Likelihood-ratio testing as a diagnostic method for small-sample regression.

It is known that under neutral mutation at a known mutation rate a sample of nucleotide sequences, within which there is assumed to be no recombination, allows estimation of the effective size of an isolated population. This paper investigates the case of very long sequences, where each pair of sequences allows a precise estimate of the divergence time of those two gene copies. The average divergence time of all pairs of copies estimates twice the effective population number and an estimate can also be derived from the number of segregating sites. One can alternatively estimate the genealogy of the copies. This paper shows how a maximum likelihood estimate of the effective population number can be derived from such a genealogical tree. The pairwise and the segregating sites estimates are shown to be much less efficient than this maximum likelihood estimate, and this is verified by computer simulation. The result implies that there is much to gain by explicitly taking the tree structure of these genealogies into account.

Likelihood Functions↗

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Random effects models with non-parametric priors.

We discuss the performance of non-parametric maximum likelihood (NPML) estimators for the distribution of a univariate random effect in the analysis of longitudinal data. For continuous data, we analyse generated and real data sets, and compare the NPML method to those that assume a Gaussian random effects distribution and to ordinary least squares. For binary outcomes we use generated data to study the moderate and large-sample performance of the NPML compared with a method based on a Gaussian random effect distribution in logistic regression. We find that estimated fixed effects are compatible for all approaches, but that appropriate standard errors for the NPML require adjusting the likelihood-based standard errors. We conclude that the non-parametric approach provides an attractive alternative to Gaussian-based methods, though additional evaluations are necessary before it can be recommended for general use.

Likelihood Functions↗