A Kolmogorov-Smirnov test for the molecular clock on Bayesian ensembles of phylogenies

Divergence date estimates are central to understand evolutionary processes and depend, in the case of molecular phylogenies, on tests of molecular clocks. Here we propose two non-parametric tests of strict and relaxed molecular clocks built upon a framework that uses the empirical cumulative distribution (ECD) of branch lengths obtained from an ensemble of Bayesian trees and well known non-parametric (one-sample and two-sample) Kolmogorov-Smirnov (KS) goodness-of-fit test. In the strict clock case, the method consists in using the one-sample Kolmogorov-Smirnov (KS) test to directly test if the phylogeny is clock-like, in other words, if it follows a Poisson law. The ECD is computed from the discretized branch lengths and the parameter $\lambda$ of the expected Poisson distribution is calculated as the average branch length over the ensemble of trees. To compensate for the auto-correlation in the ensemble of trees and pseudo-replication we take advantage of thinning and effective sample size, two features provided by Bayesian inference MCMC samplers. Finally, it is observed that tree topologies with very long or very short branches lead to Poisson mixtures and in this case we propose the use of the two-sample KS test with samples from two continuous branch length distributions, one obtained from an ensemble of clock-constrained trees and the other from an ensemble of unconstrained trees. Moreover, in this second form the test can also be applied to test for relaxed clock models. The use of a statistically equivalent ensemble of phylogenies to obtain the branch lengths ECD, instead of one consensus tree, yields considerable reduction of the effects of small sample size and provides again of power.Comment: 14 pages, 9 figures, 8 tables. Minor revision, additin of a new example and new title. Software: https://github.com/FernandoMarcon/PKS_Test.gi

Commercial real estate return distributions: a review of literature and empirical evidence

This paper review the literature on the distribution of commercial real estate returns. There is growing evidence that the assumption of normality in returns is not safe. Distributions are found to be peaked, fat-tailed and, tentatively, skewed. There is some evidence of compound distributions and non-linearity. Public traded real estate assets (such as property company or REIT shares) behave in a fashion more similar to other common stocks. However, as in equity markets, it would be unwise to assume normality uncritically. Empirical evidence for UK real estate markets is obtained by applying distribution fitting routines to IPD Monthly Index data for the aggregate index and selected sub-sectors. It is clear that normality is rejected in most cases. It is often argued that observed differences in real estate returns are a measurement issue resulting from appraiser behaviour. However, unsmoothing the series does not assist in modelling returns. A large proportion of returns are close to zero. This would be characteristic of a thinly-traded market where new information arrives infrequently. Analysis of quarterly data suggests that, over longer trading periods, return distributions may conform more closely to those found in other asset markets. These results have implications for the formulation and implementation of a multi-asset portfolio allocation strategy

Exact goodness-of-fit tests for censored dats

The statistic introduced in Fortiana and Grané (2003) is modified so that it can be used to test the goodness-of-fit of a censored sample, when the distribution function is fully specified. Exact and asymptotic distributions of three modified versions of this statistic are obtained and exact critical values are given for different sample sizes. Empirical power studies show the good performance of these statistics in detecting symmetrical alternatives

Statistical tests for whether a given set of independent, identically distributed draws does not come from a specified probability density

We discuss several tests for whether a given set of independent and identically distributed (i.i.d.) draws does not come from a specified probability density function. The most commonly used are Kolmogorov-Smirnov tests, particularly Kuiper's variant, which focus on discrepancies between the cumulative distribution function for the specified probability density and the empirical cumulative distribution function for the given set of i.i.d. draws. Unfortunately, variations in the probability density function often get smoothed over in the cumulative distribution function, making it difficult to detect discrepancies in regions where the probability density is small in comparison with its values in surrounding regions. We discuss tests without this deficiency, complementing the classical methods. The tests of the present paper are based on the plain fact that it is unlikely to draw a random number whose probability is small, provided that the draw is taken from the same distribution used in calculating the probability (thus, if we draw a random number whose probability is small, then we can be confident that we did not draw the number from the same distribution used in calculating the probability).Comment: 18 pages, 5 figures, 6 table

Asymptotic properties of a goodness-of-fit test based on maximum correlations

We study the efficiency properties of the goodness-of-fit test based on the Qn statistic introduced in Fortiana and Grané (2003) using the concepts of Bahadur asymptotic relative efficiency and Bahadur asymptotic optimality. We compare the test based on this statistic with those based on the Kolmogorov-Smirnov, the Cramér-von Mises and the Anderson-Darling statistics. We also describe the distribution families for which the test based on Qn is asymptotically optimal in the Bahadur sense and, as an application, we use this test to detect the presence of hidden periodicities in a stationary time series

Verification tools for probabilistic forecasts of continuous hydrological variables

In the present paper we describe some methods for verifying and evaluating probabilistic forecasts of hydrological variables. We propose an extension to continuous-valued variables of a verification method originated in the meteorological literature for the analysis of binary variables, and based on the use of a suitable cost-loss function to evaluate the quality of the forecasts. We find that this procedure is useful and reliable when it is complemented with other verification tools, borrowed from the economic literature, which are addressed to verify the statistical correctness of the probabilistic forecast. We illustrate our findings with a detailed application to the evaluation of probabilistic and deterministic forecasts of hourly discharge value

Two-dimensional Kolmogorov-type Goodness-of-fit Tests Based on Characterizations and their Asymptotic Efficiencies

In this paper new two-dimensional goodness of fit tests are proposed. They are of supremum-type and are based on different types of characterizations. For the first time a characterization based on independence of two statistics is used for goodness-of-fit testing. The asymptotics of the statistics is studied and Bahadur efficiencies of the tests against some close alternatives are calculated. In the process a theorem on large deviations of Kolmogorov-type statistics has been extended to the multidimensional case