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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Journal ArticleDOI
Compositional response of Amazon forests to climate change
Adriane Esquivel-Muelbert,Timothy R. Baker,Kyle G. Dexter,Simon L. Lewis,Simon L. Lewis,Roel J. W. Brienen,Ted R. Feldpausch,Jon Lloyd,Abel Monteagudo-Mendoza,Luzmila Arroyo,Esteban Álvarez-Dávila,Niro Higuchi,Beatriz Schwantes Marimon,Ben Hur Marimon-Junior,Marcos Silveira,Emilio Vilanova,Emilio Vilanova,Emanuel Gloor,Yadvinder Malhi,Jérôme Chave,Jos Barlow,Jos Barlow,Damien Bonal,Nallaret Davila Cardozo,Terry L. Erwin,Sophie Fauset,Bruno Hérault,Susan G. Laurance,Lourens Poorter,Lan Qie,Clément Stahl,Martin J. P. Sullivan,Hans ter Steege,Hans ter Steege,Vincent A. Vos,Pieter A. Zuidema,Everton Cristo de Almeida,Edmar Almeida de Oliveira,Ana Andrade,Simone Aparecida Vieira,Luiz E. O. C. Aragão,Luiz E. O. C. Aragão,Alejandro Araujo-Murakami,Eric Arets,Gerardo A. Aymard C,Christopher Baraloto,Plínio Barbosa de Camargo,Jorcely Barroso,Frans Bongers,René G. A. Boot,José Luís Camargo,Wendeson Castro,Victor Chama Moscoso,James A. Comiskey,Fernando Cornejo Valverde,Antonio Carlos Lola da Costa,Jhon del Aguila Pasquel,Jhon del Aguila Pasquel,Anthony Di Fiore,Luisa Fernanda Duque,Fernando Elias,Julien Engel,Julien Engel,Gerardo Flores Llampazo,David W. Galbraith,Rafael Herrera Fernández,Rafael Herrera Fernández,Eurídice N. Honorio Coronado,Wannes Hubau,Eliana Jimenez-Rojas,Adriano José Nogueira Lima,Ricardo Keichi Umetsu,William F. Laurance,Gabriela Lopez-Gonzalez,Thomas E. Lovejoy,Omar Aurelio Melo Cruz,Paulo S. Morandi,David A. Neill,Percy Núñez Vargas,Nadir Pallqui Camacho,Alexander Parada Gutierrez,Guido Pardo,Julie Peacock,Marielos Peña-Claros,Maria Cristina Peñuela-Mora,Pascal Petronelli,Georgia Pickavance,Nigel C. A. Pitman,Adriana Prieto,Carlos A. Quesada,Hirma Ramírez-Angulo,Maxime Réjou-Méchain,Zorayda Restrepo Correa,Anand Roopsind,Agustín Rudas,Rafael de Paiva Salomão,Natalino Silva,Javier Silva Espejo,James Singh,Juliana Stropp,John Terborgh,Raquel Thomas,Marisol Toledo,Armando Torres-Lezama,Luis Valenzuela Gamarra,Peter J. van de Meer,Geertje M. F. van der Heijden,Peter van der Hout,Rodolfo Vásquez Martínez,César I.A. Vela,Ima Célia Guimarães Vieira,Oliver L. Phillips +111 more
TL;DR: A slow shift to a more dry‐affiliated Amazonia is underway, with changes in compositional dynamics consistent with climate‐change drivers, but yet to significantly impact whole‐community composition.
Journal ArticleDOI
Various Versatile Variances: An Object-Oriented Implementation of Clustered Covariances in R
TL;DR: In R, functions for covariances in clustered or panel models have been somewhat scattered or available only for certain modeling functions, notably the (generalized) linear regression model, but now these are directly applicable to models from many packages, e.g., including MASS, pscl, countreg, betareg, among others.
Journal ArticleDOI
Antibiotic-resistant bacteria show widespread collateral sensitivity to antimicrobial peptides
Viktória Lázár,Viktória Lázár,Ana Martins,Réka Spohn,Lejla Daruka,Gábor Grézal,Gergely Fekete,Mónika Számel,Pramod Kumar Jangir,Bálint Kintses,Bálint Csörgő,Ákos Nyerges,Ádám Györkei,András Kincses,András Dér,Fruzsina R. Walter,Mária A. Deli,Edit Urbán,Zsófia Hegedűs,Gábor Olajos,Orsolya Méhi,Balázs Bálint,István Nagy,Tamás A. Martinek,Balázs Papp,Csaba Pál +25 more
TL;DR: The identification of antimicrobial peptide–antibiotic combinations that enhance antibiotic activity against multidrug-resistant bacteria and slow down de novo evolution of resistance are identified and guidelines for the development of efficient peptide-based therapies of antibiotic-resistant infections are provided.
Journal ArticleDOI
Tropospheric Ozone Assessment Report: Present-day tropospheric ozone distribution and trends relevant to vegetation
Gina Mills,Håkan Pleijel,Christopher S. Malley,Baerbel Sinha,Owen R. Cooper,Martin G. Schultz,Howard S. Neufeld,David Simpson,Katrina Sharps,Zhaozhong Feng,Giacomo Gerosa,Harry Harmens,Kazuhiko Kobayashi,Pallavi Saxena,Elena Paoletti,Vinayak Sinha,Xiaobin Xu +16 more
TL;DR: The Tropospheric Ozone Assessment Report (TOAR-Vegetation) as mentioned in this paper reports on present-day global distribution of ozone at over 3300 vegetated sites and the long-term trends at nearly 1200 sites.
Journal ArticleDOI
Reward and choice encoding in terminals of midbrain dopamine neurons depends on striatal target
Nathan F. Parker,Courtney M. Cameron,Joshua P. Taliaferro,Junuk Lee,Jung Yoon Choi,Thomas J. Davidson,Nathaniel D. Daw,Ilana B. Witten +7 more
TL;DR: Key differences in the encoding of reward and choice in dopamine terminals in dorsal versus ventral striatum are identified: DA terminals in ventralstriatum responded more strongly to reward consumption and reward-predicting cues, whereasDA terminals in dorsomedial striatum respondedMore strongly to contralateral choices.
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