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Linear Mixed-Effects Models using 'Eigen' and S4
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The core computational algorithms are implemented using the Eigen C++ library for numerical linear algebra and RcppEigen``glue''.About:
The article was published on 2015-10-06 and is currently open access. It has received 8543 citations till now.read more
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Journal ArticleDOI
Fitting Linear Mixed-Effects Models Using lme4
TL;DR: 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.
Journal ArticleDOI
Global effects of land use on local terrestrial biodiversity
Tim Newbold,Lawrence N. Hudson,Samantha L. L. Hill,Sara Contu,Igor Lysenko,Rebecca A. Senior,Luca Börger,Dominic J. Bennett,Argyrios Choimes,Ben Collen,Julie Day,Adriana De Palma,Sandra Díaz,Susy Echeverría-Londoño,Melanie J. Edgar,Anat Feldman,Morgan Garon,Michelle L K Harrison,Tamera I Alhusseini,Daniel J. Ingram,Yuval Itescu,Jens Kattge,Victoria Kemp,Lucinda Kirkpatrick,Michael Kleyer,David L P Correia,Callum D. Martin,Shai Meiri,Maria Novosolov,Yuan Pan,Helen Phillips,Drew W. Purves,Alexandra N Robinson,Jake Simpson,Sean L. Tuck,Evan Weiher,Hannah J. White,Robert M. Ewers,Georgina M. Mace,Jörn P. W. Scharlemann,Andy Purvis +40 more
TL;DR: A terrestrial assemblage database of unprecedented geographic and taxonomic coverage is analysed to quantify local biodiversity responses to land use and related changes and shows that in the worst-affected habitats, pressures reduce within-sample species richness by an average of 76.5%, total abundance by 39.5% and rarefaction-based richness by 40.3%.
Journal ArticleDOI
mediation: R Package for Causal Mediation Analysis
TL;DR: The mediation package implements a comprehensive suite of statistical tools for conducting causal mediation analysis in applied empirical research and implements a statistical method for dealing with multiple (causally dependent) mediators, which are often encountered in practice.
Journal ArticleDOI
The human transcriptome across tissues and individuals
Marta Melé,Pedro G. Ferreira,Ferran Reverter,Ferran Reverter,David S. DeLuca,Jean Monlong,Jean Monlong,Michael Sammeth,Taylor Young,Jakob M. Goldmann,Jakob M. Goldmann,Dmitri D. Pervouchine,Dmitri D. Pervouchine,Timothy J. Sullivan,Rory Johnson,Ayellet V. Segrè,Sarah Djebali,Anastasia Niarchou,Anastasia Niarchou,Fred A. Wright,Tuuli Lappalainen,Miquel Calvo,Gad Getz,Gad Getz,Emmanouil T. Dermitzakis,Emmanouil T. Dermitzakis,Kristin G. Ardlie,Roderic Guigó +27 more
TL;DR: Tissues exhibit characteristic transcriptional signatures that show stability in postmortem samples that are dominated by a relatively small number of genes, though few are exclusive to a particular tissue and vary more across tissues than individuals.
Journal ArticleDOI
Estimating the global burden of endemic canine rabies.
Katie Hampson,Laurent Coudeville,Tiziana Lembo,Maganga Sambo,Alexia Kieffer,Michaël Attlan,Jacques Barrat,Jesse D. Blanton,Deborah J. Briggs,Sarah Cleaveland,Peter Costa,Conrad M. Freuling,Elly Hiby,Lea Knopf,Fernando Leanes,François-Xavier Meslin,A. E. Metlin,Mary Elizabeth Miranda,Thomas Müller,Louis Hendrik Nel,Sergio Recuenco,Charles E. Rupprecht,Charles E. Rupprecht,Carolin L. Schumacher,Louise H. Taylor,Marco Antonio Natal Vigilato,Jakob Zinsstag,Jonathan Dushoff +27 more
TL;DR: Investment in dog vaccination, the single most effective way of reducing the disease burden, has been inadequate and that the availability and affordability of PEP needs improving, demonstrating that collaboration by medical and veterinary sectors could dramatically reduce the current large, and unnecessary, burden of rabies on affected communities.