University of California, Los Angeles

About: University of California, Los Angeles is a education organization based out in Los Angeles, California, United States. It is known for research contribution in the topics: Population & Health care. The organization has 125991 authors who have published 282429 publications receiving 15785853 citations. The organization is also known as: UCLA & UC Los Angeles.

Cutoff criteria for fit indexes in covariance structure analysis : Conventional criteria versus new alternatives

Abstract: This article examines the adequacy of the “rules of thumb” conventional cutoff criteria and several new alternatives for various fit indexes used to evaluate model fit in practice. Using a 2‐index presentation strategy, which includes using the maximum likelihood (ML)‐based standardized root mean squared residual (SRMR) and supplementing it with either Tucker‐Lewis Index (TLI), Bollen's (1989) Fit Index (BL89), Relative Noncentrality Index (RNI), Comparative Fit Index (CFI), Gamma Hat, McDonald's Centrality Index (Mc), or root mean squared error of approximation (RMSEA), various combinations of cutoff values from selected ranges of cutoff criteria for the ML‐based SRMR and a given supplemental fit index were used to calculate rejection rates for various types of true‐population and misspecified models; that is, models with misspecified factor covariance(s) and models with misspecified factor loading(s). The results suggest that, for the ML method, a cutoff value close to .95 for TLI, BL89, CFI, RNI, and G...

The Sequence Alignment/Map format and SAMtools

Abstract: Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: [email protected]

Convex Optimization

Abstract: Convex optimization problems arise frequently in many different fields. A comprehensive introduction to the subject, this book shows in detail how such problems can be solved numerically with great efficiency. The focus is on recognizing convex optimization problems and then finding the most appropriate technique for solving them. The text contains many worked examples and homework exercises and will appeal to students, researchers and practitioners in fields such as engineering, computer science, mathematics, statistics, finance, and economics.

Comparative fit indexes in structural models

Abstract: Normed and nonnormed fit indexes are frequently used as adjuncts to chi-square statistics for evaluating the fit of a structural model A drawback of existing indexes is that they estimate no known population parameters A new coefficient is proposed to summarize the relative reduction in the noncentrality parameters of two nested models Two estimators of the coefficient yield new normed (CFI) and nonnormed (FI) fit indexes CFI avoids the underestimation of fit often noted in small samples for Bentler and Bonett's (1980) normed fit index (NFI) FI is a linear function of Bentler and Bonett's non-normed fit index (NNFI) that avoids the extreme underestimation and overestimation often found in NNFI Asymptotically, CFI, FI, NFI, and a new index developed by Bollen are equivalent measures of comparative fit, whereas NNFI measures relative fit by comparing noncentrality per degree of freedom All of the indexes are generalized to permit use of Wald and Lagrange multiplier statistics An example illustrates the behavior of these indexes under conditions of correct specification and misspecification The new fit indexes perform very well at all sample sizes

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space

Abstract: Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.