On the minimum expected quantity for the validity of the chi-squared test in 2 2 2 tables

A 2 2 2 contingency table can often be analysed in an exact fashion by using Fisher's exact test and in an approximate fashion by using the chi-squared test with Yates' continuity correction, and it is traditionally held that the approximation is valid when the minimum expected quantity E is E S 5. Unfortunately, little research has been carried out into this belief, other than that it is necessary to establish a bound E>E*, that the condition E S 5 may not be the most appropriate (Martín Andrés et al., 1992) and that E* is not a constant, but usually increasing with the growth of the sample size (Martín Andrés & Herranz Tejedor, 1997). In this paper, the authors conduct a theoretical experimental study from which they ascertain that E* value (which is very variable and frequently quite a lot greater than 5) is strongly related to the magnitude of the skewness of the underlying hypergeometric distribution, and that bounding the skewness is equivalent to bounding E (which is the best control procedure). The study enables estimating the expression for the above-mentioned E* (which in turn depends on the number of tails in the test, the alpha error used, the total sample size, and the minimum marginal imbalance) to be estimated. Also the authors show that E* increases generally with the sample size and with the marginal imbalance, although it does reach a maximum. Some general and very conservative validity conditions are E S 35.53 (one-tailed test) and E S 7.45 (two-tailed test) for alpha nominal errors in 1% h f h 10%. The traditional condition E S 5 is only valid when the samples are small and one of the marginals is very balanced; alternatively, the condition E S 5.5 is valid for small samples or a very balanced marginal. Finally, it is proved that the chi-squared test is always valid in tables where both marginals are balanced, and that the maximum skewness permitted is related to the maximum value of the bound E*, to its value for tables with at least one balanced marginal and to the minimum value that those marginals must have (in non-balanced tables) for the chi-squared test to be valid.     

Estimation in an empirical bayes model for longitudinal and cross‐sectionally clustered binary data

Some studies generate data that can be grouped into clusters in more than one way. Consider for instance a smoking prevention study in which responses on smoking status are collected over several years in a cohort of students from a number of different schools. This yields longitudinal data, also cross‐sectionaliy clustered in schools. The authors present a model for analyzing binary data of this type, combining generalized estimating equations and estimation of random effects to address the longitudinal and cross‐sectional dependence, respectively. The estimation procedure for this model is discussed, as are the results of a simulation study used to investigate the properties of its estimates. An illustration using data from a smoking prevention trial is given.     

A ‘nondecimated’ lifting transform

Classical nondecimated wavelet transforms are attractive for many applications. When the data comes from complex or irregular designs, the use of second generation wavelets in nonparametric regression has proved superior to that of classical wavelets. However, the construction of a nondecimated second generation wavelet transform is not obvious. In this paper we propose a new ‘nondecimated’ lifting transform, based on the lifting algorithm which removes one coefficient at a time, and explore its behavior. Our approach also allows for embedding adaptivity in the transform, i.e. wavelet functions can be constructed such that their smoothness adjusts to the local properties of the signal. We address the problem of nonparametric regression and propose an (averaged) estimator obtained by using our nondecimated lifting technique teamed with empirical Bayes shrinkage. Simulations show that our proposed method has higher performance than competing techniques able to work on irregular data. Our construction also opens avenues for generating a ‘best’ representation, which we shall explore.     

Nonparametric control charts based on runs and Wilcoxon-type rank-sum statistics

In this article, we introduce three new distribution-free Shewhart-type control charts that exploit run and Wilcoxon-type rank-sum statistics to detect possible shifts of a monitored process. Exact formulae for the alarm rate, the run length distribution, and the average run length (ARL) are all derived. A key advantage of these charts is that, due to their nonparametric nature, the false alarm rate (FAR) and in-control run length distribution is the same for all continuous process distributions. Tables are provided for the implementation of the charts for some typical FAR values. Furthermore, a numerical study carried out reveals that the new charts are quite flexible and efficient in detecting shifts to Lehmann-type out-of-control situations.     

Bayesian unit-root tests for Stochastic Volatility models

In this article, we consider Bayesian inference procedures to test for a unit root in Stochastic Volatility (SV) models. Unit-root tests for the persistence parameter of the SV models, based on the Bayes Factor (BF), have been recently introduced in the literature. In contrast, we propose a flexible class of priors that is non-informative over the entire support of the persistence parameter (including the non-stationarity region). In addition, we show that our model fitting procedure is computationally efficient (using the software WinBUGS). Finally, we show that our proposed test procedures have good frequentist properties in terms of achieving high statistical power, while maintaining low total error rates. We illustrate the above features of our method by extensive simulation studies, followed by an application to a real data set on exchange rates.     

Diagnostic checks for discrete data regression models using posterior predictive simulations

Model checking with discrete data regressions can be difficult because the usual methods such as residual plots have complicated reference distributions that depend on the parameters in the model. Posterior predictive checks have been proposed as a Bayesian way to average the results of goodness-of-fit tests in the presence of uncertainty in estimation of the parameters. We try this approach using a variety of discrepancy variables for generalized linear models fitted to a historical data set on behavioural learning. We then discuss the general applicability of our findings in the context of a recent applied example on which we have worked. We find that the following discrepancy variables work well, in the sense of being easy to interpret and sensitive to important model failures: structured displays of the entire data set, general discrepancy variables based on plots of binned or smoothed residuals versus predictors and specific discrepancy variables created on the basis of the particular concerns arising in an application. Plots of binned residuals are especially easy to use because their predictive distributions under the model are sufficiently simple that model checks can often be made implicitly. The following discrepancy variables did not work well: scatterplots of latent residuals defined from an underlying continuous model and quantile–quantile plots of these residuals.     

Binary probability maps using a hidden conditional autoregressive Gaussian process with an application to Finnish common toad data

The Finnish common toad data of Heikkinen and Hogmander are reanalysed using an alternative fully Bayesian model that does not require a pseudolikelihood approximation and an alternative prior distribution for the true presence or absence status of toads in each 10 km×10 km square. Markov chain Monte Carlo methods are used to obtain posterior probability estimates of the square-specific presences of the common toad and these are presented as a map. The results are different from those of Heikkinen and Hogmander and we offer an explanation in terms of the prior used for square-specific presence of the toads. We suggest that our approach is more faithful to the data and avoids unnecessary confounding of effects. We demonstrate how to extend our model efficiently with square-specific covariates and illustrate this by introducing deterministic spatial changes.     

Standard errors for EM estimation

The EM algorithm is a popular method for computing maximum likelihood estimates. One of its drawbacks is that it does not produce standard errors as a by-product. We consider obtaining standard errors by numerical differentiation. Two approaches are considered. The first differentiates the Fisher score vector to yield the Hessian of the log-likelihood. The second differentiates the EM operator and uses an identity that relates its derivative to the Hessian of the log-likelihood. The well-known SEM algorithm uses the second approach. We consider three additional algorithms: one that uses the first approach and two that use the second. We evaluate the complexity and precision of these three and the SEM in algorithm seven examples. The first is a single-parameter example used to give insight. The others are three examples in each of two areas of EM application: Poisson mixture models and the estimation of covariance from incomplete data. The examples show that there are algorithms that are much simpler and more accurate than the SEM algorithm. Hopefully their simplicity will increase the availability of standard error estimates in EM applications. It is shown that, as previously conjectured, a symmetry diagnostic can accurately estimate errors arising from numerical differentiation. Some issues related to the speed of the EM algorithm and algorithms that differentiate the EM operator are identified.     

Off‐Time Pubertal Timing Predicts Physiological Reactivity to Postpuberty Interpersonal Stress

We investigated associations between retrospectively assessed timing of pubertal development, interpersonal interactions, and hypothalamic–pituitary–adrenal axis reactivity to an interpersonal stress task in 110 young adult women. Participants provided salivary cortisol samples at points prior and subsequent to a video‐taped conflict discussion with their romantic partner. Participants also provided subjective global ratings of their discussion on dimensions of conflict and support. For earlier developing girls, higher levels of interpersonal conflict were associated with greater physiological stress in anticipation of the discussion task and less physiological recovery following the discussion. In contrast, for later developing girls, low levels of conflict were associated with greater anticipatory stress and less physiological recovery. These findings have implications for understanding the influence of off‐time pubertal development on the lifetime development of young women.