Random-effect models with singular precision

We show that smoothing spline, intrinsic autoregression (IAR) and state-space model can be formulated as partially specified random-effect model with singular precision (SP). Various fitting methods have been suggested for the aforementioned models and this paper investigates the relationships among them, once the models have been placed under a single framework. Some methods have been previously shown to give the best linear unbiased predictors (BLUPs) under some random-effect models and here we show that they are in fact uniformly BLUPs (UBLUPs) under a class of models that are generated by the SP of random effects. We offer some new interpretations of the UBLUPs under models of SP and define BLUE and BLUP in these partially specified models without having to specify the covariance. We also show how the full likelihood inferences for random-effect models can be made for these models, so that the maximum likelihood (ML) and restricted maximum likelihood (REML) estimators can be used for the smoothing parameters in splines, etc.     

Lower posterior death probabilities from a quick medical response in road traffic accidents

Introduction: We use data from Spain on roads and motorways traffic accidents in May 2004 to quantify the statistical association between quick medical response time and mortality rate. Method: Probit and logit parameters are estimated by a Bayesian method in which samples from the posterior densities are obtained through an MCMC simulation scheme. We provide posterior credible intervals and posterior partial effects of a quick medical response at several time levels over which we express our prior beliefs. Results: A reduction of 5 min, from a 25-min response-time level, is associated with lower posterior probabilities of death in roads and motorways accidents of 24% and 30%, respectively.     

Parameter estimation of nonlinear mixed-effects models using first-order conditional linearization and the EM algorithm

Nonlinear mixed-effects (NLME) models are flexible enough to handle repeated-measures data from various disciplines. In this article, we propose both maximum-likelihood and restricted maximum-likelihood estimations of NLME models using first-order conditional expansion (FOCE) and the expectation–maximization (EM) algorithm. The FOCE-EM algorithm implemented in the ForStat procedure SNLME is compared with the Lindstrom and Bates (LB) algorithm implemented in both the SAS macro NLINMIX and the S-Plus/R function nlme in terms of computational efficiency and statistical properties. Two realworld data sets an orange tree data set and a Chinese fir (Cunninghamia lanceolata) data set, and a simulated data set were used for evaluation. FOCE-EM converged for all mixed models derived from the base model in the two realworld cases, while LB did not, especially for the models in which random effects are simultaneously considered in several parameters to account for between-subject variation. However, both algorithms had identical estimated parameters and fit statistics for the converged models. We therefore recommend using FOCE-EM in NLME models, particularly when convergence is a concern in model selection.     

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.     

A longitudinal analysis of infant and senescent mortality using mixture models

We construct a mixture distribution including infant, exogenous and Gompertzian/non-Gompertzian senescent mortality. Using mortality data from Swedish females 1751–, we show that this outperforms models without these features, and compare its trends in cohort and period mortality over time. We find an almost complete disappearance of exogenous mortality within the last century of period mortality, with cohort mortality approaching the same limits. Both Gompertzian and non-Gompertzian senescent mortality are consistently present, with the estimated balance between them oscillating constantly. While the parameters of the latter appear to be trending over time, the parameters of the former do not.     

A likelihood ratio test for goodness‐of‐fit of recessive and dominant models for case–control studies

Testing goodness‐of‐fit of commonly used genetic models is of critical importance in many applications including association studies and testing for departure from Hardy–Weinberg equilibrium. Case–control design has become widely used in population genetics and genetic epidemiology, thus it is of interest to develop powerful goodness‐of‐fit tests for genetic models using case–control data. This paper develops a likelihood ratio test (LRT) for testing recessive and dominant models for case–control studies. The LRT statistic has a closed‐form formula with a simple $\chi^{2}(1)$ null asymptotic distribution, thus its implementation is easy even for genome‐wide association studies. Moreover, it has the same power and optimality as when the disease prevalence is known in the population. The Canadian Journal of Statistics 41: 341–352; 2013 © 2013 Statistical Society of Canada     

Maximum Likelihood Estimation for Stochastic Differential Equations with Random Effects

Abstract. We consider N independent stochastic processes (X _i (t), t ∈ [0,T _i ]), i=1,…, N, defined by a stochastic differential equation with drift term depending on a random variable φ _i . The distribution of the random effect φ _i depends on unknown parameters which are to be estimated from the continuous observation of the processes X_i. We give the expression of the exact likelihood. When the drift term depends linearly on the random effect φ _i and φ _i has Gaussian distribution, an explicit formula for the likelihood is obtained. We prove that the maximum likelihood estimator is consistent and asymptotically Gaussian, when T _i =T for all i and N tends to infinity. We discuss the case of discrete observations. Estimators are computed on simulated data for several models and show good performances even when the length time interval of observations is not very large.     

1973 Section Officers,Committees and Association Representatives

The occurrence of missing data cells precludes a universally correct procedure for performing an analysis of variance. This is illustrated by the use of two computer routines to analyze a 2 × 3 factorial experiment with one missing cell. One of these routines does, however, provide information that may enhance the usefulness of the associated results.     

中国粮食价格波动特征研究——基于X-12-ARIMA模型和ARCH类模型

以小麦和大豆为例,研究2002年1月至2012年6月中国粮食价格波动特征。首先利用X-12-ARIMA模型对价格序列进行季节调整,然后运用ARCH类模型对剥离季节因素的价格序列进行波动分析。结果发现:中国粮食价格季节性波动逐年减弱;粮食价格具有明显的波动集簇性,前期价格波动和外部冲击对后期价格的影响具有持续性;粮食市场不存在"高风险、高回报"特征;小麦价格波动的非对称性不显著,而大豆价格波动则呈现明显的非对称特征,且上期价格上涨信息引发的波动要大于下跌信息。