Comparison of Bayesian models for production efficiency

In this paper, we use Markov Chain Monte Carlo (MCMC) methods in order to estimate and compare stochastic production frontier models from a Bayesian perspective. We consider a number of competing models in terms of different production functions and the distribution of the asymmetric error term. All MCMC simulations are done using the package JAGS (Just Another Gibbs Sampler), a clone of the classic BUGS package which works closely with the R package where all the statistical computations and graphics are done.     

On a tobit–Birnbaum–Saunders model with an application to medical data

The tobit model allows a censored response variable to be described by covariates. Its applications cover different areas such as economics, engineering, environment and medicine. A strong assumption of the standard tobit model is that its errors follow a normal distribution. However, not all applications are well modeled by this distribution. Some efforts have relaxed the normality assumption by considering more flexible distributions. Nevertheless, the presence of asymmetry could not be well described by these flexible distributions. A real-world data application of measles vaccine in Haiti is explored, which confirms this asymmetry. We propose a tobit model with errors following a Birnbaum–Saunders (BS) distribution, which is asymmetrical and has shown to be a good alternative for describing medical data. Inference based on the maximum likelihood method and a type of residual are derived for the tobit–BS model. We perform global and local influence diagnostics to assess the sensitivity of the maximum likelihood estimators to atypical cases. A Monte Carlo simulation study is carried out to empirically evaluate the performance of these estimators. We conduct a data analysis for the mentioned application of measles vaccine based on the proposed model with the help of the R software. The results show the good performance of the tobit–BS model.     

Hierarchical spatially varying coefficient and temporal dynamic process models using spTDyn

Bayesian hierarchical spatio-temporal models are becoming increasingly important due to the increasing availability of space-time data in various domains. In this paper we develop a user friendly R package, spTDyn, for spatio-temporal modelling. It can be used to fit models with spatially varying and temporally dynamic coefficients. The former is used for modelling the spatially varying impact of explanatory variables on the response caused by spatial misalignment. This issue can arise when the covariates only vary over time, or when they are measured over a grid and hence do not match the locations of the response point-level data. The latter is to examine the temporally varying impact of explanatory variables in space-time data due, for example, to seasonality or other time-varying effects. The spTDyn package uses Markov chain Monte Carlo sampling written in C, which makes computations highly efficient, and the interface is written in R making these sophisticated modelling techniques easily accessible to statistical analysts. The models and software, and their advantages, are illustrated using temperature and ozone space-time data.     

A fast algorithm for the coordinate-wise minimum distance estimation

Application of the minimum distance (MD) estimation method to the linear regression model for estimating regression parameters is a difficult and time-consuming process due to the complexity of its distance function, and hence, it is computationally expensive. To deal with the computational cost, this paper proposes a fast algorithm which makes the best use of coordinate-wise minimization technique in order to obtain the MD estimator. R package (KoulMde) based on the proposed algorithm and written in Rcpp is available online.     

Gaussian Markov random field spatial models in GAMLSS

This paper describes the modelling and fitting of Gaussian Markov random field spatial components within a Generalized AdditiveModel for Location, Scale and Shape (GAMLSS) model. This allows modelling of any or all the parameters of the distribution for the response variable using explanatory variables and spatial effects. The response variable distribution is allowed to be a non-exponential family distribution. A new package developed in R to achieve this is presented. We use Gaussian Markov random fields to model the spatial effect in Munich rent data and explore some features and characteristics of the data. The potential of using spatial analysis within GAMLSS is discussed. We argue that the flexibility of parametric distributions, ability to model all the parameters of the distribution and diagnostic tools of GAMLSS provide an ideal environment for modelling spatial features of data.     

Approximate tolerance intervals for the discrete Poisson–Lindley distribution

The Poisson–Lindley distribution is a compound discrete distribution that can be used as an alternative to other discrete distributions, like the negative binomial. This paper develops approximate one-sided and equal-tailed two-sided tolerance intervals for the Poisson–Lindley distribution. Practical applications of the Poisson–Lindley distribution frequently involve large samples, thus we utilize large-sample Wald confidence intervals in the construction of our tolerance intervals. A coverage study is presented to demonstrate the efficacy of the proposed tolerance intervals. The tolerance intervals are also demonstrated using two real data sets. The R code developed for our discussion is briefly highlighted and included in the tolerance package.     

First-order marginalised transition random effects models with probit link function

Marginalised models, also known as marginally specified models, have recently become a popular tool for analysis of discrete longitudinal data. Despite being a novel statistical methodology, these models introduce complex constraint equations and model fitting algorithms. On the other hand, there is a lack of publicly available software to fit these models. In this paper, we propose a three-level marginalised model for analysis of multivariate longitudinal binary outcome. The implicit function theorem is introduced to approximately solve the marginal constraint equations explicitly. probit link enables direct solutions to the convolution equations. Parameters are estimated by maximum likelihood via a Fisher–Scoring algorithm. A simulation study is conducted to examine the finite-sample properties of the estimator. We illustrate the model with an application to the data set from the Iowa Youth and Families Project. The R package pnmtrem is prepared to fit the model.     

On influence diagnostic in univariate elliptical linear regression models

We discuss in this paper the assessment of local influence in univariate elliptical linear regression models. This class includes all symmetric continuous distributions, such as normal, Student-t, Pearson VII, exponential power and logistic, among others. We derive the appropriate matrices for assessing the local influence on the parameter estimates and on predictions by considering as influence measures the likelihood displacement and a distance based on the Pearson residual. Two examples with real data are given for illustration.     

Influence diagnostics for the structural errors-in-variables model under the Student-t distribution

The influence of observations on the parameter estimates for the simple structural errors-in-variables model with no equation error, under the Student-t distribution, is investigated using the local influence approach. The main conclusion is that the Student-t model with small degrees of freedom is able to incorporate possible outliers and influential observations in the data. The likelihood displacement approach is useful for outlier detection, especially when a masking phenomenon is present and the degrees of freedom parameter is large. The diagnostics are illustrated with two examples.     

Comparing diagnostic tests with missing data

When missing data occur in studies designed to compare the accuracy of diagnostic tests, a common, though naive, practice is to base the comparison of sensitivity, specificity, as well as of positive and negative predictive values on some subset of the data that fits into methods implemented in standard statistical packages. Such methods are usually valid only under the strong missing completely at random (MCAR) assumption and may generate biased and less precise estimates. We review some models that use the dependence structure of the completely observed cases to incorporate the information of the partially categorized observations into the analysis and show how they may be fitted via a two-stage hybrid process involving maximum likelihood in the first stage and weighted least squares in the second. We indicate how computational subroutines written in R may be used to fit the proposed models and illustrate the different analysis strategies with observational data collected to compare the accuracy of three distinct non-invasive diagnostic methods for endometriosis. The results indicate that even when the MCAR assumption is plausible, the naive partial analyses should be avoided.     

Modeling wind energy flux by a Birnbaum–Saunders distribution with an unknown shift parameter

In this paper, we discuss a Birnbaum–Saunders distribution with an unknown shift parameter and apply it to wind energy modeling. We describe structural aspects of this distribution including properties, moments, mode and hazard and shape analyses. We also discuss estimation, goodness of fit and diagnostic methods for this distribution. A computational implementation in R language of the obtained results is provided. Finally, we apply such results to two unpublished real wind speed data from Chile, which allows us to show the characteristics of this statistical distribution and to model wind energy flux.     

Bayesian analysis of generalized elliptical semi-parametric models

In this paper, we study the statistical inference based on the Bayesian approach for regression models with the assumption that independent additive errors follow normal, Student-t, slash, contaminated normal, Laplace or symmetric hyperbolic distribution, where both location and dispersion parameters of the response variable distribution include nonparametric additive components approximated by B-splines. This class of models provides a rich set of symmetric distributions for the model error. Some of these distributions have heavier or lighter tails than the normal as well as different levels of kurtosis. In order to draw samples of the posterior distribution of the interest parameters, we propose an efficient Markov Chain Monte Carlo (MCMC) algorithm, which combines Gibbs sampler and Metropolis–Hastings algorithms. The performance of the proposed MCMC algorithm is assessed through simulation experiments. We apply the proposed methodology to a real data set. The proposed methodology is implemented in the R package BayesGESM using the function gesm().     

A novel Bayesian regression model for counts with an application to health data

Discrete data are collected in many application areas and are often characterised by highly-skewed distributions. An example of this, which is considered in this paper, is the number of visits to a specialist, often taken as a measure of demand in healthcare. A discrete Weibull regression model was recently proposed for regression problems with a discrete response and it was shown to possess desirable properties. In this paper, we propose the first Bayesian implementation of this model. We consider a general parametrization, where both parameters of the discrete Weibull distribution can be conditioned on the predictors, and show theoretically how, under a uniform non-informative prior, the posterior distribution is proper with finite moments. In addition, we consider closely the case of Laplace priors for parameter shrinkage and variable selection. Parameter estimates and their credible intervals can be readily calculated from their full posterior distribution. A simulation study and the analysis of four real datasets of medical records show promises for the wide applicability of this approach to the analysis of count data. The method is implemented in the R package BDWreg.     

A new approach to modeling positive random variables with repeated measures

In many situations, it is common to have more than one observation per experimental unit, thus generating the experiments with repeated measures. In the modeling of such experiments, it is necessary to consider and model the intra-unit dependency structure. In the literature, there are several proposals to model positive continuous data with repeated measures. In this paper, we propose one more with the generalization of the beta prime regression model. We consider the possibility of dependence between observations of the same unit. Residuals and diagnostic tools also are discussed. To evaluate the finite-sample performance of the estimators, using different correlation matrices and distributions, we conducted a Monte Carlo simulation study. The methodology proposed is illustrated with an analysis of a real data set. Finally, we create an R package for easy access to publicly available the methodology described in this paper.     

Likelihood-based risk estimation for variance-gamma models

Although the variance-gamma distribution is a flexible model for log-returns of financial assets, so far it has found rather limited applications in finance and risk management. One of the reasons is that maximum likelihood estimation of its parameters is not straightforward. We develop an EM-type algorithm based on Nitithumbundit and Chan (An ECM algorithm for skewed multivariate variance gamma distribution in normal mean–variance representation, arXiv:1504.01239, 2015) that bypasses the evaluation of the full likelihood, which may be difficult because the density is not in closed form and is unbounded for small values of the shape parameter. Moreover, we study the relative efficiency of our approach with respect to the maximum likelihood estimation procedures implemented in the VarianceGamma and ghyp R packages. Extensive simulation experiments and real-data analyses suggest that the multicycle ECM algorithm gives the best results in terms of root-mean-squared-error, for both parameter and value-at-risk estimation. The performance of the routines in the ghyp R package is similar but not as good, whereas the VarianceGamma package produces worse results, especially when the shape parameter is small.     

A new useful four-parameter extension of the Gumbel distribution: Properties,regression model and applications using the GAMLSS framework

In this paper we introduce a flexible extension of the Gumbel distribution called the odd log-logistic exponentiated Gumbel distribution. The new model was implemented in GAMLSS package of R software and a brief tutorial on how to use this package is presented throughout the paper. We provide a comprehensive treatment of its general mathematical properties. Further, we propose a new extended regression model considering four regression structures. We discuss estimation methods based on censored and uncensored data. Two simulation studies are presented and four real data sets are applied to illustrating the usefulness of the new model.     

A new class of survival regression models with heavy-tailed errors: robustness and diagnostics

Birnbaum-Saunders models have largely been applied in material fatigue studies and reliability analyses to relate the total time until failure with some type of cumulative damage. In many problems related to the medical field, such as chronic cardiac diseases and different types of cancer, a cumulative damage caused by several risk factors might cause some degradation that leads to a fatigue process. In these cases, BS models can be suitable for describing the propagation lifetime. However, since the cumulative damage is assumed to be normally distributed in the BS distribution, the parameter estimates from this model can be sensitive to outlying observations. In order to attenuate this influence, we present in this paper BS models, in which a Student-t distribution is assumed to explain the cumulative damage. In particular, we show that the maximum likelihood estimates of the Student-t log-BS models attribute smaller weights to outlying observations, which produce robust parameter estimates. Also, some inferential results are presented. In addition, based on local influence and deviance component and martingale-type residuals, a diagnostics analysis is derived. Finally, a motivating example from the medical field is analyzed using log-BS regression models. Since the parameter estimates appear to be very sensitive to outlying and influential observations, the Student-t log-BS regression model should attenuate such influences. The model checking methodologies developed in this paper are used to compare the fitted models.     

An Introduction to Practical Sequential Inferences via Single-Arm Binary Response Studies Using the binseqtest R Package

We review sequential designs, including group sequential and two-stage designs, for testing or estimating a single binary parameter. We use this simple case to introduce ideas common to many sequential designs, which in this case can be explained without explicitly using stochastic processes. We focus on methods provided by our newly developed R package, binseqtest, which exactly bound the Type I error rate of tests and exactly maintain proper coverage of confidence intervals. Within this framework, we review some allowable practical adaptations of the sequential design. We explore issues such as the following: How should the design be modified if no assessment was made at one of the planned sequential stopping times? How should the parameter be estimated if the study needs to be stopped early? What reasons for stopping early are allowed? How should inferences be made when the study is stopped for crossing the boundary, but later information is collected about responses of subjects that had enrolled before the decision to stop but had not responded by that time? Answers to these questions are demonstrated using basic methods that are available in our binseqtest R package. Supplementary materials for this article are available online.     

Developments in Maximum Likelihood Unit Root Tests

The exact maximum likelihood estimate provides a test statistic for the unit root test that is more powerful than the usual least-squares approach. In this article, a new derivation is given for the asymptotic distribution of this test statistic that is simpler and more direct than the previous method. The response surface regression method is used to obtain a fast algorithm that computes accurate finite-sample critical values. This algorithm is available in the R package mleur that is available on CRAN. The empirical power of the new test is shown to be much better than the usual test not only in the normal case but also for innovations generated from an infinite variance stable distribution as well as for innovations generated from a GARCH(1,1) process.     

A tobit model with garch errors

In the context of time series regression, we extend the standard Tobit model to allow for the possibility of conditional heteroskedastic error processes of the GARCH type. We discuss the likelihood function of the Tobit model in the presence of conditionally heteroskedastic errors. Expressing the exact likelihood function turns out to be infeasible, and we propose an approximation by treating the model as being conditionally Gaussian. The performance of the estimator is investigated by means of Monte Carlo simulations. We find that, when the error terms follow a GARCH process, the proposed estimator considerably outperforms the standard Tobit quasi maximum likelihood estimator. The efficiency loss due to the approximation of the likelihood is finally evaluated.