Estimating the variance for heterogeneity in arm‐based network meta‐analysis

Network meta‐analysis can be implemented by using arm‐based or contrast‐based models. Here we focus on arm‐based models and fit them using generalized linear mixed model procedures. Full maximum likelihood (ML) estimation leads to biased trial‐by‐treatment interaction variance estimates for heterogeneity. Thus, our objective is to investigate alternative approaches to variance estimation that reduce bias compared with full ML. Specifically, we use penalized quasi‐likelihood/pseudo‐likelihood and hierarchical (h) likelihood approaches. In addition, we consider a novel model modification that yields estimators akin to the residual maximum likelihood estimator for linear mixed models. The proposed methods are compared by simulation, and 2 real datasets are used for illustration. Simulations show that penalized quasi‐likelihood/pseudo‐likelihood and h‐likelihood reduce bias and yield satisfactory coverage rates. Sum‐to‐zero restriction and baseline contrasts for random trial‐by‐treatment interaction effects, as well as a residual ML‐like adjustment, also reduce bias compared with an unconstrained model when ML is used, but coverage rates are not quite as good. Penalized quasi‐likelihood/pseudo‐likelihood and h‐likelihood are therefore recommended.     

A Matching Prior for the Shape Parameter of the Skew‐Normal Distribution

Abstract. This paper deals with the issue of performing a default Bayesian analysis on the shape parameter of the skew‐normal distribution. Our approach is based on a suitable pseudo‐likelihood function and a matching prior distribution for this parameter, when location (or regression) and scale parameters are unknown. This approach is important for both theoretical and practical reasons. From a theoretical perspective, it is shown that the proposed matching prior is proper thus inducing a proper posterior distribution for the shape parameter, also when the likelihood is monotone. From the practical perspective, the proposed approach has the advantages of avoiding the elicitation on the nuisance parameters and the computation of multidimensional integrals.     

An MSE‐reduced estimator for the response proportion in a two‐stage clinical trial

Two‐stage design is very useful in clinical trials for evaluating the validity of a specific treatment regimen. When the second stage is allowed to continue, the method used to estimate the response rate based on the results of both stages is critical for the subsequent design. The often‐used sample proportion has an evident upward bias. However, the maximum likelihood estimator or the moment estimator tends to underestimate the response rate. A mean‐square error weighted estimator is considered here; its performance is thoroughly investigated via Simon's optimal and minimax designs and Shuster's design. Compared with the sample proportion, the proposed method has a smaller bias, and compared with the maximum likelihood estimator, the proposed method has a smaller mean‐square error. Copyright © 2010 John Wiley & Sons, Ltd.     

A Cox‐Aalen Model for Interval‐censored Data

The Cox‐Aalen model, obtained by replacing the baseline hazard function in the well‐known Cox model with a covariate‐dependent Aalen model, allows for both fixed and dynamic covariate effects. In this paper, we examine maximum likelihood estimation for a Cox‐Aalen model based on interval‐censored failure times with fixed covariates. The resulting estimator globally converges to the truth slower than the parametric rate, but its finite‐dimensional component is asymptotically efficient. Numerical studies show that estimation via a constrained Newton method performs well in terms of both finite sample properties and processing time for moderate‐to‐large samples with few covariates. We conclude with an application of the proposed methods to assess risk factors for disease progression in psoriatic arthritis.     

A new approach to estimating shelf‐life

The current approach to the estimation of shelf‐life and the determination of the label shelf‐life as detailed in the International Conference on Harmonisation guidelines to industry is presented. The shortcomings of the status quo are explained and a possible solution is offered, which gives rise to a new definition of shelf‐life. Several methods for calculating a label shelf‐life are presented and investigated using a simulation study. Recommendations to adopt the new definition and to increase sample sizes are made. Copyright © 2004 John Wiley & Sons, Ltd.     

Restricted maximum likelihood estimation of joint mean‐covariance models

The class of joint mean‐covariance models uses the modified Cholesky decomposition of the within subject covariance matrix in order to arrive to an unconstrained, statistically meaningful reparameterisation. The new parameterisation of the covariance matrix has two sets of parameters that separately describe the variances and correlations. Thus, with the mean or regression parameters, these models have three sets of distinct parameters. In order to alleviate the problem of inefficient estimation and downward bias in the variance estimates, inherent in the maximum likelihood estimation procedure, the usual REML estimation procedure adjusts for the degrees of freedom lost due to the estimation of the mean parameters. Because of the parameterisation of the joint mean covariance models, it is possible to adapt the usual REML procedure in order to estimate the variance (correlation) parameters by taking into account the degrees of freedom lost by the estimation of both the mean and correlation (variance) parameters. To this end, here we propose adjustments to the estimation procedures based on the modified and adjusted profile likelihoods. The methods are illustrated by an application to a real data set and simulation studies. The Canadian Journal of Statistics 40: 225–242; 2012 © 2012 Statistical Society of Canada     

Empirical likelihood‐based inference for genetic mixture models

The authors show how the genetic effect of a quantitative trait locus can be estimated by a nonparametric empirical likelihood method when the phenotype distributions are completely unspecified. They use an empirical likelihood ratio statistic for testing the genetic effect and obtaining confidence intervals. In addition to studying the asymptotic properties of these procedures, the authors present simulation results and illustrate their approach with a study on breast cancer resistance genes.     

Bayesian Single Changepoint Estimation in a Parameter‐driven Model

In this paper, we consider the problem of estimating a single changepoint in a parameter‐driven model. The model – an extension of the Poisson regression model – accounts for serial correlation through a latent process incorporated in its mean function. Emphasis is placed on the changepoint characterization with changes in the parameters of the model. The model is fully implemented within the Bayesian framework. We develop a RJMCMC algorithm for parameter estimation and model determination. The algorithm embeds well‐devised Metropolis–Hastings procedures for estimating the missing values of the latent process through data augmentation and the changepoint. The methodology is illustrated using data on monthly counts of claimants collecting wage loss benefit for injuries in the workplace and an analysis of presidential uses of force in the USA.     

Model Selection Criterion Based on the Multivariate Quasi‐Likelihood for Generalized Estimating Equations

The generalized estimating equations (GEE) approach has attracted considerable interest for the analysis of correlated response data. This paper considers the model selection criterion based on the multivariate quasi‐likelihood (MQL) in the GEE framework. The GEE approach is closely related to the MQL. We derive a necessary and sufficient condition for the uniqueness of the risk function based on the MQL by using properties of differential geometry. Furthermore, we establish a formal derivation of model selection criterion as an asymptotically unbiased estimator of the prediction risk under this condition, and we explicitly take into account the effect of estimating the correlation matrix used in the GEE procedure.     

A matching prior based on the modified profile likelihood in a generalized Weibull stress‐strength model

Bayesian inference of a generalized Weibull stress‐strength model (SSM) with more than one strength component is considered. For this problem, properly assigning priors for the reliabilities is challenging due to the presence of nuisance parameters. Matching priors, which are priors matching the posterior probabilities of certain regions with their frequentist coverage probabilities, are commonly used but difficult to derive in this problem. Instead, we apply an alternative method and derive a matching prior based on a modification of the profile likelihood. Simulation studies show that this proposed prior performs well in terms of frequentist coverage and estimation even when the sample sizes are minimal. The prior is applied to two real datasets. The Canadian Journal of Statistics 41: 83–97; 2013 © 2012 Statistical Society of Canada     

Learning from a lot: Empirical Bayes for high‐dimensional model‐based prediction

Empirical Bayes is a versatile approach to “learn from a lot” in two ways: first, from a large number of variables and, second, from a potentially large amount of prior information, for example, stored in public repositories. We review applications of a variety of empirical Bayes methods to several well‐known model‐based prediction methods, including penalized regression, linear discriminant analysis, and Bayesian models with sparse or dense priors. We discuss “formal” empirical Bayes methods that maximize the marginal likelihood but also more informal approaches based on other data summaries. We contrast empirical Bayes to cross‐validation and full Bayes and discuss hybrid approaches. To study the relation between the quality of an empirical Bayes estimator and p, the number of variables, we consider a simple empirical Bayes estimator in a linear model setting. We argue that empirical Bayes is particularly useful when the prior contains multiple parameters, which model a priori information on variables termed “co‐data”. In particular, we present two novel examples that allow for co‐data: first, a Bayesian spike‐and‐slab setting that facilitates inclusion of multiple co‐data sources and types and, second, a hybrid empirical Bayes–full Bayes ridge regression approach for estimation of the posterior predictive interval.     

Bias‐reduced marginal Akaike information criteria based on a Monte Carlo method for linear mixed‐effects models

In linear mixed‐effects (LME) models, if a fitted model has more random‐effect terms than the true model, a regularity condition required in the asymptotic theory may not hold. In such cases, the marginal Akaike information criterion (AIC) is positively biased for (?2) times the expected log‐likelihood. The asymptotic bias of the maximum log‐likelihood as an estimator of the expected log‐likelihood is evaluated for LME models with balanced design in the context of parameter‐constrained models. Moreover, bias‐reduced marginal AICs for LME models based on a Monte Carlo method are proposed. The performance of the proposed criteria is compared with existing criteria by using example data and by a simulation study. It was found that the bias of the proposed criteria was smaller than that of the existing marginal AIC when a larger model was fitted and that the probability of choosing a smaller model incorrectly was decreased.     

Empirical likelihood‐based inferences for a low income proportion

Low income proportion is an important index in comparisons of poverty in countries around the world. The stability of a society depends heavily on this index. An accurate and reliable estimation of this index plays an important role for government's economic policies. In this paper, the authors study empirical likelihood‐based inferences for a low income proportion under the simple random sampling and stratified random sampling designs. It is shown that the limiting distributions of the empirical likelihood ratios for the low income proportion are the scaled chi‐square distributions. The authors propose various empirical likelihood‐based confidence intervals for the low income proportion. Extensive simulation studies are conducted to evaluate the relative performance of the normal approximation‐based interval, bootstrap‐based intervals, and the empirical likelihood‐based intervals. The proposed methods are also applied to analyzing a real economic survey income dataset. The Canadian Journal of Statistics 39: 1–16; 2011 ©2011 Statistical Society of Canada     

Simultaneous confidence interval for assessing non‐inferiority with assay sensitivity in a three‐arm trial with binary endpoints

A three‐arm trial including an experimental treatment, an active reference treatment and a placebo is often used to assess the non‐inferiority (NI) with assay sensitivity of an experimental treatment. Various hypothesis‐test‐based approaches via a fraction or pre‐specified margin have been proposed to assess the NI with assay sensitivity in a three‐arm trial. There is little work done on confidence interval in a three‐arm trial. This paper develops a hybrid approach to construct simultaneous confidence interval for assessing NI and assay sensitivity in a three‐arm trial. For comparison, we present normal‐approximation‐based and bootstrap‐resampling‐based simultaneous confidence intervals. Simulation studies evidence that the hybrid approach with the Wilson score statistic performs better than other approaches in terms of empirical coverage probability and mesial‐non‐coverage probability. An example is used to illustrate the proposed approaches.     

Regression analysis for a summed missing data problem under an outcome‐dependent sampling scheme

In this paper, we consider a regression analysis for a missing data problem in which the variables of primary interest are unobserved under a general biased sampling scheme, an outcome‐dependent sampling (ODS) design. We propose a semiparametric empirical likelihood method for accessing the association between a continuous outcome response and unobservable interesting factors. Simulation study results show that ODS design can produce more efficient estimators than the simple random design of the same sample size. We demonstrate the proposed approach with a data set from an environmental study for the genetic effects on human lung function in COPD smokers. The Canadian Journal of Statistics 40: 282–303; 2012 © 2012 Statistical Society of Canada     

Confidence intervals for the mean of a population containing many zero values under unequal‐probability sampling

In many applications, a finite population contains a large proportion of zero values that make the population distribution severely skewed. An unequal‐probability sampling plan compounds the problem, and as a result the normal approximation to the distribution of various estimators has poor precision. The central‐limit‐theorem‐based confidence intervals for the population mean are hence unsatisfactory. Complex designs also make it hard to pin down useful likelihood functions, hence a direct likelihood approach is not an option. In this paper, we propose a pseudo‐likelihood approach. The proposed pseudo‐log‐likelihood function is an unbiased estimator of the log‐likelihood function when the entire population is sampled. Simulations have been carried out. When the inclusion probabilities are related to the unit values, the pseudo‐likelihood intervals are superior to existing methods in terms of the coverage probability, the balance of non‐coverage rates on the lower and upper sides, and the interval length. An application with a data set from the Canadian Labour Force Survey‐2000 also shows that the pseudo‐likelihood method performs more appropriately than other methods. The Canadian Journal of Statistics 38: 582–597; 2010 © 2010 Statistical Society of Canada