**A** chance occurrence on X validated: a question on an incomprehensible formula for Bayesian model choice: which, most unfortunately!, appeared in Bayesian Essentials with R! Eeech! It looks like one line in our *L ^{A}T_{E}X* file got erased and the likelihood part in the denominator altogether vanished. Apologies to all readers confused by this nonsensical formula!

## Archive for Bayesian Essentials with R

## a typo that went under the radar

Posted in Books, R, Statistics, University life with tags Bayesian Core, Bayesian Essentials with R, Bayesian model choice, cross validated, Jean-Michel Marin, model posterior probabilities, R, typos on January 25, 2017 by xi'an## tractable Bayesian variable selection: beyond normality

Posted in R, Statistics, University life with tags Bayesian Essentials with R, calibration, marginal density, maximum likelihood estimation, parametric family, R, two-piece error model, University of Warwick on October 17, 2016 by xi'an**D**avid Rossell and Francisco Rubio (both from Warwick) arXived a month ago a paper on non-normal variable selection. They use two-piece error models that preserve manageable inference and allow for simple computational algorithms, but also characterise the behaviour of the resulting variable selection process under model misspecification. Interestingly, they show that the existence of asymmetries or heavy tails leads to power losses when using the Normal model. The two-piece error distribution is made of two halves of location-scale transforms of the same reference density on the two sides of the common location parameter. In this paper, the density is either Gaussian or Laplace (i.e., exponential?). In both cases the (log-)likelihood has a nice compact expression (although it does not allow for a useful sufficient statistic). One is the L¹ version versus the other which is the L² version. Which is the main reason for using this formalism based on only two families of parametric distributions, I presume. (As mentioned in an earlier post, I do not consider those distributions as mixtures because the component of a given observation can always be identified. And because as shown in the current paper, maximum likelihood estimates can be easily derived.) The prior construction follows the non-local prior principles of Johnson and Rossell (2010, 2012) also discussed in earlier posts. The construction is very detailed and hence highlights how many calibration steps are needed in the process.

“Bayes factor rates are the same as when the correct model is assumed [but] model misspecification often causes a decrease in the power to detect truly active variables.”

When there are too many models to compare at once, the authors propose a random walk on the finite set of models (which does not require advanced measure-theoretic tools like reversible jump MCMC). One interesting aspect is that moving away from the normal to another member of this small family is driven by the density of the data under the marginal densities, which means moving only to interesting alternatives. But also sticking to the normal only for adequate datasets. In a sense this is not extremely surprising given that the marginal likelihoods (model-wise) are available. It is also interesting that on real datasets, one of the four models is heavily favoured against the others, be it Normal (6.3) or Laplace (6.4). And that the four model framework returns almost identical values when compared with a single (most likely) model. Although not immensely surprising when acknowledging that the frequency of the most likely model is 0.998 and 0.998, respectively.

“Our framework represents a middle-ground to add flexibility in a parsimonious manner that remains analytically and computationally tractable, facilitating applications where either p is large or n is too moderate to fit more flexible models accurately.”

Overall, I find the experiment quite conclusive and do not object [much] to this choice of parametric family in that it is always more general and generic than the sempiternal Gaussian model. That we picked in our Bayesian Essentials, following tradition. In a sense, it would be natural to pick the most general possible parametric family that allows for fast computations, if this notion does make any sense…

## Bayesian Essentials with R [book review]

Posted in Books, R, Statistics, University life with tags Bayesian Core, Bayesian Essentials with R, book review, Jean-Michel Marin, Kent State University, R, Technometrics, time series on July 28, 2016 by xi'an[A review of Bayesian Essentials that appeared in Technometrics two weeks ago, with the first author being rechristened Jean-Michael!]

“Overall this book is a very helpful and useful introduction to Bayesianmethods of data analysis. I found the use of R, the code in the book, and thecompanion R package, bayess, to be helpful to those who want to begin usingBayesian methods in data analysis. One topic that I would like to see added isthe use of Bayesian methods in change point problems, a topic that we founduseful in a recent article and which could be added to the time series chapter.Overall this is a solid book and well worth considering by its intended audience.”

David E. BOOTH

Kent State University

## Statistical rethinking [book review]

Posted in Books, Kids, R, Statistics, University life with tags Amazon, Bayes theorem, Bayesian data analysis, Bayesian Essentials with R, book review, CHANCE, code, convergence diagnostics, E.T. Jaynes, generalised linear models, golem, maths, matrix algebra, MCMC algorithms, mixtures of distributions, Monte Carlo Statistical Methods, Prague, R, robots, STAN, statistical modelling, Statistical rethinking on April 6, 2016 by xi'anStatistical Rethinking: A Bayesian Course with Examples in R and Stan is a new book by Richard McElreath that CRC Press sent me for review in CHANCE. While the book was already discussed on Andrew’s blog three months ago, and [rightly so!] enthusiastically recommended by Rasmus Bååth on Amazon, here are the reasons why I am quite impressed by Statistical Rethinking!

“Make no mistake: you will wreck Prague eventually.” (p.10)

While the book has a lot in common with Bayesian Data Analysis, from being in the same CRC series to adopting a pragmatic and weakly informative approach to Bayesian analysis, to supporting the use of STAN, it also nicely develops its own ecosystem and idiosyncrasies, with a noticeable Jaynesian bent. To start with, I like the highly personal style with clear attempts to make the concepts memorable for students by resorting to external concepts. The best example is the call to the myth of the golem in the first chapter, which McElreath uses as an warning for the use of statistical models (which almost are anagrams to golems!). Golems and models [and robots, another concept invented in Prague!] are man-made devices that strive to accomplish the goal set to them without heeding the consequences of their actions. This first chapter of Statistical Rethinking is setting the ground for the rest of the book and gets quite philosophical (albeit in a readable way!) as a result. In particular, there is a most coherent call against hypothesis testing, which by itself justifies the title of the book. Continue reading

## Introduction to Monte Carlo methods with R and Bayesian Essentials with R

Posted in Books, R, Statistics, University life with tags Bayesian Essentials with R, book sales, Brazil, copyright, Introduction to Monte Carlo Methods with R, Saudi Arabia, Springer-Verlag on June 26, 2015 by xi'an**H**ere are the download figures for my e-book with George as sent to me last week by my publisher Springer-Verlag. With an interesting surge in the past year. Maybe simply due to new selling strategies of the published rather to a wider interest in the book. (My royalties have certainly not increased!) Anyway thanks to all readers. As an aside for wordpress wannabe bloggers, I realised it is now almost impossible to write tables with WordPress, another illustration of the move towards small-device-supported blogs. Along with a new annoying “simpler” (or more accurately dumber) interface and a default font far too small for my eyesight. So I advise alternatives to wordpress that are more sympathetic to maths contents (e.g., using MathJax) and comfortable editing.

And the same for the e-book with Jean-Michel, which only appeared in late 2013. And contains more chapters than Introduction to Monte Carlo methods with R. Incidentally, a reader recently pointed out to me the availability of a pirated version of *The Bayesian Choice* on a Saudi (religious) university website. And of a pirated version of Introducing Monte Carlo with R on a Saõ Paulo (Brazil) university website. This may be alas inevitable, given the diffusion by publishers of e-chapters that can be copied with no limitations…

## Statistics month in Marseilles (CIRM)

Posted in Books, Kids, Mountains, pictures, Running, Statistics, Travel, University life, Wines with tags Bayesian Essentials with R, Bayesian statistics, bouillabaisse, calanques, Cassis, CIRM, CNRS, copulas, extremes, France, machine learning, Marseille, minicourse, SMF, stochastic processes on June 24, 2015 by xi'an**N**ext February, the fabulous Centre International de Recherche en Mathématiques (CIRM) in Marseilles, France, will hold a Statistics month, with the following programme over five weeks

- 1 – 6 February, 2016 Learning
- 8 – 12 February, 2016 Mathématical statistics
- 15 – 19 February, 2016 Processes
- 22 – 26 February, 2016 Extremes, Copulas and Actuarial Science
- 29 February – 4 March, 2016 Bayesian statistics and algorithms

Each week will see minicourses of a few hours (2-3) and advanced talks, leaving time for interactions and collaborations. (I will give one of those minicourses on Bayesian foundations.) The scientific organisers of the B’ week are Gilles Celeux and Nicolas Chopin.

The CIRM is a wonderful meeting place, in the mountains between Marseilles and Cassis, with many trails to walk and run, and hundreds of fantastic climbing routes in the Calanques at all levels. (In February, the sea is too cold to contemplate swimming. The good side is that it is not too warm to climb and the risk of bush fire is very low!) We stayed there with Jean-Michel Marin a few years ago when preparing Bayesian Essentials. The maths and stats library is well-provided, with permanent access for quiet working sessions. This is the French version of the equally fantastic German Mathematik Forschungsinstitut Oberwolfach. There will be financial support available from the supporting societies and research bodies, at least for young participants and the costs if any are low, for excellent food and excellent lodging. Definitely not a scam conference!

## solution manual for Bayesian Essentials with R

Posted in Books, Kids, Statistics, University life with tags Bayesian Core, Bayesian Essentials with R, lag polynomial, Lemer-Schur algorithm, solution manual, Springer-Verlag, stationarity on March 18, 2015 by xi'anThe solution manual to our *Bayesian Essentials with R* has just been arXived. If I link this completion with the publication date of the book itself, it sure took an unreasonable time to come out and sadly with no obvious reason or even less justification for the delay… Given the large overlap with the solution manual of the previous edition, *Bayesian Core*, this version should have been completed much much earlier but, paradoxically if in-line with the lengthy completion of the book istelf, this previous manual is one of the causes for the delay, as we thought the overlap allowed for self-study readers to check some of the exercises. Prodded by Hannah Bracken from Springer-Verlag, and unable to hire an assistant towards this task, I eventually decided to spend the few days required to clean up this solution manual, with the unintentional help from my sorry excuse for an Internet provider who accidentally cutting my home connection for a whole week so far…!

In the course of writing solutions, I stumbled upon one inexplicably worded exercise about the Lemer-Schur algorithm for testing stationarity, exercise that I had to rewrite from scratch. Apologies to any reader of *Bayesian Essentials with R* getting stuck on that exercise!!!