Comment: Bayesian Checking of the Second Levels of Hierarchical Models

Comment: Bayesian Checking of the Second Levels of Hierarchical Models [arXiv:0802.0743]Comment: Published in at http://dx.doi.org/10.1214/07-STS235D the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

A Bayesian \chi^2 test for goodness-of-fit

This article describes an extension of classical \chi^2 goodness-of-fit tests to Bayesian model assessment. The extension, which essentially involves evaluating Pearson's goodness-of-fit statistic at a parameter value drawn from its posterior distribution, has the important property that it is asymptotically distributed as a \chi^2 random variable on K-1 degrees of freedom, independently of the dimension of the underlying parameter vector. By examining the posterior distribution of this statistic, global goodness-of-fit diagnostics are obtained. Advantages of these diagnostics include ease of interpretation, computational convenience and favorable power properties. The proposed diagnostics can be used to assess the adequacy of a broad class of Bayesian models, essentially requiring only a finite-dimensional parameter vector and conditionally independent observations.Comment: Published at http://dx.doi.org/10.1214/009053604000000616 in the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

A simple model of unbounded evolutionary versatility as a largest-scale trend in organismal evolution

The idea that there are any large-scale trends in the evolution of biological organisms is highly controversial. It is commonly believed, for example, that there is a large-scale trend in evolution towards increasing complexity, but empirical and theoretical arguments undermine this belief. Natural selection results in organisms that are well adapted to their local environments, but it is not clear how local adaptation can produce a global trend. In this paper, I present a simple computational model, in which local adaptation to a randomly changing environment results in a global trend towards increasing evolutionary versatility. In this model, for evolutionary versatility to increase without bound, the environment must be highly dynamic. The model also shows that unbounded evolutionary versatility implies an accelerating evolutionary pace. I believe that unbounded increase in evolutionary versatility is a large-scale trend in evolution. I discuss some of the testable predictions about organismal evolution that are suggested by the model

Bayes factor functions for reporting outcomes of hypothesis tests

Bayes factors represent the ratio of probabilities assigned to data by competing scientific hypotheses. Drawbacks of Bayes factors are their dependence on prior specifications that define null and alternative hypotheses and difficulties encountered in their computation. To address these problems, we define Bayes factor functions (BFF) directly from common test statistics. BFFs depend on a single non-centrality parameter that can be expressed as a function of standardized effect sizes, and plots of BFFs versus effect size provide informative summaries of hypothesis tests that can be easily aggregated across studies. Such summaries eliminate the need for arbitrary P-value thresholds to define ``statistical significance.'' BFFs are available in closed form and can be computed easily from z, t, chi-squared, and F statistics