Bayesian factor models in characterizing molecular adaptation

Assessing the selective influence of amino acid properties is important in understanding evolution at the molecular level. A collection of methods and models has been developed in recent years to determine if amino acid sites in a given DNA sequence alignment display substitutions that are altering or conserving a prespecified set of amino acid properties. Residues showing an elevated number of substitutions that favorably alter a physicochemical property are considered targets of positive natural selection. Such approaches usually perform independent analyses for each amino acid property under consideration, without taking into account the fact that some of the properties may be highly correlated. We propose a Bayesian hierarchical regression model with latent factor structure that allows us to determine which sites display substitutions that conserve or radically change a set of amino acid properties, while accounting for the correlation structure that may be present across such properties. We illustrate our approach by analyzing simulated data sets and an alignment of lysin sperm DNA.     

Robust location estimation with missing data

In a missing data setting, we have a sample in which a vector of explanatory variables ${\bf x}_i$ is observed for every subject i, while scalar responses $y_i$ are missing by happenstance on some individuals. In this work we propose robust estimators of the distribution of the responses assuming missing at random (MAR) data, under a semiparametric regression model. Our approach allows the consistent estimation of any weakly continuous functional of the response's distribution. In particular, strongly consistent estimators of any continuous location functional, such as the median, L‐functionals and M‐functionals, are proposed. A robust fit for the regression model combined with the robust properties of the location functional gives rise to a robust recipe for estimating the location parameter. Robustness is quantified through the breakdown point of the proposed procedure. The asymptotic distribution of the location estimators is also derived. The proofs of the theorems are presented in Supplementary Material available online. The Canadian Journal of Statistics 41: 111–132; 2013 © 2012 Statistical Society of Canada     

Generalized estimating equations for mixtures with varying concentrations

A finite mixture model is considered in which the mixing probabilities vary from observation to observation. A parametric model is assumed for one mixture component distribution, while the others are nonparametric nuisance parameters. Generalized estimating equations (GEE) are proposed for the semi‐parametric estimation. Asymptotic normality of the GEE estimates is demonstrated and the lower bound for their dispersion (asymptotic covariance) matrix is derived. An adaptive technique is developed to derive estimates with nearly optimal small dispersion. An application to the sociological analysis of voting results is discussed. The Canadian Journal of Statistics 41: 217–236; 2013 © 2013 Statistical Society of Canada     

Discrete Multicolour Random Mosaics with an Application to Network Extraction

We introduce a class of random fields that can be understood as discrete versions of multicolour polygonal fields built on regular linear tessellations. We focus first on a subclass of consistent polygonal fields, for which we show Markovianity and solvability by means of a dynamic representation. This representation is used to design new sampling techniques for Gibbsian modifications of such fields, a class which covers lattice‐based random fields. A flux‐based modification is applied to the extraction of the field tracks network from a Synthetic Aperture Radar image of a rural area.     

The asymptotic distribution of the partial attributable risk in cross-sectional studies

The partial attributable risk (PAR) has been introduced as a tool for partitioning the responsibility for causing an adverse event between various risk factors. It has arisen from epidemiology, but it is also a valid general risk allocation concept, which can, for example, be applied to data from customer satisfaction surveys. So far, a variance formula for the PAR has been missing so that the confidence intervals were not directly available. This paper provides the asymptotic normal distribution for the PAR determined from a cross-sectional study.     

Non-linear models 1

This is the first application of a new method for testing stationary random point processes. Consider the class of all stationary ergodic point processes on the real line with arbitrary dependences among the inter–point distances (spacing).The hypothesis is :The observed process φ is a homogeneous Poisson process or more (resp.less) regular than a Poisson process.The sample is the vector of the first n points t₁, …,t_n.There is a close relation between our method for testing and queueing theory: For finding an appropriate test statistic, we observe the behaviour of a single server queue with the input φ.A table of critical values is given.     

Adaptive Test for Periodicity in Self-Exciting Threshold Autoregressive Models

This article is devoted to the study of the periodicity testing problem in a self-exciting threshold autoregressive (SETAR) model. The local asymptotic normality (LAN) property is shown via the adapted sufficient conditions due to Swensen (1985 Swensen , A. R. ( 1985 ). The asymptotic distribution of the likelihood ratio for autoregressive time series with a regression trend . Journal of Multivariate Analysis 16 : 54 – 70 .[Crossref], [Web of Science ®] , [Google Scholar]). Moreover, the LAN of the central sequence is established. First, we consider the case where the innovation density is specified and we obtain a parametric local asymptotic test. Second, we construct an adaptive test in the case where this density is unspecified but symmetric. The performances of these established tests are shown via simulation studies.     

Transformed Logit Confidence Intervals for Small Populations in Single Capture–Recapture Estimation

The good performance of logit confidence intervals for the odds ratio with small samples is well known. This is true unless the actual odds ratio is very large. In single capture–recapture estimation the odds ratio is equal to 1 because of the assumption of independence of the samples. Consequently, a transformation of the logit confidence intervals for the odds ratio is proposed in order to estimate the size of a closed population under single capture–recapture estimation. It is found that the transformed logit interval, after adding .5 to each observed count before computation, has actual coverage probabilities near to the nominal level even for small populations and even for capture probabilities near to 0 or 1, which is not guaranteed for the other capture–recapture confidence intervals proposed in statistical literature. Thus, given that the .5 transformed logit interval is very simple to compute and has a good performance, it is appropriate to be implemented by most users of the single capture–recapture method.     

Composite Marginal Likelihoods to the Normal Bradley-Terry Model

Inference in generalized linear mixed models with crossed random effects is often made cumbersome by the high-dimensional intractable integrals involved in the marginal likelihood. This article presents two inferential approaches based on the marginal composite likelihood for the normal Bradley-Terry model. The two approaches are illustrated by a simulation study to evaluate their performance. Thereafter, the asymptotic variances of the estimated variance component are compared.     

EGARCH Model with Weighted Liquidity

We analyze a variant of the EGARCH model which captures the variation of the intra-day price. We study the asymptotic behavior of the estimators for the parameters of the model. We also illustrate our theoretical results by empirical studies.