Minimal auxiliary Markov chains through sequential elimination of states

When using an auxiliary Markov chain to compute the distribution of a pattern statistic, the computational complexity is directly related to the number of Markov chain states. Theory related to minimal deterministic finite automata have been applied to large state spaces to reduce the number of Markov chain states so that only a minimal set remains. In this paper, a characterization of equivalent states is given so that extraneous states are deleted during the process of forming the state space, improving computational efficiency. The theory extends the applicability of Markov chain based methods for computing the distribution of pattern statistics.     

A simulation approach to convergence rates for Markov chain Monte Carlo algorithms

Markov chain Monte Carlo (MCMC) methods, including the Gibbs sampler and the Metropolis–Hastings algorithm, are very commonly used in Bayesian statistics for sampling from complicated, high-dimensional posterior distributions. A continuing source of uncertainty is how long such a sampler must be run in order to converge approximately to its target stationary distribution. A method has previously been developed to compute rigorous theoretical upper bounds on the number of iterations required to achieve a specified degree of convergence in total variation distance by verifying drift and minorization conditions. We propose the use of auxiliary simulations to estimate the numerical values needed in this theorem. Our simulation method makes it possible to compute quantitative convergence bounds for models for which the requisite analytical computations would be prohibitively difficult or impossible. On the other hand, although our method appears to perform well in our example problems, it cannot provide the guarantees offered by analytical proof.     

Approximations for Multiple Scan Statistics on the Circle

Multiple scan statistic is usually used by epidemiologist to test the uniformity or clustering of data. In this article, we extend the work of Lin (1999) to give a general expression for the moments of multiple scan statistic on a circle, and use these moments to approximate its distribution using Markov chain and compound Poisson approximations proposed by Huffer and Lin (1997a) and Lin (1993). Numerical results are presented to evaluate the performance of these approximations.     

Bayesian scanning of spatial disease rates with integrated nested Laplace approximation (INLA)

Among the many tools suited to detect local clusters in group-level data, Kulldorff–Nagarwalla’s spatial scan statistic gained wide popularity (Kulldorff and Nagarwalla in Stat Med 14(8):799–810, 1995). The underlying assumptions needed for making statistical inference feasible are quite strong, as counts in spatial units are assumed to be independent Poisson distributed random variables. Unfortunately, outcomes in spatial units are often not independent of each other, and risk estimates of areas that are close to each other will tend to be positively correlated as they share a number of spatially varying characteristics. We therefore introduce a Bayesian model-based algorithm for cluster detection in the presence of spatially autocorrelated relative risks. Our approach has been made possible by the recent development of new numerical methods based on integrated nested Laplace approximation, by which we can directly compute very accurate approximations of posterior marginals within short computational time (Rue et al. in JRSS B 71(2):319–392, 2009). Simulated data and a case study show that the performance of our method is at least comparable to that of Kulldorff–Nagarwalla’s statistic.     

Generalized order statistic processes and Pfeifer records

We introduce a uniform generalized order statistic process. It is a simple Markov process whose initial segment can be identified with a set of uniform generalized order statistics. A standard marginal transformation leads to a generalized order statistic process related to non-uniform generalized order statistics. It is then demonstrated that the nth variable in such a process has the same distribution as an nth Pfeifer record value. This process representation of Pfeifer records facilitates discussion of the possible limit laws for Pfeifer records and, in some cases, of sums thereof. Because of the close relationship between Pfeifer records and generalized order statistics, the results shed some light on the problem of determining the nature of the possible limiting distributions of the largest generalized order statistic.     

Multiple Window Discrete Scan Statistics

In this article, multiple scan statistics of variable window sizes are derived for independent and identically distributed 0-1 Bernoulli trials. Both one and two dimensional, as well as, conditional and unconditional cases are treated. The advantage in using multiple scan statistics, as opposed to single fixed window scan statistics, is that they are more sensitive in detecting a change in the underlying distribution of the observed data. We show how to derive simple approximations for the significance level of these testing procedures and present numerical results to evaluate their performance.     

Minimal Markov Basis for Tests of Main Effect Models for 2p-1 Fractional Factorial Designs of Resolution p

We consider conditional exact tests of factor effects in design of experiments for discrete response variables. Similarly to the analysis of contingency tables, Markov chain Monte Carlo methods can be used to perform exact tests, especially when large-sample approximations of the null distributions are poor and the enumeration of the conditional sample space is infeasible. In order to construct a connected Markov chain over the appropriate sample space, one approach is to compute a Markov basis. Theoretically, a Markov basis can be characterized as a generator of a well-specified toric ideal in a polynomial ring and is computed by computational algebraic software. However, the computation of a Markov basis sometimes becomes infeasible, even for problems of moderate sizes. In the present article, we obtain the closed-form expression of minimal Markov bases for the main effect models of 2^{p ? 1} fractional factorial designs of resolution p.     

Hypothesis Testing in Functional Comparative Calibration Models

The purpose of this article is to investigate hypothesis testing in functional comparative calibration models. Wald type statistics are considered which are asymptotically distributed according to the chi-square distribution. The statistics are based on maximum likelihood, corrected score approach, and method of moment estimators of the model parameters, which are shown to be consistent and asymptotically normally distributed. Results of analytical and simulation studies seem to indicate that the Wald statistics based on the method of moment estimators and the corrected score estimators are, as expected, less efficient than the Wald type statistic based on the maximum likelihood estimators for small n. Wald statistic based on moment estimators are simpler to compute than the other Wald statistics tests and their performance improves significantly as n increases. Comparisons with an alternative F statistics proposed in the literature are also reported.     

A continuous-time HMM approach to modeling the magnitude-frequency distribution of earthquakes

The magnitude-frequency distribution (MFD) of earthquake is a fundamental statistic in seismology. The so-called b-value in the MFD is of particular interest in geophysics. A continuous time hidden Markov model (HMM) is proposed for characterizing the variability of b-values. The HMM-based approach to modeling the MFD has some appealing properties over the widely used sliding-window approach. Often, large variability appears in the estimation of b-value due to window size tuning, which may cause difficulties in interpretation of b-value heterogeneities. Continuous-time hidden Markov models (CT-HMMs) are widely applied in various fields. It bears some advantages over its discrete time counterpart in that it can characterize heterogeneities appearing in time series in a finer time scale, particularly for highly irregularly-spaced time series, such as earthquake occurrences. We demonstrate an expectation–maximization algorithm for the estimation of general exponential family CT-HMM. In parallel with discrete-time hidden Markov models, we develop a continuous time version of Viterbi algorithm to retrieve the overall optimal path of the latent Markov chain. The methods are applied to New Zealand deep earthquakes. Before the analysis, we first assess the completeness of catalogue events to assure the analysis is not biased by missing data. The estimation of b-value is stable over the selection of magnitude thresholds, which is ideal for the interpretation of b-value variability.     

Space‐time cluster identification in point processes

The authors propose a new type of scan statistic to test for the presence of space‐time clusters in point processes data, when the goal is to identify and evaluate the statistical significance of localized clusters. Their method is based only on point patterns for cases; it does not require any specific knowledge of the underlying population. The authors propose to scan the three‐dimensional space with a score test statistic under the null hypothesis that the underlying point process is an inhomogeneous Poisson point process with space and time separable intensity. The alternative is that there are one or more localized space‐time clusters. Their method has been implemented in a computationally efficient way so that it can be applied routinely. They illustrate their method with space‐time crime data from Belo Horizonte, a Brazilian city, in addition to presenting a Monte Carlo study to analyze the power of their new test.     

Comparison of Two Methods for Calculating the Partition Functions of Various Spatial Statistical Models

Likelihood computation in spatial statistics requires accurate and efficient calculation of the normalizing constant (i.e. partition function) of the Gibbs distribution of the model. Two available methods to calculate the normalizing constant by Markov chain Monte Carlo methods are compared by simulation experiments for an Ising model, a Gaussian Markov field model and a pairwise interaction point field model.     

A spatial scan statistic for survival data based on generalized life distribution

ABSTRACT

For many years, detection of clusters has been of great public health interest and widely studied. Several methods have been developed to detect clusters and their performance has been evaluated in various contexts. Spatial scan statistics are widely used for geographical cluster detection and inference. Different types of discrete or continuous data can be analyzed using spatial scan statistics for Bernoulli, Poisson, ordinal, exponential, and normal models. In this paper, we propose a scan statistic for survival data which is based on generalized life distribution model that provides three important life distributions, viz. Weibull, exponential, and Rayleigh. The proposed method is applied to the survival data of tuberculosis patients in Nainital district of Uttarakhand, India, for the year 2004–05. The Monte Carlo simulation studies reveal that the proposed method performs well for different survival distributions.     

Exact distributions of two non-central generalized Wilks's statistics

We derive the exact expressions of the probability density function (pdf) and the cumulative distribution function (cdf) of Wilks's likelihood ratio criterion Λ and Wilks-Lawley's statistic U in the non-central linear and the non-central planar cases. Those expressions are given in rapidly converging infinite series and can be used for numerical computation. For applications, we compute the exact power of these statistics in a multivariate analysis of variance exercise, and show by simulation the precision of our analytic formulae.     

An Efficient Method to Generate Data and Compute Exact P-Values in Goodness-of-Fit Testing

In this article, we use a characterization of the set of sample counts that do not match with the null hypothesis of the test of goodness of fit. Two direct applications arise: first, to instantaneously generate data sets whose corresponding asymptotic P-values belong to a certain pre-defined range; and second, to compute exact P-values for this test in an efficient way. We present both issues before illustrating them by analyzing a couple of data sets. Method's efficiency is also assessed by means of simulations. We focus on Pearson's X ² statistic but the case of likelihood-ratio statistic is also discussed.     

REVERSIBLE JUMP MARKOV CHAIN MONTE CARLO METHODS AND SEGMENTATION ALGORITHMS IN HIDDEN MARKOV MODELS

We consider hidden Markov models with an unknown number of regimes for the segmentation of the pixel intensities of digital images that consist of a small set of colours. New reversible jump Markov chain Monte Carlo algorithms to estimate both the dimension and the unknown parameters of the model are introduced. Parameters are updated by random walk Metropolis–Hastings moves, without updating the sequence of the hidden Markov chain. The segmentation (i.e. the estimation of the hidden regimes) is a further aim and is performed by means of a number of competing algorithms. We apply our Bayesian inference and segmentation tools to digital images, which are linearized through the Peano–Hilbert scan, and perform experiments and comparisons on both synthetic images and a real brain magnetic resonance image.     

Bayesian inversion of geoelectrical resistivity data

Summary. Enormous quantities of geoelectrical data are produced daily and often used for large scale reservoir modelling. To interpret these data requires reliable and efficient inversion methods which adequately incorporate prior information and use realistically complex modelling structures. We use models based on random coloured polygonal graphs as a powerful and flexible modelling framework for the layered composition of the Earth and we contrast our approach with earlier methods based on smooth Gaussian fields. We demonstrate how the reconstruction algorithm may be efficiently implemented through the use of multigrid Metropolis–coupled Markov chain Monte Carlo methods and illustrate the method on a set of field data.     

Detecting clusters with increased mean using scan windows with variable radius

Applying spatiotemporal scan statistics is an effective method to detect the clustering of mean shifts in many application fields. Although several exponentially weighted moving average (EWMA) based scan statistics have been proposed, the existing methods generally require a fixed scan window size or apply the weighting technique across the temporal axis only. However, the size of shift coverage is often unavailable in practical problems. Using a mismatching scan radius may mislead the size of cluster coverage in space or delay the time to detection. This research proposed an stEWMA method by applying the weighting technique across both temporal and spatial axes with variable scan radius. The simulation analysis showed that the stEWMA method can have a significantly shorter time to detection than the likelihood ratio-based scan statistic using variable scan radius, especially when cluster coverage size is small. The application to detecting the increase of male thyroid cancer in the New Mexico state also showed the effectiveness of the proposed method.     

Gap-ratio goodness of fit tests for weibull or extreme value distribution assumptions with left or right censored data

With data collection in environmental science and bioassay, left censoring because of nondetects is a problem. Similarly in reliability and life data analysis right censoring frequently occurs. There is a need for goodness of fit tests that can adapt to left or right censored data and be used to check important distributional assumptions without becoming too difficult to regularly implement in practice. A new test statistic is derived from a plot of the standardized spacings between the order statistics versus their ranks. Any linear or curvilinear pattern is evidence against the null distribution. When testing the Weibull or extreme value null hypothesis this statistic has a null distribution that is approximately F for most combinations of sample size and censoring of practical interest. Our statistic is compared to the Mann-Scheuer-Fertig statistic which also uses the standardized spacings between the order statistics. The results of a simulation study show the two tests are competitive in terms of power. Although the Mann-Scheuer-Fertig statistic is somewhat easier to compute, our test enjoys advantages in the accuracy of the F approximation and the availability of a graphical diagnostic.     

Parameter estimation and prediction of order statistics for the Burr Type XII distribution with Type II censoring

This article deals with the statistical inference and prediction on Burr Type XII parameters based on Type II censored sample. It is observed that the maximum likelihood estimators (MLEs) cannot be obtained in closed form. We use the expectation-maximization algorithm to compute the MLEs. We also obtain the Bayes estimators under symmetric and asymmetric loss functions such as squared error and Linex By applying Lindley's approximation and Markov chain Monte Carlo (MCMC) technique. Further, MCMC samples are used to calculate the highest posterior density credible intervals. Monte Carlo simulation study and two real-life data-sets are presented to illustrate all of the methods developed here. Furthermore, we obtain a prediction of future order statistics based on the observed ordered because of its important application in different fields such as medical and engineering sciences. A numerical example carried out to illustrate the procedures obtained for prediction of future order statistics.     

Estimation with right‐censored observations under a semi‐Markov model

The semi‐Markov process often provides a better framework than the classical Markov process for the analysis of events with multiple states. The purpose of this paper is twofold. First, we show that in the presence of right censoring, when the right end‐point of the support of the censoring time is strictly less than the right end‐point of the support of the semi‐Markov kernel, the transition probability of the semi‐Markov process is nonidentifiable, and the estimators proposed in the literature are inconsistent in general. We derive the set of all attainable values for the transition probability based on the censored data, and we propose a nonparametric inference procedure for the transition probability using this set. Second, the conventional approach to constructing confidence bands is not applicable for the semi‐Markov kernel and the sojourn time distribution. We propose new perturbation resampling methods to construct these confidence bands. Different weights and transformations are explored in the construction. We use simulation to examine our proposals and illustrate them with hospitalization data from a recent cancer survivor study. The Canadian Journal of Statistics 41: 237–256; 2013 © 2013 Statistical Society of Canada