Changes in protein function can lead to changes in the selection acting on specific residues. This can often be detected as evolutionary rate changes at the sites in question. A maximum-likelihood method for detecting evolutionary rate shifts at specific protein positions is presented. The method determines significance values of the rate differences to give a sound statistical foundation for t...

We examine a test of a nonparametric regression function based on penalized spline smoothing. We show that, similarly to a penalized spline estimator, the asymptotic power of the penalized spline test falls into a small- K or a large-K scenarios characterized by the number of knots K and the smoothing parameter. However, the optimal rate of K and the smoothing parameter maximizing power for tes...

Latimer et al. (Reports, 9 September 2005, p. 1722) used an approximate likelihood function to estimate parameters of Hubbell's neutral model of biodiversity. Reanalysis with the exact likelihood not only yields different estimates but also shows that two similar likelihood maxima for very different parameter combinations can occur. This reveals a limitation of using species abundance data to g...

Autoregressive moving average (ARMA) models are useful statistical tools to examine the dynamical characteristics of ecological time-series data. Here, we illustrate the utility and challenges of applying ARMA (p,q) models, where p is the dimension of the autoregressive component of the model, and q is the dimension of the moving average component. We focus on parameter estimation and model sel...

Estimators of the conditional expectation, i.e., prediction, function involve a global bias-variance trade off. In some cases, an estimator that yields unbiased estimates of the conditional expectation for a particular partitioning of the data may be desirable. Such estimators are calibrated with respect to the partitioning. We identify the conditional expectation given a particular partitionin...

By introducing the asymptotic logarithmic likelihood ratio as a measure of the Markov approximation of arbitrary random fields on a uniformly bounded tree, by constructing a non-negative martingale on a uniformly bounded tree, a class of small deviation theorems of functionals and a class of small deviation theorems of the frequencies of occurrence of states for random fields on a uniformly bou...

After the Shewhart method was suggested for industrial applications, other applications such as surveillance for bioterrorism and financial transactions have come into focus. Also other methods for surveillance have followed. The relation between the Shewhart method and the followers is examined. A uniform presentation of methods, by expressions of likelihood ratios, facilitates the comparisons...

We study in this paper some nonparametric inference problems where the nonparametric maximum likelihood estimator (NPMLE) are not well defined. However, if we enlarge the parameter space, the NPMLE will be well defined. We propose to gradually shrink the enlarged parameter space by placing more and more restrictions on the parameter space, producing a sequence of (envelope) estimators. The appr...

We propose a class of transformation models for multivariate failure times. The class of transformation models generalize the usual gamma frailty model and yields a marginally linear transformation model for each failure time. Nonparametric maximum likelihood estimation is used for inference. The maximum likelihood estimators for the regression coefficients are shown to be consistent and asympt...