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Search Results: 1 - 10 of 406183 matches for " Douglas M Bates "
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Fitting Linear Mixed-Effects Models using lme4
Douglas Bates,Martin M?chler,Ben Bolker,Steve Walker
Statistics , 2014,
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.
Fast and Elegant Numerical Linear Algebra Using the RcppEigen Package
Douglas Bates,Dirk Eddlebuettel
Journal of Statistical Software , 2013,
Abstract: The RcppEigen package provides access from R (R Core Team 2012a) to the Eigen (Guennebaud, Jacob, and others 2012) C++ template library for numerical linear algebra. Rcpp (Eddelbuettel and Fran ois 2011, 2012) classes and specializations of the C++ templated functions as and wrap from Rcpp provide the "glue" for passing objects from R to C++ and back. Several introductory examples are presented. This is followed by an in-depth discussion of various available approaches for solving least-squares problems, including rank-revealing methods, concluding with an empirical run-time comparison. Last but not least, sparse matrix methods are discussed.
Prolonged Exposure to a Mer Ligand in Leukemia: Gas6 Favors Expression of a Partial Mer Glycoform and Reveals a Novel Role for Mer in the Nucleus
Justine Migdall-Wilson, Christine Bates, Jennifer Schlegel, Luis Brand?o, Rachel M. A. Linger, Deborah DeRyckere, Douglas K. Graham
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0031635
Abstract: Mer tyrosine kinase is ectopically expressed in acute lymphoblastic leukemia and associated with enhanced chemoresistance and disease progression. While such effects are generally ascribed to increased engagement of oncogenic pathways downstream of Mer stimulation by its ligand, Gas6, Mer has not been characterized beyond the scope of its signaling activity. The present study explores Mer behavior following prolonged exposure to Gas6, a context similar to the Gas6-enriched microenvironment of the bone marrow, where a steady supply of ligand facilitates continuous engagement of Mer and likely sustains the presence of leukemic cells. Long-term Gas6 exposure induced production of a partially N-glycosylated form of Mer from newly synthesized stores of protein. Preferential expression of the partial Mer glycoform was associated with diminished levels of Mer on the cell surface and altered Mer localization within the nuclear-soluble and chromatin-bound fractions. The presence of Mer in the nucleus is a novel finding for this receptor, and the glycoform-specific preferences observed in each nuclear compartment suggest that glycosylation may influence Mer function within particular subcellular locales. Previous studies have established Mer as an attractive cancer biologic target, and understanding the complexity of its activity has important implications for potential strategies of Mer inhibition in leukemia therapy. Our results identify several novel features of Mer that expand the breadth of its functions and impact the development of therapeutic modalities designed to target Mer.
The Effect of Heterogeneity on Invasion in Spatial Epidemics: From Theory to Experimental Evidence in a Model System
Franco M. Neri ,Anne Bates,Winnie S. Füchtbauer,Francisco J. Pérez-Reche,Sergei N. Taraskin,Wilfred Otten,Douglas J. Bailey,Christopher A. Gilligan
PLOS Computational Biology , 2011, DOI: 10.1371/journal.pcbi.1002174
Abstract: Heterogeneity in host populations is an important factor affecting the ability of a pathogen to invade, yet the quantitative investigation of its effects on epidemic spread is still an open problem. In this paper, we test recent theoretical results, which extend the established “percolation paradigm” to the spread of a pathogen in discrete heterogeneous host populations. In particular, we test the hypothesis that the probability of epidemic invasion decreases when host heterogeneity is increased. We use replicated experimental microcosms, in which the ubiquitous pathogenic fungus Rhizoctonia solani grows through a population of discrete nutrient sites on a lattice, with nutrient sites representing hosts. The degree of host heterogeneity within different populations is adjusted by changing the proportion and the nutrient concentration of nutrient sites. The experimental data are analysed via Bayesian inference methods, estimating pathogen transmission parameters for each individual population. We find a significant, negative correlation between heterogeneity and the probability of pathogen invasion, thereby validating the theory. The value of the correlation is also in remarkably good agreement with the theoretical predictions. We briefly discuss how our results can be exploited in the design and implementation of disease control strategies.
A provisional check list of the reptiles and amphibians of Golden Gate Highlands National Park
M.F. Bates
Koedoe : African Protected Area Conservation and Science , 1991, DOI: 10.4102/koedoe.v34i2.431
Abstract: A provisional check list of 26 reptile and amphibian species (8 frog, 8 lizard and 10 snake species) occurring in Golden Gate Highlands National Park is presented. The list does not reflect the results of an intensive survey, but is a record of specimens collected in the park and preserved at the National Museum, Bloemfontein.
Taxonomic status and distribution of the South African lizard Tetradactylus breyeri Roux (Gerrhosauridae)
M.F. Bates
African Zoology , 2011,
Abstract: The taxonomic status of the poorly known South African gerrhosaurid Tetradactylus breyeri, described by Roux in 1907 on the basis of a single specimen from the Transvaal, was investigated. The holotype and 14 other preserved specimens were examined and are described in detail. Prior to this study, only six specimens had been described in the literature. No evidence was found to warrant subspecific status for lizards from any part of the species' range, despite the apparently isolated nature of populations, and T breyer; is thus considered monotypic. The species occurs as three apparently isolated montane grassland to highveld grassland populations in the South African provinces of Mpumalanga, north-eastern Free State and KwaZulu-Natal. Despite recent surveys, very few specimens have been found, and the 'rare' status afforded the species in the South African Red Data Book should be retained.
A Systematic Process for Educational Policy Development: Based on a Systems Approach to Training and Project Management
Catherine M Bates
Brock Education : a Journal of Educational Research and Practice , 2007,
Abstract: In the Canadian Forces leadership is considered to be the paramount skill of all members. For Training Development Officers, one method of displaying leadership is through the careful consideration of educational policy and its skilful implementation. If we do not take the time to write carefully considered policy, then students and their issues are managed according to the values and beliefs of individual decision makers. Normally this is fine, but when it negatively impacts students or teachers then neither equality nor equity is achieved.
The Mnn2 Mannosyltransferase Family Modulates Mannoprotein Fibril Length, Immune Recognition and Virulence of Candida albicans
Rebecca A. Hall,Steven Bates,Megan D. Lenardon,Donna M. MacCallum,Jeanette Wagener,Douglas W. Lowman,Michael D. Kruppa,David L. Williams,Frank C. Odds,Alistair J. P. Brown,Neil A. R. Gow
PLOS Pathogens , 2013, DOI: 10.1371/journal.ppat.1003276
Abstract: The fungal cell wall is the first point of interaction between an invading fungal pathogen and the host immune system. The outer layer of the cell wall is comprised of GPI anchored proteins, which are post-translationally modified by both N- and O-linked glycans. These glycans are important pathogen associated molecular patterns (PAMPs) recognised by the innate immune system. Glycan synthesis is mediated by a series of glycosyl transferases, located in the endoplasmic reticulum and Golgi apparatus. Mnn2 is responsible for the addition of the initial α1,2-mannose residue onto the α1,6-mannose backbone, forming the N-mannan outer chain branches. In Candida albicans, the MNN2 gene family is comprised of six members (MNN2, MNN21, MNN22, MNN23, MNN24 and MNN26). Using a series of single, double, triple, quintuple and sextuple mutants, we show, for the first time, that addition of α1,2-mannose is required for stabilisation of the α1,6-mannose backbone and hence regulates mannan fibril length. Sequential deletion of members of the MNN2 gene family resulted in the synthesis of lower molecular weight, less complex and more uniform N-glycans, with the sextuple mutant displaying only un-substituted α1,6-mannose. TEM images confirmed that the sextuple mutant was completely devoid of the outer mannan fibril layer, while deletion of two MNN2 orthologues resulted in short mannan fibrils. These changes in cell wall architecture correlated with decreased proinflammatory cytokine induction from monocytes and a decrease in fungal virulence in two animal models. Therefore, α1,2-mannose of N-mannan is important for both immune recognition and virulence of C. albicans.
Estimating the Multilevel Rasch Model: With the lme4 Package
Harold Doran,Douglas Bates,Paul Bliese,Maritza Dowling
Journal of Statistical Software , 2007,
Abstract: Traditional Rasch estimation of the item and student parameters via marginal maximum likelihood, joint maximum likelihood or conditional maximum likelihood, assume individuals in clustered settings are uncorrelated and items within a test that share a grouping structure are also uncorrelated. These assumptions are often violated, particularly in educational testing situations, in which students are grouped into classrooms and many test items share a common grouping structure, such as a content strand or a reading passage. Consequently, one possible approach is to explicitly recognize the clustered nature of the data and directly incorporate random effects to account for the various dependencies. This article demonstrates how the multilevel Rasch model can be estimated using the functions in R for mixed-effects models with crossed or partially crossed random effects. We demonstrate how to model the following hierarchical data structures: a) individuals clustered in similar settings (e.g., classrooms, schools), b) items nested within a particular group (such as a content strand or a reading passage), and c) how to estimate a teacher × content strand interaction.
Out of the Cage of Shadows
Harald Baayen,Shravan Vasishth,Douglas Bates,Reinhold Kliegl
Statistics , 2015,
Abstract: Unlike molecules or plots of barley, subjects in psycholinguistic experiments are intelligent beings that depend for their survival on constant adaptation to their environment. This study presents three data sets documenting the presence of adaptive processes in psychological experiments. These adaptive processes leave a statistical footprint in the form of autocorrelations in the residual error associated with by-subject time series of trial-to-trial responses. Generalized additive mixed models (GAMMs) provide a unified framework within which both factorial predictors and covariates given with the experimental design, as well as non-linear random effects and interactions with experimental time can be uncovered and evaluated. GAMMs not only provide substantially improved fits to experimental data with time series structure, but also provide improved insight into predictors of theoretical interest, as well as a more refined window on the random effects structure. Our results challenge the standard advocated by Barr et al. (2013). The analytical cage of the maximal linear mixed model to which this standard confines the analyst is motivated by simulation studies which presuppose experimental data to be sterile, and free of any adaptive processes. However, when adaptive processes are present in real data, the simulation results of Barr et al. are no longer informative. For such data, the method of analysis cannot be purely design-driven, but must be in part driven by the data.
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