Inference on local average treatment effects for misclassified treatment

We develop point-identification for the local average treatment effect when the binary treatment contains a measurement error. The standard instrumental variable estimator is inconsistent for the parameter since the measurement error is nonclassical by construction. We correct the problem by identifying the distribution of the measurement error based on the use of an exogenous variable that can even be a binary covariate. The moment conditions derived from the identification lead to generalized method of moments estimation with asymptotically valid inferences. Monte Carlo simulations and an empirical illustration demonstrate the usefulness of the proposed procedure.     

On Bayesian lasso variable selection and the specification of the shrinkage parameter

We propose a Bayesian implementation of the lasso regression that accomplishes both shrinkage and variable selection. We focus on the appropriate specification for the shrinkage parameter λ through Bayes factors that evaluate the inclusion of each covariate in the model formulation. We associate this parameter with the values of Pearson and partial correlation at the limits between significance and insignificance as defined by Bayes factors. In this way, a meaningful interpretation of λ is achieved that leads to a simple specification of this parameter. Moreover, we use these values to specify the parameters of a gamma hyperprior for λ. The parameters of the hyperprior are elicited such that appropriate levels of practical significance of the Pearson correlation are achieved and, at the same time, the prior support of λ values that activate the Lindley-Bartlett paradox or lead to over-shrinkage of model coefficients is avoided. The proposed method is illustrated using two simulation studies and a real dataset. For the first simulation study, results for different prior values of λ are presented as well as a detailed robustness analysis concerning the parameters of the hyperprior of λ. In all examples, detailed comparisons with a variety of ordinary and Bayesian lasso methods are presented.     

The use of predicted values for item parameters in item response theory models: an application in intelligence tests

In testing, item response theory models are widely used in order to estimate item parameters and individual abilities. However, even unidimensional models require a considerable sample size so that all parameters can be estimated precisely. The introduction of empirical prior information about candidates and items might reduce the number of candidates needed for parameter estimation. Using data for IQ measurement, this work shows how empirical information about items can be used effectively for item calibration and in adaptive testing. First, we propose multivariate regression trees to predict the item parameters based on a set of covariates related to the item-solving process. Afterwards, we compare the item parameter estimation when tree-fitted values are included in the estimation or when they are ignored. Model estimation is fully Bayesian, and is conducted via Markov chain Monte Carlo methods. The results are two-fold: (a) in item calibration, it is shown that the introduction of prior information is effective with short test lengths and small sample sizes and (b) in adaptive testing, it is demonstrated that the use of the tree-fitted values instead of the estimated parameters leads to a moderate increase in the test length, but provides a considerable saving of resources.     

The Bayesian choice of crop variety and fertilizer dose

Recent contributions to the theory of optimizing fertilizer doses in agricultural crop production have introduced Bayesian ideas to incorporate information on crop yield from several environments and on soil nutrients from a soil test, but they have not used a fully Bayesian formulation. We present such a formulation and demonstrate how the resulting Bayes decision procedure can be evaluated in practice by using Markov chain Monte Carlo methods. The approach incorporates expert knowledge of the crop and of regional and local soil conditions and allows a choice of crop variety as well as of fertilizer level. Alternative dose–response functions are expressed in terms of a common interpretable set of parameters to facilitate model comparisons and the specification of prior distributions. The approach is illustrated with a set of yield data from spring barley nitrogen–response trials and is found to be robust to changes in the dose–response function and the prior distribution for indigenous soil nitrogen.     

Pre-checking for non-monotonicity of the Wald statistic

The non-monotonic behaviour of the Wald test in some finite-sample applications leads to low power when the null hypothesis needs rejection most. This article proposes a simple check for discerning if the Wald statistic for testing significance of regression coefficients is non-monotonic in the neighbourhood of the parameter space from which the sample data are drawn. Monte Carlo simulations show that this method works rather well for detecting situations where the Wald test can be safely applied. An example is provided to illustrate the use of this check.     

Estimating crop yield via Gaussian quadrature

The present study proposes a method to estimate the yield of a crop. The proposed Gaussian quadrature (GQ) method makes it possible to estimate the crop yield from a smaller subsample. Identification of plots and corresponding weights to be assigned to the yield of plots comprising a subsample is done with the help of information about the full sample on certain auxiliary variables relating to biometrical characteristics of the plant. Computational experience reveals that the proposed method leads to about 78% reduction in sample size with absolute percentage error of 2.7%. Performance of the proposed method has been compared with that of random sampling on the basis of the values of average absolute percentage error and standard deviation of yield estimates obtained from 40 samples of comparable size. Interestingly, average absolute percentage error as well as standard deviation is considerably smaller for the GQ estimates than for the random sample estimates. The proposed method is quite general and can be applied for other crops as well-provided information on auxiliary variables relating to yield contributing biometrical characteristics is available.     

Objective Priors for Parameters in a Normal Linear Regression with Measurement Error

We investigate certain objective priors for the parameters in a normal linear regression models with one of the explanatory variables subject to measurement error. We first show that the use of the standard non informative prior for normal linear regression without measurement error leads to an improper posterior in the measurement error model. We then derive the Jeffreys prior and reference priors, and show that they lead to proper posteriors. We use simulation study to compare the frequentist performance of the estimates derived using these priors, and the MLE.     

Performance of Interval Estimators for the Inverse Hypergeometric Distribution

The inverse hypergeometric distribution is of interest in applications of inverse sampling without replacement from a finite population where a binary observation is made on each sampling unit. Thus, sampling is performed by randomly choosing units sequentially one at a time until a specified number of one of the two types is selected for the sample. Assuming the total number of units in the population is known but the number of each type is not, we consider the problem of estimating this parameter. We use the Delta method to develop approximations for the variance of three parameter estimators. We then propose three large sample confidence intervals for the parameter. Based on these results, we selected a sampling of parameter values for the inverse hypergeometric distribution to empirically investigate performance of these estimators. We evaluate their performance in terms of expected probability of parameter coverage and confidence interval length calculated as means of possible outcomes weighted by the appropriate outcome probabilities for each parameter value considered. The unbiased estimator of the parameter is the preferred estimator relative to the maximum likelihood estimator and an estimator based on a negative binomial approximation, as evidenced by empirical estimates of closeness to the true parameter value. Confidence intervals based on the unbiased estimator tend to be shorter than the two competitors because of its relatively small variance but at a slight cost in terms of coverage probability.     

A bayesian wls approach to generalized linear models

We use a Bayesian approach to fitting a linear regression model to transformations of the natural parameter for the exponential class of distributions. The usual Bayesian approach is to assume that a linear model exactly describes the relationship among the natural parameters. We assume only that a linear model is approximately in force. We approximate the theta-links by using a linear model obtained by minimizing the posterior expectation of a loss function.While some posterior results can be obtained analytically considerable generality follows from an exact Monte Carlo method for obtaining random samples of parameter values or functions of parameter values from their respective posterior distributions. The approach that is presented is justified for small samples, requires only one-dimensional numerical integrations, and allows for the use of regression matrices with less than full column rank. Two numerical examples are provided.     

On the Choice of a Prior for Bayesian D-Optimal Designs for the Logistic Regression Model with a Single Predictor

The Bayesian design approach accounts for uncertainty of the parameter values on which optimal design depends, but Bayesian designs themselves depend on the choice of a prior distribution for the parameter values. This article investigates Bayesian D-optimal designs for two-parameter logistic models, using numerical search. We show three things: (1) a prior with large variance leads to a design that remains highly efficient under other priors, (2) uniform and normal priors lead to equally efficient designs, and (3) designs with four or five equidistant equally weighted design points are highly efficient relative to the Bayesian D-optimal designs.     

The two-sided power distribution for the treatment of the uncertainty in PERT

The aim of this paper is to include the Two-Sided Power (TSP) distribution in the PERT methodology making use of the advantages that this four-parameter distribution offers. In order to be completely determined, a distribution of this type needs, the same as the beta distribution, a new datum apart from the three usual values a (pessimistic), m (most likely) and b (optimistic). To solve this question, when using the beta distribution in the PERT context, we are looking for the maximum similarity with the normal and so it is required that the distribution has the same variance as the normal or its same kurtosis, giving rise to the constant variance and mesokurtic families, respectively. Nevertheless, while this approach can be only applied to the beta distribution for some values in the range of the standardized mode, in the case of the TSP distribution this methodology leads always to a solution. A detailed analysis comparing the beta and TSP distribution based on their PERT means and variances is presented indicating better results for the second. We are very grateful for the comments and suggestions of two anonymous referees.     

Attenuation of treatment effect due to measurement variability in assessment of progression-free survival

For normally distributed data analyzed with linear models, it is well known that measurement error on an independent variable leads to attenuation of the effect of the independent variable on the dependent variable. However, for time‐to‐event variables such as progression‐free survival (PFS), the effect of the measurement variability in the underlying measurements defining the event is less well understood. We conducted a simulation study to evaluate the impact of measurement variability in tumor assessment on the treatment effect hazard ratio for PFS and on the median PFS time, for different tumor assessment frequencies. Our results show that scan measurement variability can cause attenuation of the treatment effect (i.e. the hazard ratio is closer to one) and that the extent of attenuation may be increased with more frequent scan assessments. This attenuation leads to inflation of the type II error. Therefore, scan measurement variability should be minimized as far as possible in order to reveal a treatment effect that is closest to the truth. In disease settings where the measurement variability is shown to be large, consideration may be given to inflating the sample size of the study to maintain statistical power. Copyright © 2012 John Wiley & Sons, Ltd.     

Extended generalised Pareto models for tail estimation

The most popular approach in extreme value statistics is the modelling of threshold exceedances using the asymptotically motivated generalised Pareto distribution. This approach involves the selection of a high threshold above which the model fits the data well. Sometimes, few observations of a measurement process might be recorded in applications and so selecting a high quantile of the sample as the threshold leads to almost no exceedances. In this paper we propose extensions of the generalised Pareto distribution that incorporate an additional shape parameter while keeping the tail behaviour unaffected. The inclusion of this parameter offers additional structure for the main body of the distribution, improves the stability of the modified scale, tail index and return level estimates to threshold choice and allows a lower threshold to be selected. We illustrate the benefits of the proposed models with a simulation study and two case studies.     

A comparison study on modeling of clustered and overdispersed count data for multiple comparisons

Data collected in various scientific fields are count data. One way to analyze such data is to compare the individual levels of the factor treatment using multiple comparisons. However, the measured individuals are often clustered – e.g. according to litter or rearing. This must be considered when estimating the parameters by a repeated measurement model. In addition, ignoring the overdispersion to which count data is prone leads to an increase of the type one error rate. We carry out simulation studies using several different data settings and compare different multiple contrast tests with parameter estimates from generalized estimation equations and generalized linear mixed models in order to observe coverage and rejection probabilities. We generate overdispersed, clustered count data in small samples as can be observed in many biological settings. We have found that the generalized estimation equations outperform generalized linear mixed models if the variance-sandwich estimator is correctly specified. Furthermore, generalized linear mixed models show problems with the convergence rate under certain data settings, but there are model implementations with lower implications exists. Finally, we use an example of genetic data to demonstrate the application of the multiple contrast test and the problems of ignoring strong overdispersion.     

Fitting Emax models to clinical trial dose–response data when the high dose asymptote is ill defined

We consider fitting the so‐called Emax model to continuous response data from clinical trials designed to investigate the dose–response relationship for an experimental compound. When there is insufficient information in the data to estimate all of the parameters because of the high dose asymptote being ill defined, maximum likelihood estimation fails to converge. We explore the use of either bootstrap resampling or the profile likelihood to make inferences about effects and doses required to give a particular effect, using limits on the parameter values to obtain the value of the maximum likelihood when the high dose asymptote is ill defined. The results obtained show these approaches to be comparable with or better than some others that have been used when maximum likelihood estimation fails to converge and that the profile likelihood method outperforms the method of bootstrap resampling used. Copyright © 2014 John Wiley & Sons, Ltd.     

On a data-dependent choice of the tuning parameter appearing in certain goodness-of-fit tests

We propose a data-dependent method for choosing the tuning parameter appearing in many recently developed goodness-of-fit test statistics. The new method, based on the bootstrap, is applicable to a class of distributions for which the null distribution of the test statistic is independent of unknown parameters. No data-dependent choice for this parameter exists in the literature; typically, a fixed value for the parameter is chosen which can perform well for some alternatives, but poorly for others. The performance of the new method is investigated by means of a Monte Carlo study, employing three tests for exponentiality. It is found that the Monte Carlo power of these tests, using the data-dependent choice, compares favourably to the maximum achievable power for the tests calculated over a grid of values of the tuning parameter.     

Notes on the two-stage procedure under an incomplete block two-period crossover design

Abstract

Under an incomplete block crossover design with two periods, we derive the least-squares estimators for the period effect, treatment effects and carry-over effects in explicit formulae based on within-patient differences. Using the commonly-used strategy of searching a base model for making inferences in regression analysis, we define a two-stage test procedure in studying treatment effects. On the basis of Monte Carlo simulation, we evaluate the performance of the two-stage procedure for hypothesis testing, point and interval estimation of treatment effects in a variety of situations. We note that use of the two-stage procedure can be potentially misleading and hence one should not apply a test procedure to exclusively determine whether he/she needs to account for the carry-over effect in studying treatment effects. We use the double-blind crossover trial comparing two different doses of formoterol with placebo on the forced expiratory volume in 1 second (FEV₁) readings to illustrate the use of the two-stage procedure, as well as the distinction between use of two-stage procedure and the approach with assuming no carry-over effects based on one's subjective knowledge.     

A Kernel Variogram Estimator for Clustered Data

Abstract.  The variogram provides an important method for measuring the dependence of attribute values between spatial locations. Suppose that the nature of the sampling process leads to the presence of clustered data; it would be advisable to use a variogram estimator that aims to adjust for clustering of samples. In this setting, the use of a non-parametric weighted estimator, obtained by considering an inverse weight to a given neighbourhood density combined with the kernel method, seems to have a satisfactory behaviour in practice. This paper pursues a theoretical study of the cluster robust estimator, by proving that it is asymptotically unbiased as well as consistent and by providing criteria for selection of the bandwidth parameter and the neighbourhood radius. Numerical studies are also included to illustrate the performance of the considered estimator and the suggested approaches.     

Optimal design of experimental epidemics

We consider the optimal design of controlled experimental epidemics or transmission experiments, whose purpose is to inform the practitioner about disease transmission and recovery rates. Our methodology employs Gaussian diffusion approximations, applicable to epidemics that can be modeled as density-dependent Markov processes and involving relatively large numbers of organisms. We focus on finding (i) the optimal times at which to collect data about the state of the system for a small number of discrete observations, (ii) the optimal numbers of susceptible and infective individuals to begin an experiment with, and (iii) the optimal number of replicate epidemics to use. We adopt the popular D-optimality criterion as providing an appropriate objective function for designing our experiments, since this leads to estimates with maximum precision, subject to valid assumptions about parameter values. We demonstrate the broad applicability of our methodology using a diverse array of compartmental epidemic models: a time-homogeneous SIS epidemic, a time-inhomogeneous SI epidemic with exponentially decreasing transmission rates and a partially observed SIR epidemic where the infectious period for an individual has a gamma distribution.