Archive for R-bloggers


Posted in R, Statistics, University life with tags , , , , , , , on June 4, 2017 by xi'an

A few weeks ago and then some, I [as occasional blogger!] got contacted by to write a piece on this data-sharing platform. I then went and checked what this was all about, having the vague impression this was a platform where I could store and tun R codes, besides dropping collective projects, but from what I quickly read, it sounds more like being able to run R scripts from one’s machine using data and code stored on But after reading just one more blog entry I finally understood it is also possible to run R, SQL, NotebookJS (and LaTeX) directly on that platform, without downloading code or data to one’s machine. Which makes it a definitive plus with this site, as users can experiment with no transfer to their computer. Hence on a larger variety of platforms. While personally I do not [yet?] see how to use it for my research or [limited] teaching, it seems like an [yet another] interesting exploration of the positive uses of Internet to collaborate and communicate on scientific issues! With no opinion on privacy and data protection offered by the site, of course.

R for dummies

Posted in Books, R, Statistics, University life with tags , , , , , , , , on October 20, 2012 by xi'an

Just saw this nice review of R for dummies. And thought after this afternoon class that my students in the simulation course at Paris-Dauphine could clearly benefit from reading it! They in fact had a terrible time simulating a truncated normal distribution by accept-reject. As they could not get the notion of normalising constants… (Yes, indeed, this very truncated normal distribution!) Even the validity of simulating a normal variate until the truncation is satisfied was not obvious to them and they took forever to program the corresponding code. Anyway, I will certainly order the book to check for myself (after receiving Genetics for dummies to make sure I use the right vocabulary, even though it is a bit too light in the end…)! And write a review for CHANCE if it generates enough interest in doing so…

Planet Particle Physics [blog aggregator]

Posted in pictures, Statistics, University life with tags , , , , on January 16, 2012 by xi'an

I just received an email from Austria that the ‘Og is now part of a blog aggregator, Particle physics planet, along with an impressive list of particle physics blogs. It is certainly an honour to be associated with this blog, even though I fear my random ratiocinations very rarely reach the shore of the particle physics universe…. (I think this is my third “aggregation” after becoming part of R-bloggers and of

1500th, 3000th, &tc

Posted in Books, R, Statistics, University life with tags , , , , , , , , , , , , on January 8, 2012 by xi'an

As the ‘Og reached its 1500th post and 3000th comment at exactly the same time, a wee and only mildly interesting Sunday morning foray in what was posted so far and attracted the most attention (using the statistics provided by wordpress). The most visited posts:

Title Views
Home page 203,727
In{s}a(ne)!! 7,422
“simply start over and build something better” 6,264
Julien on R shortcomings 2,676
Sudoku via simulated annealing 2,402
About 1,876
Of black swans and bleak prospects 1,768
Solution manual to Bayesian Core on-line 1,628
Parallel processing of independent Metropolis-Hastings algorithms 1,625
Bayesian p-values 1,595
Bayes’ Theorem 1,537
#2 blog for the statistics geek?! 1,526
Do we need an integrated Bayesian/likelihood inference? 1,501
Coincidence in lotteries 1,396
Solution manual for Introducing Monte Carlo Methods with R 1,340
Julian Besag 1945-2010 1,293
Tornado in Central Park 1,093
The Search for Certainty 1,016

Hence, three R posts (incl. one by Julien and one by Ross Ihaka), three (critical) book reviews, two solution manuals, two general Bayesian posts, two computational entries, one paper (with Pierre Jacob and Murray Smith), one obituary, and one photograph news report… Altogether in line with the main purpose of the ‘Og. The most commented posts:

Post Comments
In{s}a(ne)!! 31
“simply start over and build something better” 30
That the likelihood principle does not hold… 23
Incoherent inference 23
Lack of confidence in ABC model choice 20
Parallel processing of independent Metropolis-Hastings algorithms 19
ABC model choice not to be trusted 17
MCMC with errors 16
Coincidence in lotteries 16
Bessel integral 14
Numerical analysis for statisticians 14

Not exactly the same as above! In particular, the posts about ABC model choice and our PNAS paper got into the list. At last, the top search terms:

Search Views
surfers paradise 1,050
benidorm 914
introducing monte carlo methods with r 514
andrew wyeth 398
mistborn 352
abele blanc 350
nested sampling 269
particle mcmc 269
bayesian p-value 263
julian besag 257
rites of love and math 249
millenium 237
bayesian p value 222
marie curie 221
bonsai 200

(out of which I removed the dozens of variations on xian’s blog). I find it rather sad that both top entries are beach towns that are completely unrelated to my lifestyle and to my vacation places. Overall, more than a  half of those entries do not strongly relate to the contents of the ‘Og (even though I did post at length about Saunderson’s Mistborn and Larsson’s Millenium trilogies). At last, the most popular clicks are

URL Clicks 1,243 1,039 583 575 531 529 505 404 395 372 298 298 288 282 279 257 256 253 243 216 203

which include links to my books on Amazon, Andrew Gelman’s, Terry Tao’s, Radford Neal’s and Romain François’s blogs, the CREST stat students collective blog, and a few arXiv papers of mine’s…

quantum forest

Posted in Books, R, Statistics, Travel, University life with tags , , , , , , , , on December 1, 2011 by xi'an

Thanks to a link on R-bloggers, I was introduced to Luis Apiolaza’s blog, Quantum Forest, which covers data analyses and R comments he encounters in his research as a quantitative forester/geneticist. And he works at the University of Canterbury, Christchurch, where I first taught from Bayesian Core in 2006. Which may be why he chose Bayesian Core as one of the three books he is currently reading to understand Bayesian statistics better. (The other two are Jim Albert’s Bayesian computation with R, and Bill Bolstad’s Introduction to Bayesian Statistics, which is not the one I reviewed recently.) Luis has just started the book but he mentions that “the book has managed to capture my interest”, which is real nice, and being annoyed by the self-contained label we put on the back cover. Which is a reaction I also got from some students when teaching the book for a week in Australia, as they thought they could take it without a probability background. Hopefully, we’ll manage to complete our revision before next summer!

A dubious statistic

Posted in Books, R, Statistics with tags , , on June 1, 2011 by xi'an

Following a link on R-bloggers, I ended up on this page (with a completely useless graph that only contained the pieces of information 5% in 1900 and 55% in 2000). The author (Ralph Keeney) reports on “A remarkable 55 percent of deaths for people age 15 to 64 can be attributed to decisions with readily available alternatives.” This sounded to me like a highly dubious finding… So I looked at the paper itself, reading that

“A personal decision is a situation where an individual can make a choice among two or more alternatives. This assumes that the individual recognizes that he or she has a choice and has control of this choice. Readily available alternatives are alternatives that the decision maker would have known about and could have chosen without investing much time or money.” Ralph Keeney

This categorisation of deaths is highly debatable, in that choice is not always that available! So I do not see how the author can assert which percentage of the individuals truly have control of the choice… (For instance, can people refuse doing dangerous jobs when they desperately need a job? or when the dangerousness is an abstract concept as, say, for a Fukushima worker? Is obesity a sheer matter of will?) Furthermore, the jump from 5% to 55% is also highly shaky: “Clearly, one should not put much credibility in this 22% for 1950 or the corresponding 5% for 1900”.  In the end, tt seems that the whole issue of the paper is about the amount of information: “in 1900 the knowledge about and ability to avoid many of the causes of death would seem to be much lower than in 2000”. So life has not been getting more dangerous or people sillier, simply information about the causes of deaths has become more widespread. I am thus surprised at the low level of academic input contained in the paper (look at the “life-saving decisions’!), which may actually explain for the echo it found on the blogosphere. (This post also appeared on the Statistics Forum.)

R-ecap [-16]

Posted in Books, R, University life with tags , , , , , , , on March 27, 2011 by xi'an

This morning, I noticed that none of my R related posts had appeared on R-bloggers for the past fortnight… After investigating, this was caused by…cut-and-paste! Indeed, when advertising about the special issue of TOMACS Arnaud Doucet and I edit about Monte Carlo methods in Statistics, I copied the main parts from the pdf announcement, straight out of Acrobat, and the word “field” was used, involving a ligature between the f and the i that did not get copied in proper UTF-8:

error on line 434 at column 330: Input is not proper UTF-8, indicate encoding ! Bytes: 0x0C 0×65 0x6C 0×64

So here are the entries in the ‘Og for the past 16 days that could have been of interest for R-bloggers readers: