Archive for philogenetics

Nature tea[dbits]

Posted in Books, pictures, University life, Wines with tags , , , , , , , , , , , , , , , , on February 28, 2019 by xi'an

A very special issue of Nature (7 February 2019, vol. 556, no. 7742). With an outlook section on tea, plus a few research papers (and ads) on my principal beverage. News about the REF, Elsevier’s and Huawei’s woes with the University of California, the dangerous weakening of Title IX by the Trump administration, and a long report on the statistical analysis of Hurricane Maria deaths, involving mostly epidemiologists, but also Patrick Ball who took part in our Bayes for Good workshop at CIRM. Plus China’s food crisis and ways to reduce cropland losses and food waste. Concerning the tea part(y), a philogenetic study of different samples led to the theory that tea was domesticated thrice, twice in Yunnan (China) and once in Assam (India), with a divergence estimated at more than twenty thousand years ago. Another article on Pu-Ehr, with the potential impacts of climate change on this very unique tea. With a further remark that higher altitudes increase the anti-oxydant level of tea… And a fascinating description of agro-forestry where tea and vegetables are grown in a forest that regulates sun exposure, moisture evaporation, and soil nutrients.

nested sampling for philogenies

Posted in Statistics with tags , , , , , , , on March 3, 2017 by xi'an

“Methods to estimate the marginal likelihood should be sensitive to the prior choice. Non-informative priors should increase the contribution of low-likelihood regions of parameter space in the estimated marginal likelihood. Consequently, the prior choice should affect the estimated evidence.”

 In a most recent arXival, Maturana, Brewer, and Klaere discuss of the appeal of nested sampling for conducting model choice in philogenetic models. In comparison with the “generalized steppingstone sampling” method, which represents the evidence as a product of ratios of evidences (Fan et al., 2011). And which I do not think I have previously met, with all references provided therein relating to Bayesian philogenetics, apparently. The stepping stone approach relies on a sequence of tempered targets, moving from a reference distribution to the real target as a temperature β goes from zero to one. (The paper also mentions thermodynamic integration as too costly.) Nested sampling—much discussed on this blog!—is presented in this paper as having the ability to deal with partly convex likelihoods, although I do not really get how or why. (As there is nothing new in the fairly pedagogical pretentation of nested sampling therein.) Nothing appears to be mentioned about the difficulty to handle multimodal as high likelihood isolated regions are unlikely to be sampled from poorly weighted priors (by which I mean that a region with significant likelihood mass is unlikely to get sampled if the prior distribution gives little prior weight to that region). The novelty in the paper is to compare nested sampling with generalized steppingstone sampling and path sampling on several phylogenetic examples. I did not spot computing time mentioned there. As usual with examples, my reservation is that the conclusions drawn for one particular analysis of one (three) particular example(s) does not convey a general method about the power and generality of a method. Even though I acknowledge that nested sampling is on principle operational in wide generality.