Estimation of a covariance matrix or its inverse plays a central role in many statistical methods. For these methods to work reliably, estimated matrices must not only be invertible but also well-conditioned. The current paper introduces a novel prior to ensure a well-conditioned maximum a posteriori (MAP) covariance estimate. The prior shrinks the sample covariance estimator towards a stable target and leads to a MAP estimator that is consistent and asymptotically efficient. Thus, the MAP estimator gracefully transitions towards the sample covariance matrix as the number of samples grows relative to the number of covariates. The utility of the MAP estimator is demonstrated in two standard applications-discriminant analysis and EM clustering-in challenging sampling regimes.
Many applied problems require a covariance matrix estimator that is not only invertible, but also well-conditioned (that is, inverting it does not amplify estimation error). For large-dimensional covariance matrices, the usual estimator--the sample covariance matrix--is typically not well-conditioned and may not even be invertible. This paper introduces an estimator that is both well-conditioned and more accurate than the sample covariance matrix asymptotically. This estimator is distribution-free and has a simple explicit formula that is easy to compute and interpret. It is the asymptotically optimal convex linear combination of the sample covariance matrix with the identity matrix. Optimality is meant with respect to a quadratic loss function, asymptotically as the number of observations and the number of variables go to infinity together. Extensive Monte Carlo confirm that the asymptotic results tend to hold well in finite sample. Many statistical applications require an estimate of a covariance matrix and or its inverse. When the matrix dimension is large compared to the sample size, which happens frequently, the sample covariance matrix is known to perform poorly and may suffer from ill-conditioning. There already exists an extensive literature concerning improved estimators in such situations. In the absence of further knowledge about the structure of the true covariance matrix, the most successful approach so far, arguably, has been shrinkage estimation. Shrinking the sample covariance matrix to a multiple of the identity, by taking a weighted average of the two, turns out to be equivalent to linearly shrinking the sample eigenvalues to their grand mean, while retaining the sample eigenvectors. Our paper extends this approach by considering nonlinear transformations of the sample eigenvalues. We show how to construct an estimator that is asymptotically equivalent to an oracle estimator suggested in previous work. As demonstrated in extensive Monte Carlo simulations, the resulting bona fide estimator can result in sizeable improvements over the sample covariance matrix and also over linear shrinkage. A method for simultaneous modelling of the Cholesky decomposition of several covariance matrices is presented. We highlight the conceptual and computational advantages of the unconstrained parameterization of the Cholesky decomposition and compare the results with those obtained using the classical spectral (eigenvalue) and variance-correlation decompositions. All these methods amount to decomposing complicated covariance matrices into ''dependence'' and ''variance'' components, and then modelling them virtually separately using regression techniques. The entries of the ''dependence'' component of the Cholesky decomposition have the unique advantage of being unconstrained so that further reduction of the dimension of its parameter space is fairly simple. Normal theory maximum likelihood estimates for complete and incomplete data are presented using iterative methods such as the EM (Expectation-Maximization) algorithm and their improvements. These procedures are illustrated using a dataset from a growth hormone longitudinal clinical trial.