Bayesian fractional polynomials

This paper sets out to implement the Bayesian paradigm for fractional polynomial models under the assumption of normally distributed error terms. Fractional polynomials widen the class of ordinary polynomials and offer an additive and transportable modelling approach. The methodology is based on a Bayesian linear model with a quasi-default hyper-g prior and combines variable selection with parametric modelling of additive effects. A Markov chain Monte Carlo algorithm for the exploration of the model space is presented. This theoretically well-founded stochastic search constitutes a substantial improvement to ad hoc stepwise procedures for the fitting of fractional polynomial models. The method is applied to a data set on the relationship between ozone levels and meteorological parameters, previously analysed in the literature.     

A Semi‐parametric Transformation Frailty Model for Semi‐competing Risks Survival Data

In the analysis of semi‐competing risks data interest lies in estimation and inference with respect to a so‐called non‐terminal event, the observation of which is subject to a terminal event. Multi‐state models are commonly used to analyse such data, with covariate effects on the transition/intensity functions typically specified via the Cox model and dependence between the non‐terminal and terminal events specified, in part, by a unit‐specific shared frailty term. To ensure identifiability, the frailties are typically assumed to arise from a parametric distribution, specifically a Gamma distribution with mean 1.0 and variance, say, σ². When the frailty distribution is misspecified, however, the resulting estimator is not guaranteed to be consistent, with the extent of asymptotic bias depending on the discrepancy between the assumed and true frailty distributions. In this paper, we propose a novel class of transformation models for semi‐competing risks analysis that permit the non‐parametric specification of the frailty distribution. To ensure identifiability, the class restricts to parametric specifications of the transformation and the error distribution; the latter are flexible, however, and cover a broad range of possible specifications. We also derive the semi‐parametric efficient score under the complete data setting and propose a non‐parametric score imputation method to handle right censoring; consistency and asymptotic normality of the resulting estimators is derived and small‐sample operating characteristics evaluated via simulation. Although the proposed semi‐parametric transformation model and non‐parametric score imputation method are motivated by the analysis of semi‐competing risks data, they are broadly applicable to any analysis of multivariate time‐to‐event outcomes in which a unit‐specific shared frailty is used to account for correlation. Finally, the proposed model and estimation procedures are applied to a study of hospital readmission among patients diagnosed with pancreatic cancer.     

An evaluation of a non-parametric method of estimating semi-variograms of isotropic spatial processes

Semi-variograms are useful for describing the correlation strucure of spatial random variables. Valid semi-variograms must be conditionally negative definite. To ensure this restriction when estimating these functions, a valid parametric model is typically fitted to a sample semi-variogram. Recently, a method of fitting valid semi-variograms without having to choose a parametric family has been described in the literature. The method is based on the spectral representation of positive definite functions. In this paper, the method is evaluated using simulated data. The fits obtained using the non-parametric method are compared with fits obtained by fitting four parametric models (exponential, Gaussian, rational quadratic and power) to simulated data using non-linear least squares. The comparisons are based on the integrated squared errors of the resulting fits. The non-parametric estimator always resulted in fits that were as good as those obtained using the parametric models. The non-parametric method is faster, easier to use and more objective than the parametric methods. Some examples are presented.     

Bayesian analysis of longitudinal ordered data with flexible random effects using McMC: application to diabetic macular Edema data

In the analysis of correlated ordered data, mixed-effect models are frequently used to control the subject heterogeneity effects. A common assumption in fitting these models is the normality of random effects. In many cases, this is unrealistic, making the estimation results unreliable. This paper considers several flexible models for random effects and investigates their properties in the model fitting. We adopt a proportional odds logistic regression model and incorporate the skewed version of the normal, Student's t and slash distributions for the effects. Stochastic representations for various flexible distributions are proposed afterwards based on the mixing strategy approach. This reduces the computational burden being performed by the McMC technique. Furthermore, this paper addresses the identifiability restrictions and suggests a procedure to handle this issue. We analyze a real data set taken from an ophthalmic clinical trial. Model selection is performed by suitable Bayesian model selection criteria.     

Bayesian image analysis with Markov chain Monte Carlo and coloured continuum triangulation models

It is now possible to carry out Bayesian image segmentation from a continuum parametric model with an unknown number of regions. However, few suitable parametric models exist. We set out to model processes which have realizations that are naturally described by coloured planar triangulations. Triangulations are already used, to represent image structure in machine vision, and in finite element analysis, for domain decomposition. However, no normalizable parametric model, with realizations that are coloured triangulations, has been specified to date. We show how this must be done, and in particular we prove that a normalizable measure on the space of triangulations in the interior of a fixed simple polygon derives from a Poisson point process of vertices. We show how such models may be analysed by using Markov chain Monte Carlo methods and we present two case-studies, including convergence analysis.     

Nonlinear voxel-based modelling of the haemodynamic response in fMRI

A common assumption for data analysis in functional magnetic resonance imaging is that the response signal can be modelled as the convolution of a haemodynamic response (HDR) kernel with a stimulus reference function. Early approaches modelled spatially constant HDR kernels, but more recently spatially varying models have been proposed. However, convolution limits the flexibility of these models and their ability to capture spatial variation. Here, a range of (nonlinear) parametric curves are fitted by least squares minimisation directly to individual voxel HDRs (i.e., without using convolution). A ‘constrained gamma curve’ is proposed as an efficient form for fitting the HDR at each individual voxel. This curve allows for spatial variation in the delay of the HDR, but places a global constraint on the temporal spread. The approach of directly fitting individual parameters of HDR shape is demonstrated to lead to an improved fit of response estimates.     

Computational methods for local regression

Local regression is a nonparametric method in which the regression surface is estimated by fitting parametric functions locally in the space of the predictors using weighted least squares in a moving fashion similar to the way that a time series is smoothed by moving averages. Three computational methods for local regression are presented. First, fast surface fitting and evaluation is achieved by building ak-d tree in the space of the predictors, evaluating the surface at the corners of the tree, and then interpolating elsewhere by blending functions. Second, surfaces are made conditionally parametric in any proper subset of the predictors by a simple alteration of the weighting scheme. Third degree-of-freedom quantities that would be extremely expensive to compute exactly are approximated, not by numerical methods, but through a statistical model that predicts the quantities from the trace of the hat matrix, which can be computed easily.     

Estimation on semi-functional linear errors-in-variables models

Abstract

Semi-functional linear regression models are important in practice. In this paper, their estimation is discussed when function-valued and real-valued random variables are all measured with additive error. By means of functional principal component analysis and kernel smoothing techniques, the estimators of the slope function and the non parametric component are obtained. To account for errors in variables, deconvolution is involved in the construction of a new class of kernel estimators. The convergence rates of the estimators of the unknown slope function and non parametric component are established under suitable norm and conditions. Simulation studies are conducted to illustrate the finite sample performance of our method.     

Empirical likelihood based variable selection

Information criteria form an important class of model/variable selection methods in statistical analysis. Parametric likelihood is a crucial part of these methods. In some applications such as the generalized linear models, the models are only specified by a set of estimating functions. To overcome the non-availability of well defined likelihood function, the information criteria under empirical likelihood are introduced. Under this setup, we successfully solve the existence problem of the profile empirical likelihood due to the over constraint in variable selection problems. The asymptotic properties of the new method are investigated. The new method is shown to be consistent at selecting the variables under mild conditions. Simulation studies find that the proposed method has comparable performance to the parametric information criteria when a suitable parametric model is available, and is superior when the parametric model assumption is violated. A real data set is also used to illustrate the usefulness of the new method.     

Bayesian calibration of computer models

We consider prediction and uncertainty analysis for systems which are approximated using complex mathematical models. Such models, implemented as computer codes, are often generic in the sense that by a suitable choice of some of the model's input parameters the code can be used to predict the behaviour of the system in a variety of specific applications. However, in any specific application the values of necessary parameters may be unknown. In this case, physical observations of the system in the specific context are used to learn about the unknown parameters. The process of fitting the model to the observed data by adjusting the parameters is known as calibration. Calibration is typically effected by ad hoc fitting, and after calibration the model is used, with the fitted input values, to predict the future behaviour of the system. We present a Bayesian calibration technique which improves on this traditional approach in two respects. First, the predictions allow for all sources of uncertainty, including the remaining uncertainty over the fitted parameters. Second, they attempt to correct for any inadequacy of the model which is revealed by a discrepancy between the observed data and the model predictions from even the best-fitting parameter values. The method is illustrated by using data from a nuclear radiation release at Tomsk, and from a more complex simulated nuclear accident exercise.     

Boosting techniques for nonlinear time series models

Many of the popular nonlinear time series models require a priori the choice of parametric functions which are assumed to be appropriate in specific applications. This approach is mainly used in financial applications, when sufficient knowledge is available about the nonlinear structure between the covariates and the response. One principal strategy to investigate a broader class on nonlinear time series is the Nonlinear Additive AutoRegressive (NAAR) model. The NAAR model estimates the lags of a time series as flexible functions in order to detect non-monotone relationships between current and past observations. We consider linear and additive models for identifying nonlinear relationships. A componentwise boosting algorithm is applied for simultaneous model fitting, variable selection, and model choice. Thus, with the application of boosting for fitting potentially nonlinear models we address the major issues in time series modelling: lag selection and nonlinearity. By means of simulation we compare boosting to alternative nonparametric methods. Boosting shows a strong overall performance in terms of precise estimations of highly nonlinear lag functions. The forecasting potential of boosting is examined on the German industrial production (IP); to improve the model’s forecasting quality we include additional exogenous variables. Thus we address the second major aspect in this paper which concerns the issue of high dimensionality in models. Allowing additional inputs in the model extends the NAAR model to a broader class of models, namely the NAARX model. We show that boosting can cope with large models which have many covariates compared to the number of observations.     

Fitting linear regression models to censored data by least squares and maximum likelihood methods

Several approaches have been suggested for fitting linear regression models to censored data. These include Cox's propor­tional hazard models based on quasi-likelihoods. Methods of fitting based on least squares and maximum likelihoods have also been proposed. The methods proposed so far all require special purpose optimization routines. We describe an approach here which requires only a modified standard least squares routine.

We present methods for fitting a linear regression model to censored data by least squares and method of maximum likelihood. In the least squares method, the censored values are replaced by their expectations, and the residual sum of squares is minimized. Several variants are suggested in the ways in which the expect­ation is calculated. A parametric (assuming a normal error model) and two non-parametric approaches are described. We also present a method for solving the maximum likelihood equations in the estimation of the regression parameters in the censored regression situation. It is shown that the solutions can be obtained by a recursive algorithm which needs only a least squares routine for optimization. The suggested procesures gain considerably in computational officiency. The Stanford Heart Transplant data is used to illustrate the various methods.     

Semiparametric Negative Binomial Regression Models

Negative-binomial (NB) regression models have been widely used for analysis of count data displaying substantial overdispersion (extra-Poisson variation). However, no formal lack-of-fit tests for a postulated parametric model for a covariate effect have been proposed. Therefore, a flexible parametric procedure is used to model the covariate effect as a linear combination of fixed-knot cubic basis splines or B-splines. Within the proposed modeling framework, a log-likelihood ratio test is constructed to evaluate the adequacy of a postulated parametric form of the covariate effect. Simulation experiments are conducted to study the power performance of the proposed test.     

Mixtures of general location model with factor analyzer covariance structure for clustering mixed type data

Cluster analysis is one of the most widely used method in statistical analyses, in which homogeneous subgroups are identified in a heterogeneous population. Due to the existence of the continuous and discrete mixed data in many applications, so far, some ordinary clustering methods such as, hierarchical methods, k-means and model-based methods have been extended for analysis of mixed data. However, in the available model-based clustering methods, by increasing the number of continuous variables, the number of parameters increases and identifying as well as fitting an appropriate model may be difficult. In this paper, to reduce the number of the parameters, for the model-based clustering mixed data of continuous (normal) and nominal data, a set of parsimonious models is introduced. Models in this set are extended, using the general location model approach, for modeling distribution of mixed variables and applying factor analyzer structure for covariance matrices. The ECM algorithm is used for estimating the parameters of these models. In order to show the performance of the proposed models for clustering, results from some simulation studies and analyzing two real data sets are presented.     

A parametric model fitting time to first event for overdispersed data: application to time to relapse in multiple sclerosis

In this article, we propose a parametric model for the distribution of time to first event when events are overdispersed and can be properly fitted by a Negative Binomial distribution. This is a very common situation in medical statistics, when the occurrence of events is summarized as a count for each patient and the simple Poisson model is not adequate to account for overdispersion of data. In this situation, studying the time of occurrence of the first event can be of interest. From the Negative Binomial distribution of counts, we derive a new parametric model for time to first event and apply it to fit the distribution of time to first relapse in multiple sclerosis (MS). We develop the regression model with methods for covariate estimation. We show that, as the Negative Binomial model properly fits relapse counts data, this new model matches quite perfectly the distribution of time to first relapse, as tested in two large datasets of MS patients. Finally we compare its performance, when fitting time to first relapse in MS, with other models widely used in survival analysis (the semiparametric Cox model and the parametric exponential, Weibull, log-logistic and log-normal models).     

A new semiparametric Weibull cure rate model: fitting different behaviors within GAMLSS

ABSTRACT

We propose a new semiparametric Weibull cure rate model for fitting nonlinear effects of explanatory variables on the mean, scale and cure rate parameters. The regression model is based on the generalized additive models for location, scale and shape, for which any or all distribution parameters can be modeled as parametric linear and/or nonparametric smooth functions of explanatory variables. We present methods to select additive terms, model estimation and validation, where all computational codes are presented in a simple way such that any R user can fit the new model. Biases of the parameter estimates caused by models specified erroneously are investigated through Monte Carlo simulations. We illustrate the usefulness of the new model by means of two applications to real data. We provide computational codes to fit the new regression model in the R software.     

The glm log-rank test:general linear modeling of log-rank scores as a method of analysis for survival data

The use of general linear modeling (GLM) procedures based on log-rank scores is proposed for the analysis of survival data and compared to standard survival analysis procedures. For the comparison of two groups, this approach performed similarly to the traditional log-rank test. In the case of more complicated designs - without ties in the survival times - the approach was only marginally less powerful than tests from proportional hazards models, and clearly less powerful than a likelihood ratio test for a fully parametric model; however, with ties in the survival time, the approach proved more powerful than tests from Cox's semi-parametric proportional hazards procedure. The method appears to provide a reasonably powerful alternative for the analysis of survival data, is easily used in complicated study designs, avoids (semi-)parametric assumptions, and is quite computationally easy and inexpensive to employ.     

Exploratory data analysis for counts using the empirical probability generating function 1

We present a graphical method based on the empirical probability generating function for preliminary statistical analysis of distributions for counts. The method is especially useful in fitting a Poisson model, or for identifying alternative models as well as possible outlying observations from general discrete distributions.     

An extension of parametric ROC analysis for calculating diagnostic accuracy when underlying distributions are mixture of Gaussian

The semiparametric LABROC approach of fitting binormal model for estimating AUC as a global index of accuracy has been justified (except for bimodal forms), while for estimating a local index of accuracy such as TPF, it may lead to a bias in severe departure of data from binormality. We extended parametric ROC analysis for quantitative data when one or both pair members are mixture of Gaussian (MG) in particular for bimodal forms. We analytically showed that AUC and TPF are a mixture of weighting parameters of different components of AUCs and TPFs of a mixture of underlying distributions. In a simulation study of six configurations of MG distributions:{bimodal, normal} and {bimodal, bimodal} pairs, the parameters of MG distributions were estimated using the EM algorithm. The results showed that the estimated AUC from our proposed model was essentially unbiased, and that the bias in the estimated TPF at a clinically relevant range of FPF was roughly 0.01 for a sample size of n=100/100. In practice, with severe departures from binormality, we recommend an extension of the LABROC and software development for future research to allow for each member of the pair of distributions to be a mixture of Gaussian that is a more flexible parametric form.     

Fitting multiplicative models by robust alternating regressions

In this paper a robust approach for fitting multiplicative models is presented. Focus is on the factor analysis model, where we will estimate factor loadings and scores by a robust alternating regression algorithm. The approach is highly robust, and also works well when there are more variables than observations. The technique yields a robust biplot, depicting the interaction structure between individuals and variables. This biplot is not predetermined by outliers, which can be retrieved from the residual plot. Also provided is an accompanying robust R ²-plot to determine the appropriate number of factors. The approach is illustrated by real and artificial examples and compared with factor analysis based on robust covariance matrix estimators. The same estimation technique can fit models with both additive and multiplicative effects (FANOVA models) to two-way tables, thereby extending the median polish technique.