Lateral transfer in Stochastic Dollo models

Lateral transfer, a process whereby species exchange evolutionary traits through non-ancestral relationships, is a frequent source of model misspecification in phylogenetic inference. Lateral transfer obscures the phylogenetic signal in the data as the histories of affected traits are mosaics of the overall phylogeny. We control for the effect of lateral transfer in a Stochastic Dollo model and a Bayesian setting. Our likelihood is highly intractable as the parameters are the solution of a sequence of large systems of differential equations representing the expected evolution of traits along a tree. We illustrate our method on a data set of lexical traits in Eastern Polynesian languages and obtain an improved fit over the corresponding model without lateral transfer.Comment: Improvements suggested by reviewer

Coins falling in water

When a coin falls in water, its trajectory is one of four types determined by its dimensionless moment of inertia $I^\ast$ and Reynolds number Re: (A) steady; (B) fluttering; (C) chaotic; or (D) tumbling. The dynamics induced by the interaction of the water with the surface of the coin, however, makes the exact landing site difficult to predict a priori. Here, we describe a carefully designed experiment in which a coin is dropped repeatedly in water, so that we can determine the probability density functions (pdf) associated with the landing positions for each of the four trajectory types, all of which are radially symmetric about the center-drop line. In the case of the steady mode, the pdf is approximately Gaussian distributed, with variances that are small, indicating that the coin is most likely to land at the center, right below the point it is dropped from. For the other falling modes, the center is one of the least likely landing sites. Indeed, the pdf's of the fluttering, chaotic and tumbling modes are characterized by a "dip" around the center. For the tumbling mode, the pdf is a ring configuration about the center-line, with a ring width that depends on the dimensionless parameters $I^\ast$ and Re and height from which the coin is dropped. For the chaotic mode, the pdf is generally a broadband distribution spread out radially symmetrically about the center-line. For the steady and fluttering modes, the coin never flips, so the coin lands with the same side up as was dropped. For the chaotic mode, the probability of heads or tails is close to 0.5. In the case of the tumbling mode, the probability of heads or tails based on the height of the drop which determines whether the coin flips an even or odd number of times during descent

Low-coverage heats of adsorption. iii - alkali metal ions on tungsten, atom-metal interaction theory

Heats of adsorption of sodium, rubidium, and cesium ions on tungsten substrat

Exact Tests for Two-Way Contingency Tables with Structural Zeros

Fisher's exact test, named for Sir Ronald Aylmer Fisher, tests contingency tables for homogeneity of proportion. This paper discusses a generalization of Fisher's exact test for the case where some of the table entries are constrained to be zero. The resulting test is useful for assessing cases where the null hypothesis of conditional multinomial distribution is suspected to be false. The test is implemented in the form of a new R package, aylmer.