Generalized Additive Models for Zero‐Inflated Data with Partial Constraints

Abstract. Zero‐inflated data abound in ecological studies as well as in other scientific fields. Non‐parametric regression with zero‐inflated response may be studied via the zero‐inflated generalized additive model (ZIGAM) with a probabilistic mixture distribution of zero and a regular exponential family component. We propose the (partially) constrained ZIGAM, which assumes that some covariates affect the probability of non‐zero‐inflation and the regular exponential family distribution mean proportionally on the link scales. When the assumption obtains, the new approach provides a unified framework for modelling zero‐inflated data, which is more parsimonious and efficient than the unconstrained ZIGAM. We develop an iterative estimation algorithm, and discuss the confidence interval construction of the estimator. Some asymptotic properties are derived. We also propose a Bayesian model selection criterion for choosing between the unconstrained and constrained ZIGAMs. The new methods are illustrated with both simulated data and a real application in jellyfish abundance data analysis.     

Augmented-limited regression models with an application to the study of the risk perceived using continuous scales

Studies of risk perceived using continuous scales of [0,100] were recently introduced in psychometrics, which can be transformed to the unit interval, but the presence of zeros or ones are commonly observed. Motivated by this, we introduce a full inferential set of tools that allows for augmented and limited data modeling. We considered parameter estimation, residual analysis, influence diagnostic and model selection for zero-and/or-one augmented beta rectangular (ZOABR) regression models and their particular nested models, which is based on a new parameterization of the beta rectangular distribution. Different from other alternatives, we performed maximum-likelihood estimation using a combination of the EM algorithm (for the continuous part) and Fisher scoring algorithm (for the discrete part). Also, we perform an additional step, by considering other link functions, besides the usual logistic link, for modeling the response mean. By considering randomized quantile residuals, (local) influence diagnostics and model selection tools, we identified that the ZOABR regression model is the best one. We also conducted extensive simulations studies, which indicate that all developed tools work properly. Finally, we discuss the use of this type of models to treat psychometric data. It is worthwhile to mention that applications of the developed methods go beyond to Psychometric data. Indeed, they can be useful when the response variable in bounded, including or not the respective limits.     

Interval robust design under contaminated and non normal data

Abstract

Robust parameter design (RPD) is an effective tool, which involves experimental design and strategic modeling to determine the optimal operating conditions of a system. The usual assumptions of RPD are that normally distributed experimental data and no contamination due to outliers. And generally the parameter uncertainties in response models are neglected. However, using normal theory modeling methods for a skewed data and ignoring parameter uncertainties can create a chain of degradation in optimization and production phases such that misleading fit, poor estimated optimal operating conditions, and poor quality products. This article presents a new approach based on confidence interval (CI) response modeling for the process mean. The proposed interval robust design makes the system median unbiased for the mean and uses midpoint of the interval as a measure of location performance response. As an alternative robust estimator for the process variance response modeling, using biweight midvariance is proposed which is both resistant and robust of efficiency where normality is not met. The results further show that the proposed interval robust design gives a robust solution to the skewed structure of the data and to contaminated data. The procedure and its advantages are illustrated using two experimental design studies.     

Test inversion bootstrap confidence intervals

In this paper we explore the theoretical and practical implications of using bootstrap test inversion to construct confidence intervals. In the presence of nuisance parameters, we show that the coverage error of such intervals is O ( n ^−1/2) which may be reduced to O ( n ⁻¹) if a Studentized statistic is used. We present three simulation studies and compare the performance of test inversion methods with established methods on the problem of estimating a confidence interval for the dose–response parameter in models of the Japanese atomic bomb survivors data.     

Bayesian generalized varying coefficient models for longitudinal proportional data with errors-in-covariates

This paper is motivated from a neurophysiological study of muscle fatigue, in which biomedical researchers are interested in understanding the time-dependent relationships of handgrip force and electromyography measures. A varying coefficient model is appealing here to investigate the dynamic pattern in the longitudinal data. The response variable in the study is continuous but bounded on the standard unit interval (0, 1) over time, while the longitudinal covariates are contaminated with measurement errors. We propose a generalization of varying coefficient models for the longitudinal proportional data with errors-in-covariates. We describe two estimation methods with penalized splines, which are formalized under a Bayesian inferential perspective. The first method is an adaptation of the popular regression calibration approach. The second method is based on a joint likelihood under the hierarchical Bayesian model. A simulation study is conducted to evaluate the efficacy of the proposed methods under different scenarios. The analysis of the neurophysiological data is presented to demonstrate the use of the methods.     

Maximum likelihood estimation of bivariate survival probabilities and its existence and uniqueness

Nonparametric maximum likelihood estimation of bivariate survival probabilities is developed for interval censored survival data. We restrict our attention to the situation where response times within pairs are not distinguishable, and the univariate survival distribution is the same for any individual within any pair. Campbell's (1981) model is modified to incorporate this restriction. Existence and uniqueness of maximum likelihood estimators are discussed. This methodology is illustrated with a bivariate life table analysis of an angioplasty study where each patient undergoes two procedures.     

A transformation approach for the analysis of interval-censored failure time data

This paper discusses the analysis of interval-censored failure time data, which has recently attracted a great amount of attention (Li and Pu, Lifetime Data Anal 9:57–70, 2003; Sun, The statistical analysis of interval-censored data, 2006; Tian and Cai, Biometrika 93(2):329–342, 2006; Zhang et al., Can J Stat 33:61–70, 2005). Interval-censored data mean that the survival time of interest is observed only to belong to an interval and they occur in many fields including clinical trials, demographical studies, medical follow-up studies, public health studies and tumorgenicity experiments. A major difficulty with the analysis of interval-censored data is that one has to deal with a censoring mechanism that involves two related variables. For the inference, we present a transformation approach that transforms general interval-censored data into current status data, for which one only needs to deal with one censoring variable and the inference is thus much easy. We apply this general idea to regression analysis of interval-censored data using the additive hazards model and numerical studies indicate that the method performs well for practical situations. An illustrative example is provided.     

A comparative study of confidence intervals for negative binomial proportion

In this paper, we investigate four existing and three new confidence interval estimators for the negative binomial proportion (i.e., proportion under inverse/negative binomial sampling). An extensive and systematic comparative study among these confidence interval estimators through Monte Carlo simulations is presented. The performance of these confidence intervals are evaluated in terms of their coverage probabilities and expected interval widths. Our simulation studies suggest that the confidence interval estimator based on saddlepoint approximation is more appealing for large coverage levels (e.g., nominal level≤1% ) whereas the score confidence interval estimator is more desirable for those commonly used coverage levels (e.g., nominal level>1% ). We illustrate these confidence interval construction methods with a real data set from a maternal congenital heart disease study.     

Functional Analysis of Variance,Discriminant Analysis,and Clustering in a Manifold of Elastic Curves

We develop functional data analysis techniques using the differential geometry of a manifold of smooth elastic functions on an interval in which the functions are represented by a log-speed function and an angle function. The manifold's geometry provides a method for computing a sample mean function and principal components on tangent spaces. Using tangent principal component analysis, we estimate probability models for functional data and apply them to functional analysis of variance, discriminant analysis, and clustering. We demonstrate these tasks using a collection of growth curves from children from ages 1–18.     

Beta Regression for Modelling Rates and Proportions

This paper proposes a regression model where the response is beta distributed using a parameterization of the beta law that is indexed by mean and dispersion parameters. The proposed model is useful for situations where the variable of interest is continuous and restricted to the interval (0, 1) and is related to other variables through a regression structure. The regression parameters of the beta regression model are interpretable in terms of the mean of the response and, when the logit link is used, of an odds ratio, unlike the parameters of a linear regression that employs a transformed response. Estimation is performed by maximum likelihood. We provide closed-form expressions for the score function, for Fisher's information matrix and its inverse. Hypothesis testing is performed using approximations obtained from the asymptotic normality of the maximum likelihood estimator. Some diagnostic measures are introduced. Finally, practical applications that employ real data are presented and discussed.     

Extending the inference function for augmented margins method to implement trivariate Clayton copula-based SUR Tobit models

Abstract

In this paper, we perform the analysis of the SUR Tobit model for three left-censored dependent variables by modeling its nonlinear dependence structure through the one-parameter Clayton copula. For unbiased parameter estimation, we propose an extension of the Inference Function for Augmented Margins (IFAM) method to the trivariate case. The interval estimation for the model parameters using resampling procedures is also discussed. We perform simulation and empirical studies, whose satisfactory results indicate the good performance of the proposed model and methods. Our procedure is illustrated using real data on consumption of food items (salad dressings, lettuce, tomato) by Americans.     

A semiparametric regression cure model for interval-censored and left-truncated data

Medical advancements have made it possible for patients to be cured of certain types of diseases. In follow-up studies, the disease event time can be subject to left truncation and interval censoring. In this article, we propose a semiparametric nonmixture cure model for the regression analysis of left-truncated and interval-censored (LTIC) data. We develop semiparametric maximum likelihood estimation for the nonmixture cure model with LTIC data. A simulation study is conducted to investigate the performance of the proposed estimators.     

Estimation of proportion ratio in non-compliance randomized trials with repeated measurements in binary data

It is not uncommon to encounter a randomized clinical trial (RCT) in which each patient is treated with several courses of therapies and his/her response is taken after treatment with each course because of the nature of a treatment design for a disease. On the basis of a simple multiplicative risk model proposed elsewhere for repeated binary measurements, we derive the maximum likelihood estimator (MLE) for the proportion ratio (PR) of responses between two treatments in closed form without the need of modeling the complicated relationship between patient’s compliance and patient’s response. We further derive the asymptotic variance of the MLE and propose an asymptotic interval estimator for the PR using the logarithmic transformation. We also consider two other asymptotic interval estimators. One is derived from the principle of Fieller’s Theorem and the other is derived by using the randomization-based approach suggested elsewhere. To evaluate and compare the finite-sample performance of these interval estimators, we apply the Monte Carlo simulation. We find that the interval estimator using the logarithmic transformation of the MLE consistently outperforms the other two estimators with respect to efficiency. This gain in efficiency can be substantial especially when there are patients not complying with their assigned treatments. Finally, we employ the data regarding the trial of using macrophage colony stimulating factor (M-CSF) over three courses of intensive chemotherapies to reduce febrile neutropenia incidence for acute myeloid leukemia patients to illustrate the use of these estimators.     

Likelihood‐based Inference with Missing Data Under Missing‐at‐Random

Likelihood‐based inference with missing data is challenging because the observed log likelihood is often an (intractable) integration over the missing data distribution, which also depends on the unknown parameter. Approximating the integral by Monte Carlo sampling does not necessarily lead to a valid likelihood over the entire parameter space because the Monte Carlo samples are generated from a distribution with a fixed parameter value. We consider approximating the observed log likelihood based on importance sampling. In the proposed method, the dependency of the integral on the parameter is properly reflected through fractional weights. We discuss constructing a confidence interval using the profile likelihood ratio test. A Newton–Raphson algorithm is employed to find the interval end points. Two limited simulation studies show the advantage of the Wilks inference over the Wald inference in terms of power, parameter space conformity and computational efficiency. A real data example on salamander mating shows that our method also works well with high‐dimensional missing data.     

Nonparametric estimation of the mean function of a stochastic process with missing observations

In an attempt to identify similarities between methods for estimating a mean function with different types of response or observation processes, we explore a general theoretical framework for nonparametric estimation of the mean function of a response process subject to incomplete observations. Special cases of the response process include quantitative responses and discrete state processes such as survival processes, counting processes and alternating binary processes. The incomplete data are assumed to arise from a general response-independent observation process, which includes right- censoring, interval censoring, periodic observation, and mixtures of these as special cases. We explore two criteria for defining nonparametric estimators, one based on the sample mean of available data and the other inspired by the construction of Kaplan-Meier (or product-limit) estimator [J. Am. Statist. Assoc. 53 (1958) 457] for right-censored survival data. We show that under regularity conditions the estimated mean functions resulting from both criteria are consistent and converge weakly to Gaussian processes, and provide consistent estimators of their covariance functions. We then evaluate these general criteria for specific responses and observation processes, and show how they lead to familiar estimators for some response and observation processes and new estimators for others. We illustrate the latter with data from an recently completed AIDS clinical trial.     

A Spline‐Based Semiparametric Maximum Likelihood Estimation Method for the Cox Model with Interval‐Censored Data

Abstract. We propose a spline‐based semiparametric maximum likelihood approach to analysing the Cox model with interval‐censored data. With this approach, the baseline cumulative hazard function is approximated by a monotone B‐spline function. We extend the generalized Rosen algorithm to compute the maximum likelihood estimate. We show that the estimator of the regression parameter is asymptotically normal and semiparametrically efficient, although the estimator of the baseline cumulative hazard function converges at a rate slower than root‐n. We also develop an easy‐to‐implement method for consistently estimating the standard error of the estimated regression parameter, which facilitates the proposed inference procedure for the Cox model with interval‐censored data. The proposed method is evaluated by simulation studies regarding its finite sample performance and is illustrated using data from a breast cosmesis study.     

Benchmark profile and inferences for joint-exposure quantal data in quantitative risk assessment

Abstract

In risk assessment, it is often desired to make inferences on the minimum dose levels (benchmark doses or BMDs) at which a specific benchmark risk (BMR) is attained. The estimation and inferences of BMDs are well understood in the case of an adverse response to a single-exposure agent. However, the theory of finding BMDs and making inferences on the BMDs is much less developed for cases where the adverse effect of two hazardous agents is studied simultaneously. Deutsch and Piegorsch [2012. Benchmark dose profiles for joint-action quantal data in quantitative risk assessment. Biometrics 68(4):1313–22] proposed a benchmark modeling paradigm in dual exposure setting—adapted from the single-exposure setting—and developed a strategy for conducting full benchmark analysis with joint-action quantal data, and they further extended the proposed benchmark paradigm to continuous response outcomes [Deutsch, R. C., and W. W. Piegorsch. 2013. Benchmark dose profiles for joint-action continuous data in quantitative risk assessment. Biometrical Journal 55(5):741–54]. In their 2012 article, Deutsch and Piegorsch worked exclusively with the complementary log link for modeling the risk with quantal data. The focus of the current paper is on the logit link; particularly, we consider an Abbott-adjusted [A method of computing the effectiveness of an insecticide. Journal of Economic Entomology 18(2):265–7] log-logistic model for the analysis of quantal data with nonzero background response. We discuss the estimation of the benchmark profile (BMP)—a collection of benchmark points which induce the prespecified BMR—and propose different methods for building benchmark inferences in studies involving two hazardous agents. We perform Monte Carlo simulation studies to evaluate the characteristics of the confidence limits. An example is given to illustrate the use of the proposed methods.     

Semiparametric Inference for ROC Curves with Censoring

Abstract.  Comparison of two samples can sometimes be conducted on the basis of analysis of receiver operating characteristic (ROC) curves. A variety of methods of point estimation and confidence intervals for ROC curves have been proposed and well studied. We develop smoothed empirical likelihood-based confidence intervals for ROC curves when the samples are censored and generated from semiparametric models. The resulting empirical log-likelihood function is shown to be asymptotically chi-squared. Simulation studies illustrate that the proposed empirical likelihood confidence interval is advantageous over the normal approximation-based confidence interval. A real data set is analysed using the proposed method.     

BAYESIAN BETA REGRESSION: APPLICATIONS TO HOUSEHOLD EXPENDITURE DATA AND GENETIC DISTANCE BETWEEN FOOT-AND-MOUTH DISEASE VIRUSES

There is considerable interest in understanding how factors such as time and geographic distance between isolates might influence the evolutionary direction of foot‐and‐mouth disease. Genetic differences between viruses can be measured as the proportion of nucleotides that differ for a given sequence or gene. We present a Bayesian hierarchical regression model for the statistical analysis of continuous data with sample space restricted to the interval (0, 1). The data are modelled using beta distributions with means that depend on covariates through a link function. We discuss methodology for: (i) the incorporation of informative prior information into an analysis; (ii) fitting the model using Markov chain Monte Carlo sampling; (iii) model selection using Bayes factors; and (iv) semiparametric beta regression using penalized splines. The model was applied to two different datasets.     

Nonparametric confidence intervals for location in time series data

We extend the confidence interval construction procedure for location for symmetric iid data using the one-sample Wilcoxon signed rank statistic (T⁺) to stationary time series data. We propose a normal approximation procedure when explicit knowledge of the underlying dependence structure/distribution is unknown. By conducting extensive simulations from linear and nonlinear time series models, we show that the extended procedure is a strong contender for use in the construction of confidence intervals in time series analysis. Finally we demonstrate real application implementations in two case studies.