Estimation and tests for a longitudinal regression model based on the Markov chain

In this paper, the dependence of transition probabilities on covariates and a test procedure for covariate dependent Markov models are examined. The nonparametric test for the role of waiting time proposed by Jones and Crowley [M. Jones, J. Crowley, Nonparametric tests of the Markov model for survival data Biometrika 79 (3) (1992) 513–522] has been extended here to transitions and reverse transitions. The limitation of the Jones and Crowley method is that it does not take account of other covariates that might have association with the probabilities of transition. A simple test procedure is proposed that can be employed for testing: (i) the significance of association between covariates and transition probabilities, and (ii) the impact of waiting time on the transition probabilities. The procedure is illustrated using panel data on hospitalization of the elderly population in the USA from the Health and Retirement Survey (HRS).     

Testing lumpability for marginal discrete hidden Markov models

When some states of a Markov chain are aggregated (or lumped) and the new process, with lumped states, inherits the Markov property, the original chain is said to be lumpable. We discuss the notion of lumpability for discrete hidden Markov models (DHMMs) and we explain why, in general, testing this hypothesis leads to non-standard problems. Nevertheless, we present a case where lumpability in DHMMs is a regular problem of comparing nested models. Finally, some simulation results assessing the performance of the proposed test and an application to two real data sets are given.     

Goodness-of-fit testing for the marginal distribution of regime-switching models with an application to electricity spot prices

This paper complements a recently published study (Janczura and Weron in AStA-Adv Stat Anal 96(3):385–407, 2012) on efficient estimation of Markov regime-switching models. Here, we propose a new goodness-of-fit testing scheme for the marginal distribution of such models. We consider models with an observable (like threshold autoregressions) as well as a latent state process (like Markov regime-switching). The test is based on the Kolmogorov–Smirnov supremum-distance statistic and the concept of the weighted empirical distribution function. The motivation for this research comes from a recent stream of literature in energy economics concerning electricity spot price models. While the existence of distinct regimes in such data is generally unquestionable (due to the supply stack structure), the actual goodness-of-fit of the models requires statistical validation. We illustrate the proposed scheme by testing whether commonly used Markov regime-switching models fit deseasonalized electricity prices from the NEPOOL (US) day-ahead market.     

Exact Goodness‐of‐Fit Testing for the Ising Model

The Ising model is one of the simplest and most famous models of interacting systems. It was originally proposed to model ferromagnetic interactions in statistical physics and is now widely used to model spatial processes in many areas such as ecology, sociology, and genetics, usually without testing its goodness of fit. Here, we propose various test statistics and an exact goodness‐of‐fit test for the finite‐lattice Ising model. The theory of Markov bases has been developed in algebraic statistics for exact goodness‐of‐fit testing using a Monte Carlo approach. However, finding a Markov basis is often computationally intractable. Thus, we develop a Monte Carlo method for exact goodness‐of‐fit testing for the Ising model that avoids computing a Markov basis and also leads to a better connectivity of the Markov chain and hence to a faster convergence. We show how this method can be applied to analyze the spatial organization of receptors on the cell membrane.     

Bayesian analysis of panel data using an MTAR model

Bayesian analysis of panel data using a class of momentum threshold autoregressive (MTAR) models is considered. Posterior estimation of parameters of the MTAR models is done by using a simple Markov Chain Monte Carlo (MCMC) algorithm. Selection of appropriate differenced variables, test for asymmetry and unit roots are recast as model selections and a simple way of computing posterior probabilities of the candidate models is proposed. The proposed method is applied to the yearly unemployment rates of 51 US states and the results show strong evidence of stationarity and asymmetry.     

Fitting DNA sequences through log-linear modelling with linear constraints

For some discrete state series, such as DNA sequences, it can often be postulated that its probabilistic behaviour is given by a Markov chain. For making the decision on whether or not an uncharacterized piece of DNA is part of the coding region of a gene, under the Markovian assumption, there are two statistical tools that are essential to be considered: the hypothesis testing of the order in a Markov chain and the estimators of transition probabilities. In order to improve the traditional statistical procedures for both of them when stationarity assumption can be considered, a new version for understanding the homogeneity hypothesis is proposed so that log-linear modelling is applied for conditional independence jointly with homogeneity restrictions on the expected means of transition counts in the sequence. In addition we can consider a variety of test-statistics and estimators by using φ-divergence measures. As special case of them the well-known likelihood ratio test-statistics and maximum-likelihood estimators are obtained.     

Non-mixture cure correlated frailty models in Bayesian approach

In this article, we develop a Bayesian approach for the estimation of two cure correlated frailty models that have been extended to the cure frailty models introduced by Yin [34]. We used the two different type of frailty with bivariate log-normal distribution instead of gamma distribution. A likelihood function was constructed based on a piecewise exponential distribution function. The model parameters were estimated by the Markov chain Monte Carlo method. The comparison of models is based on the Cox correlated frailty model with log-normal distribution. A real data set of bilateral corneal graft rejection was used to compare these models. The results of this data, based on deviance information criteria, showed the advantage of the proposed models.     

Economic and economic statistical designs for three-level control charts

In some situations, an appropriate quality measure uses three or more discrete levels to classify a product characteristic. For these situations, some control charts have been developed based on statistical criteria regardless of economic considerations. In this paper, we develop economic and economic statistical designs (ESD) for 3-level control charts. We apply the cost model proposed by Costa and Rahim.[Economic design of X charts with variable parameters: the Markov chain approach, J Appl Stat 28 (2001), 875–885] Furthermore, we assume that the length of time that the process remains in control is exponentially distributed which allows us to apply the Markov chain approach for developing the cost model. We apply a genetic algorithm to determine the optimal values of model parameters by minimizing the cost function. A numerical example is provided to illustrate the performance of the proposed models and to compare the cost of the pure economic and ESD for three-level control charts. A sensitivity analysis is also conducted in this numerical example.     

Unit roots and double smooth transitions

Techniques for testing the null hypothesis of difference stationarity against stationarity around some deterministic function have received much attention. In particular, unit root tests where the alternative is stationarity around a smooth transition in a linear trend have recently been proposed to permit the possibility of non-instantaneous structural change. In this paper we develop tests extending such an approach in order to admit more than one structural change. The analysis is motivated by time series that appear to undergo two smooth transitions in the linear trend, and the application of the new tests to two such series (average global temperature and US consumer prices) highlights the benefits of this double transition extension.     

Testing a markov chain for independence

A bootstrap procedure is proposed for testing whether an observed Markov chain is actually an independent process, based on the observed transition probability matrix. The results of simulations showing the power and size of the bootstrap test are presented. The asymptotic distribution of the non-unit eigenvalues is given under the null hypothesis.     

Modeling statistical dependence of Markov chains via copula models

Conditional probability distributions have been commonly used in modeling Markov chains. In this paper we consider an alternative approach based on copulas to investigate Markov-type dependence structures. Based on the realization of a single Markov chain, we estimate the parameters using one- and two-stage estimation procedures. We derive asymptotic properties of the marginal and copula parameter estimators and compare performance of the estimation procedures based on Monte Carlo simulations. At low and moderate dependence structures the two-stage estimation has comparable performance as the maximum likelihood estimation. In addition we propose a parametric pseudo-likelihood ratio test for copula model selection under the two-stage procedure. We apply the proposed methods to an environmental data set.     

Likelihood Ratio Testing for Hidden Markov Models Under Non-standard Conditions

Abstract.  In practical applications, when testing parametric restrictions for hidden Markov models (HMMs), one frequently encounters non-standard situations such as testing for zero entries in the transition matrix, one-sided tests for the parameters of the transition matrix or for the components of the stationary distribution of the underlying Markov chain, or testing boundary restrictions on the parameters of the state-dependent distributions. In this paper, we briefly discuss how the relevant asymptotic distribution theory for the likelihood ratio test (LRT) when the true parameter is on the boundary extends from the independent and identically distributed situation to HMMs. Then we concentrate on discussing a number of relevant examples. The finite-sample performance of the LRT in such situations is investigated in a simulation study. An application to series of epileptic seizure counts concludes the paper.     

Markov chain Monte Carlo estimation of a mixture item response theory model

Markov chain Monte Carlo (MCMC) algorithms have been shown to be useful for estimation of complex item response theory (IRT) models. Although an MCMC algorithm can be very useful, it also requires care in use and interpretation of results. In particular, MCMC algorithms generally make extensive use of priors on model parameters. In this paper, MCMC estimation is illustrated using a simple mixture IRT model, a mixture Rasch model (MRM), to demonstrate how the algorithm operates and how results may be affected by some commonly used priors. Priors on the probabilities of mixtures, label switching, model selection, metric anchoring, and implementation of the MCMC algorithm using WinBUGS are described, and their effects illustrated on parameter recovery in practical testing situations. In addition, an example is presented in which an MRM is fitted to a set of educational test data using the MCMC algorithm and a comparison is illustrated with results from three existing maximum likelihood estimation methods.     

F-tests for seasonal differencing with a break-point

The classification between stochastic trend stationarity and deterministic broken trend stationarity is important because incorrect inferences can follow if a stationary series with a broken trend is incorrectly classified as integrated. In this paper, we consider joint tests for regular and seasonal unit roots null hypothesis against broken trend stationarity alternatives where the location of the break is known or unknown. Based on the F-test proposed by Hasza and Fuller (1982, Ann. Statist. 10, 1209–1216), we develop testing procedures for distinguishing these two types of process. The asymptotic distributions of test statistics are derived as functions of Wiener processes. A response surface regression analysis directed to relating the finite sample distributions and the breaking position is studied. Simulation experiments suggest that the power of the test is reasonable. The testing procedure is illustrated by the Canadian consumer price index series.     

Trace Class Markov Chains for Bayesian Inference with Generalized Double Pareto Shrinkage Priors

Bayesian shrinkage methods have generated a lot of interest in recent years, especially in the context of high‐dimensional linear regression. In recent work, a Bayesian shrinkage approach using generalized double Pareto priors has been proposed. Several useful properties of this approach, including the derivation of a tractable three‐block Gibbs sampler to sample from the resulting posterior density, have been established. We show that the Markov operator corresponding to this three‐block Gibbs sampler is not Hilbert–Schmidt. We propose a simpler two‐block Gibbs sampler and show that the corresponding Markov operator is trace class (and hence Hilbert–Schmidt). Establishing the trace class property for the proposed two‐block Gibbs sampler has several useful consequences. Firstly, it implies that the corresponding Markov chain is geometrically ergodic, thereby implying the existence of a Markov chain central limit theorem, which in turn enables computation of asymptotic standard errors for Markov chain‐based estimates of posterior quantities. Secondly, because the proposed Gibbs sampler uses two blocks, standard recipes in the literature can be used to construct a sandwich Markov chain (by inserting an appropriate extra step) to gain further efficiency and to achieve faster convergence. The trace class property for the two‐block sampler implies that the corresponding sandwich Markov chain is also trace class and thereby geometrically ergodic. Finally, it also guarantees that all eigenvalues of the sandwich chain are dominated by the corresponding eigenvalues of the Gibbs sampling chain (with at least one strict domination). Our results demonstrate that a minor change in the structure of a Markov chain can lead to fundamental changes in its theoretical properties. We illustrate the improvement in efficiency resulting from our proposed Markov chains using simulated and real examples.     

Semiparametric score test for varying copula parameter in Markov time series

This article examines a semiparametric test for checking the constancy of serial dependence via copula models for Markov time series. A semiparametric score test is proposed for testing the constancy of the copula parameter against stochastically varying copula parameter. The asymptotic null distribution of the test is established. A semiparametric bootstrap procedure is employed for the estimation of the variance of the proposed score test. Illustrations are given based on simulated series and historic interest rate data.     

A bayesian method in determining the order of a finite state markov chain

In this paper, we use the Bayesian method in the application of hypothesis testing and model selection to determine the order of a Markov chain. The criteria used are based on Bayes factors with noninformative priors. Com¬parisons with the commonly used AIC and BIC criteria are made through an example and computer simulations. The results show that the proposed method is better than the AIC and BIC criteria, especially for Markov chains with higher orders and larger state spaces.     

Reversible jump, birth-and-death and more general continuous time Markov chain Monte Carlo samplers

Summary. Reversible jump methods are the most commonly used Markov chain Monte Carlo tool for exploring variable dimension statistical models. Recently, however, an alternative approach based on birth-and-death processes has been proposed by Stephens for mixtures of distributions. We show that the birth-and-death setting can be generalized to include other types of continuous time jumps like split-and-combine moves in the spirit of Richardson and Green. We illustrate these extensions both for mixtures of distributions and for hidden Markov models. We demonstrate the strong similarity of reversible jump and continuous time methodologies by showing that, on appropriate rescaling of time, the reversible jump chain converges to a limiting continuous time birth-and-death process. A numerical comparison in the setting of mixtures of distributions highlights this similarity.     

Reversible jump and the label switching problem in hidden Markov models

Reversible jump Markov chain Monte Carlo (RJMCMC) algorithms can be efficiently applied in Bayesian inference for hidden Markov models (HMMs), when the number of latent regimes is unknown. As for finite mixture models, when priors are invariant to the relabelling of the regimes, HMMs are unidentifiable in data fitting, because multiple ways to label the regimes can alternate during the MCMC iterations; this is the so-called label switching problem. HMMs with an unknown number of regimes are considered here and the goal of this paper is the comparison, both applied and theoretical, of five methods used for tackling label switching within a RJMCMC algorithm; they are: post-processing, partial reordering, permutation sampling, sampling from a Markov prior and rejection sampling. The five strategies we compare have been proposed mostly in the literature of finite mixture models and only two of them, i.e. rejection sampling and partial reordering, have been presented in RJMCMC algorithms for HMMs. We consider RJMCMC algorithms in which the parameters are updated by Gibbs sampling and the dimension of the model changes in split-and-merge and birth-and-death moves. Finally, an example illustrates and compares the five different methodologies.     

Maximum Likelihood Estimation in Gaussian Chain Graph Models under the Alternative Markov Property

Abstract.  The Andersson–Madigan–Perlman (AMP) Markov property is a recently proposed alternative Markov property (AMP) for chain graphs. In the case of continuous variables with a joint multivariate Gaussian distribution, it is the AMP rather than the earlier introduced Lauritzen–Wermuth–Frydenberg Markov property that is coherent with data-generation by natural block-recursive regressions. In this paper, we show that maximum likelihood estimates in Gaussian AMP chain graph models can be obtained by combining generalized least squares and iterative proportional fitting to an iterative algorithm. In an appendix, we give useful convergence results for iterative partial maximization algorithms that apply in particular to the described algorithm.