An Object-Oriented Framework for Robust Multivariate Analysis

Taking advantage of the S4 class system of the programming environment R, which facilitates the creation and maintenance of reusable and modular components, an object-oriented framework for robust multivariate analysis was developed. The framework resides in the packages robustbase and rrcov and includes an almost complete set of algorithms for computing robust multivariate location and scatter, various robust methods for principal component analysis as well as robust linear and quadratic discriminant analysis. The design of these methods follows common patterns which we call statistical design patterns in analogy to the design patterns widely used in software engineering. The application of the framework to data analysis as well as possible extensions by the development of new methods is demonstrated on examples which themselves are part of the package rrcov.

Properties of principal component methods for functional and longitudinal data analysis

The use of principal component methods to analyze functional data is appropriate in a wide range of different settings. In studies of ``functional data analysis,'' it has often been assumed that a sample of random functions is observed precisely, in the continuum and without noise. While this has been the traditional setting for functional data analysis, in the context of longitudinal data analysis a random function typically represents a patient, or subject, who is observed at only a small number of randomly distributed points, with nonnegligible measurement error. Nevertheless, essentially the same methods can be used in both these cases, as well as in the vast number of settings that lie between them. How is performance affected by the sampling plan? In this paper we answer that question. We show that if there is a sample of $n$ functions, or subjects, then estimation of eigenvalues is a semiparametric problem, with root-$n$ consistent estimators, even if only a few observations are made of each function, and if each observation is encumbered by noise. However, estimation of eigenfunctions becomes a nonparametric problem when observations are sparse. The optimal convergence rates in this case are those which pertain to more familiar function-estimation settings. We also describe the effects of sampling at regularly spaced points, as opposed to random points. In particular, it is shown that there are often advantages in sampling randomly. However, even in the case of noisy data there is a threshold sampling rate (depending on the number of functions treated) above which the rate of sampling (either randomly or regularly) has negligible impact on estimator performance, no matter whether eigenfunctions or eigenvectors are being estimated.Comment: Published at http://dx.doi.org/10.1214/009053606000000272 in the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Principal arc analysis on direct product manifolds

We propose a new approach to analyze data that naturally lie on manifolds. We focus on a special class of manifolds, called direct product manifolds, whose intrinsic dimension could be very high. Our method finds a low-dimensional representation of the manifold that can be used to find and visualize the principal modes of variation of the data, as Principal Component Analysis (PCA) does in linear spaces. The proposed method improves upon earlier manifold extensions of PCA by more concisely capturing important nonlinear modes. For the special case of data on a sphere, variation following nongeodesic arcs is captured in a single mode, compared to the two modes needed by previous methods. Several computational and statistical challenges are resolved. The development on spheres forms the basis of principal arc analysis on more complicated manifolds. The benefits of the method are illustrated by a data example using medial representations in image analysis.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS370 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Robust functional principal components: A projection-pursuit approach

In many situations, data are recorded over a period of time and may be regarded as realizations of a stochastic process. In this paper, robust estimators for the principal components are considered by adapting the projection pursuit approach to the functional data setting. Our approach combines robust projection-pursuit with different smoothing methods. Consistency of the estimators are shown under mild assumptions. The performance of the classical and robust procedures are compared in a simulation study under different contamination schemes.Comment: Published in at http://dx.doi.org/10.1214/11-AOS923 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Covariance Estimation: The GLM and Regularization Perspectives

Finding an unconstrained and statistically interpretable reparameterization of a covariance matrix is still an open problem in statistics. Its solution is of central importance in covariance estimation, particularly in the recent high-dimensional data environment where enforcing the positive-definiteness constraint could be computationally expensive. We provide a survey of the progress made in modeling covariance matrices from two relatively complementary perspectives: (1) generalized linear models (GLM) or parsimony and use of covariates in low dimensions, and (2) regularization or sparsity for high-dimensional data. An emerging, unifying and powerful trend in both perspectives is that of reducing a covariance estimation problem to that of estimating a sequence of regression problems. We point out several instances of the regression-based formulation. A notable case is in sparse estimation of a precision matrix or a Gaussian graphical model leading to the fast graphical LASSO algorithm. Some advantages and limitations of the regression-based Cholesky decomposition relative to the classical spectral (eigenvalue) and variance-correlation decompositions are highlighted. The former provides an unconstrained and statistically interpretable reparameterization, and guarantees the positive-definiteness of the estimated covariance matrix. It reduces the unintuitive task of covariance estimation to that of modeling a sequence of regressions at the cost of imposing an a priori order among the variables. Elementwise regularization of the sample covariance matrix such as banding, tapering and thresholding has desirable asymptotic properties and the sparse estimated covariance matrix is positive definite with probability tending to one for large samples and dimensions.Comment: Published in at http://dx.doi.org/10.1214/11-STS358 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org