In an ideal world, all bioinformatics tools would be made available via the Web as a web service with an API, as well as a standalone package to download for local use. This is rarely the case and sometimes, even where one or the other is available, factors such as ... [Read more...]

Check them out. Here are thirty homoskedastic ones: __ homo.wiener for (j in 1:30) {  for (i in 2:length(homo.wiener)) {          homo.wiener[i,j] for (j in 1:30) {        plot( homo.wiener[,j],           type = "l", col = rgb(.1,.... [Read more...]

After a terrific run this morning to the top of Arthur’s Seat, and then around (the ribs are feeling fine, now!), the Bayes-250 talks were exhilarating and challenging. Jim Smith gave an introduction to the challenges of getting different experts to collaborate on a complex risk assessment, much in ... [Read more...]

When I received this book, Handbook of fitting statistical distributions with R, by Z. Karian and E.J. Dudewicz,  from/for the Short Book Reviews section of the International Statistical Review, I was obviously impressed by its size (around 1700 pages and 3 kilos…). From briefly glancing at the table of contents, ... [Read more...]

Like last year, here are the most popular posts since last August: Home page 92,982 In{s}a(ne)!! 6,803 “simply start over and build something better” 5,834 Julien on R shortcomings 2,373 Parallel processing of independent Metropolis-Hastings algorithms 1,455 Do we need an integrated Bayesian/likelihood inference? 1,361 Coincidence in lotteries 1,256 #2 blog for the statistics ... [Read more...]

Once again, meaningless figures are published about a man who won the French lottery (Le Loto) for the second time. The reported probability of the event is indeed one chance out of 363 (US) trillions (i.e., billions in the metric system. or 1012)… This number is simply the square of which ... [Read more...]

“In the end, it really is just a matter of choosing the relevant parts of mathematics and ignoring the rest. Of course, the hard part is deciding what is irrelevant.” Somehow, I had missed the first edition of this book and thus I started reading it this afternoon with a ... [Read more...]

“My interpretation of [Leland Wilkinson’s] grammar [of statistical graphics]: —Data is the most important thing, and the thing that you bring to the table. —Geometric objects … what you actually see on the plot: points, lines, polygons, etc. ... [Read more...]

“My interpretation of [Leland Wilkinson’s] grammar [of statistical graphics]: —Data is the most important thing, and the thing that you bring to the table. —Geometric objects … what you actually see on the plot: points, lines, polygons, etc. ... [Read more...]

Here is an email I received from Umberto: I have a doubt regarding the tempered transitions method you considered in your JASA article with Celeux and Hurn. On page 961 you detail the several steps for building a proposal for a given distribution by simulating through l tempered power densities. I ... [Read more...]

The title says “things” but conferences are mainly about people. Some of it can be serendipitous.  For example, one day I sat next to Jonathan Rougier at lunch because I had a question for him about climate models.  When Jonathan left, I started a conversation with the person on my ... [Read more...]

For once, here is a book review I wrote in French about the book Le logiciel R, written by Pierre Lafaye de Micheaux (Université de Montréal), Rémy Drouilhet (Université de Grenoble 2) and Benoît Liquet (Université de Bordeaux 2): Ce livre édité par Springer (dans la même collection ... [Read more...]

“It seems quite absurd to reject an EP-based approach, if the only alternative is an ABC approach based on summary statistics, which introduces a bias which seems both larger (according to our numerical examples) and more arbitrary, in the sense that in real-world applications one has little intuition and even ... [Read more...]

Which topics are the most popular at the BioStar bioinformatics Q&A site? One source of data is the tags used for questions. Tags are somewhat arbitrary of course, but fortunately BioStar has quite an active community, so “bad” tags are usually edited to improve them. Hint: if your question ... [Read more...]

Over at the ExploringDataBlog, Ron Pearson just wrote a post about the cases when means are useless. In fact, it’s possible to calculate a whole load of stats on your data and still not really understand it. The canonical dataset for demonstrating this (spoiler alert: if you are doing ... [Read more...]

Decision Science News is no stranger to misleading infographics in free New York newspapers. We could stop reading them entirely, but we find that playing "spot the infographic flaw" makes time fly on the subway. Recently we saw the above graphic in a paper called Metro. Can you spot the ... [Read more...]

I’ve been thinking a lot about what it means for two variables to be correlated.  Scientists throw around the term like it’s uniformly understood, but I fear that an understanding of the concept is elusive to substantive researchers who aren’t interested in empirical methods, except as a ... [Read more...]

A surprising paper came out in the last issue of Statistical Science, linking martingales and Bayes factors. In the historical part, the authors (Shafer, Shen, Vereshchagin and Vovk) recall that martingales were popularised by Martin-Löf, who is also influential in the theory of algorithmic randomness. A property of test ... [Read more...]

Programmers should definitely know how to use R. I don’t mean they should switch from their current language to R, but they should think of R as a handy tool during development.Again and again I find myself working with Java code like the following. td.linenos { background-color: #f0... [Read more...]

I got a paper (unavailable online) to referee about testing for the order (i.e. the number of components) of a normal mixture. Although this is an easily spelled problem, namely estimate k in I came to the conclusion that it is a kind of ill-posed problem. Without a clear ... [Read more...]