Cognitive radio is viewed as a novel approach for improving the utilization of a precious natural resource: the radio electromagnetic spectrum. The cognitive radio, built on a software-defined radio, is defined as an intelligent wireless communication system that is aware of its environment and uses the methodology of understanding-by-building to learn from the environment and adapt to statistical variations in the input stimuli, with two primary objectives in mind: /spl middot/ highly reliable communication whenever and wherever needed; /spl middot/ efficient utilization of the radio spectrum. Following the discussion of interference temperature as a new metric for the quantification and management of interference, the paper addresses three fundamental cognitive tasks. 1) Radio-scene analysis. 2) Channel-state estimation and predictive modeling. 3) Transmit-power control and dynamic spectrum management. This work also discusses the emergent behavior of cognitive radio.

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Cognitive radio: brain-empowered wireless communications

Summary. We consider the problem of comparing complex hierarchical models in which the number of parameters is not clearly defined. Using an information theoretic argument we derive a measure pD for the effective number of parameters in a model as the difference between the posterior mean of the deviance and the deviance at the posterior means of the parameters of interest. In general pD approximately corresponds to the trace of the product of Fisher's information and the posterior covariance, which in normal models is the trace of the ‘hat’ matrix projecting observations onto fitted values. Its properties in exponential families are explored. The posterior mean deviance is suggested as a Bayesian measure of fit or adequacy, and the contributions of individual observations to the fit and complexity can give rise to a diagnostic plot of deviance residuals against leverages. Adding pD to the posterior mean deviance gives a deviance information criterion for comparing models, which is related to other information criteria and has an approximate decision theoretic justification. The procedure is illustrated in some examples, and comparisons are drawn with alternative Bayesian and classical proposals. Throughout it is emphasized that the quantities required are trivial to compute in a Markov chain Monte Carlo analysis.

/pdf/bayesian-measures-of-model-complexity-and-fit-1ouzmtfu7x.pdf

Bayesian measures of model complexity and fit

Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.

/pdf/phyloseq-an-r-package-for-reproducible-interactive-analysis-1ez1xx3dlr.pdf

phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.

An essential textbook for any student or researcher in biology needing to design experiments, sample programs or analyse the resulting data The text begins with a revision of estimation and hypothesis testing methods, covering both classical and Bayesian philosophies, before advancing to the analysis of linear and generalized linear models Topics covered include linear and logistic regression, simple and complex ANOVA models (for factorial, nested, block, split-plot and repeated measures and covariance designs), and log-linear models Multivariate techniques, including classification and ordination, are then introduced Special emphasis is placed on checking assumptions, exploratory data analysis and presentation of results The main analyses are illustrated with many examples from published papers and there is an extensive reference list to both the statistical and biological literature The book is supported by a website that provides all data sets, questions for each chapter and links to software

/pdf/experimental-design-and-data-analysis-for-biologists-8ybva8d53x.pdf

Experimental Design and Data Analysis for Biologists

Presents the likelihood methods for the analysis of cointegration in VAR models with Gaussian errors, seasonal dummies, and constant terms. Discusses likelihood ratio tests of cointegration rank and find the asymptotic distribution of the test statistics. Shows that the asymptotic distribution of the maximum likelihood estimator is mixed Gausssian.

Estimation and hypothesis testing of cointegration vectors in Gaussian vector autoregressive models / Søren Johansen

Often sports announcers, particularly in baseball, provide the listener with exaggerated information concerning a player's performance. For example, we may be told that Dave Winfield, a popular baseball player, has hit safely in 8 of his last 17 chances (a batting average of .471). This is biased, or selected information, as the “17” was chosen to maximize the reported percentage. We model this as observing a maximum success rate of a Bernoulli process and show how to construct the likelihood function for a player's true batting ability. The likelihood function is a high-degree polynomial, but it can be computed exactly. Alternatively, the problem yields to solutions based on either the EM algorithm or Gibbs sampling. Using these techniques, we compute maximum likelihood estimators, Bayes estimators, and associated measures of error. We also show how to approximate the likelihood using a Brownian motion calculation. We find that although constructing good estimators from selected information is d...

/pdf/estimation-with-selected-binomial-information-or-do-you-4q1ei4n2cp.pdf

Estimation with Selected Binomial Information or do you Really Believe that Dave Winfield is Batting .471

/pdf/gibbs-sampling-with-improper-prior-distributions-13xz7fnmxl.pdf

Gibbs Sampling with Improper Prior Distributions

Association testing aims to discover the underlying relationship between genotypes (usually Single Nucleotide Polymorphisms, or SNPs) and phenotypes (attributes, or traits). The typically large data sets used in association testing often contain missing values. Standard statistical methods either impute the missing values using relatively simple assumptions, or delete them, or both, which can generate biased results. Here we describe the Bayesian hierarchical model BAMD (Bayesian Association with Missing Data). BAMD is a Gibbs sampler, in which missing values are multiply imputed based upon all of the available information in the data set. We estimate the parameters and prove that updating one SNP at each iteration preserves the ergodic property of the Markov chain, and at the same time improves computational speed. We also implement a model selection option in BAMD, which enables potential detection of SNP interactions. Simulations show that unbiased estimates of SNP effects are recovered with missing genotype data. Also, we validate associations between SNPs and a carbon isotope discrimination phenotype that were previously reported using a family based method, and discover an additional SNP associated with the trait. BAMD is available as an R-package from this http URL

Simultaneous SNP identification in association studies with missing data

The usual confidence interval, based on Student's t distribution, has conditional confidence that is larger than the nominal confidence level. Although this fact is known, along with the fact that increased conditional confidence can be used to improve a confidence assertion, the confidence assertion of Student's t interval has never been critically examined. We do so here, and construct a confidence estimator that allows uniformly higher confidence in the interval and is closer (than 1 - a) to the indicator of coverage. 1. Introduction and summary. The usual confidence interval for a normal mean, when the population variance is unknown, is based on Student's

/pdf/increasing-the-confidence-in-student-s-t-interval-5p5ykcw097.pdf

Increasing the Confidence in Student's $t$ Interval

Association testing aims to discover the underlying relationship between genotypes (usually Single Nucleotide Polymorphisms, or SNPs) and phenotypes (attributes, or traits). The typically large data sets used in association testing often contain missing values. Standard statistical methods either impute the missing values using relatively simple assumptions, or delete them, or both, which can generate biased results. Here we describe the Bayesian hierarchical model BAMD (Bayesian Association with Missing Data). BAMD is a Gibbs sampler, in which missing values are multiply imputed based upon all of the available information in the data set. We estimate the parameters and prove that updating one SNP at each iteration preserves the ergodic property of the Markov chain, and at the same time improves computational speed. We also implement a model selection option in BAMD, which enables potential detection of SNP interactions. Simulations show that unbiased estimates of SNP effects are recovered with missing genotype data. Also, we validate associations between SNPs and a carbon isotope discrimination phenotype that were previously reported using a family based method, and discover an additional SNP associated with the trait. BAMD is available as an R-package from http://cran.r-project.org/package=BAMD.

/pdf/simultaneous-snp-identification-in-association-studies-with-3dk8zua1cf.pdf

George Casella

Papers

Estimation with Selected Binomial Information or do you Really Believe that Dave Winfield is Batting .471

Gibbs Sampling with Improper Prior Distributions

Simultaneous SNP identification in association studies with missing data

Increasing the Confidence in Student's $t$ Interval

Simultaneous SNP identification in association studies with missing data