C. Lee,Michael B. Brenner,Soumya Raychaudhuri +22 more
TL;DR: Mixed-effects regression of single-cell data accounts for confounding variation and reveals an expanded CD4+ T cell population in rheumatoid arthritis patients that was later seen to contract upon treatment, and could be a potentially widely applied tool for the analysis of high-dimensional single- cell data.
Journal ArticleDOI
Are robots becoming unpopular? Changes in attitudes towards autonomous robotic systems in europe
TL;DR: Attitudes towards robots in the European Union between 2012 and 2017 showed that public opinions regarding robots exhibited a marked negative trend, particularly strong for robots at the workplace, which are, despite the drop, still more positively evaluated than robots performing surgeries or autonomous cars.
Journal ArticleDOI
Beyond green: Broad support for biodiversity in multicultural European cities
Leonie K. Fischer,Jasmin Honold,Rozalija Cvejić,Tim Delshammar,Sven Hilbert,Sven Hilbert,Raffaele Lafortezza,Raffaele Lafortezza,Mojca Nastran,Anders Busse Nielsen,Anders Busse Nielsen,Marina Pintar,Alexander P.N. van der Jagt,Ingo Kowarik +13 more
TL;DR: In this article, a field survey revealed that biodiversity matters: people largely prefer higher plant species richness in urban greenspaces (i.e., parks, wastelands, streetscapes).
Journal ArticleDOI
Evaluation of Maternal, Embryo, and Placental Effects in CD-1 Mice following Gestational Exposure to Perfluorooctanoic Acid (PFOA) or Hexafluoropropylene Oxide Dimer Acid (HFPO-DA or GenX).
Bevin E. Blake,Bevin E. Blake,Harlie A. Cope,Samantha M. Hall,Robert D. Keys,Beth W. Mahler,James McCord,Brittany Scott,Heather M. Stapleton,Mark J. Strynar,Susan A. Elmore,Suzanne E. Fenton +11 more
TL;DR: Gestational exposure to GenX recapitulated many documented effects of PFOA in CD-1 mice, regardless of its much shorter reported half-life; however, adverse effects toward the placenta appear to have compound-specific signatures.
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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