Archive for book review

implementing reproducible research [short book review]

Posted in Books, Kids, pictures, R, Statistics, Travel, University life with tags , , , , , , , , , , , on July 15, 2014 by xi'an

As promised, I got back to this book, Implementing reproducible research (after the pigeons had their say). I looked at it this morning while monitoring my students taking their last-chance R exam (definitely last chance as my undergraduate R course is not reconoduced next year). The book is in fact an edited collection of papers on tools, principles, and platforms around the theme of reproducible research. It obviously links with other themes like open access, open data, and open software. All positive directions that need more active support from the scientific community. In particular the solutions advocated through this volume are mostly Linux-based. Among the tools described in the first chapter, knitr appears as an alternative to sweave. I used the later a while ago and while I like its philosophy. it does not extend to situations where the R code within takes too long to run… (Or maybe I did not invest enough time to grasp the entire spectrum of sweave.) Note that, even though the book is part of the R Series of CRC Press, many chapters are unrelated to R. And even more [unrelated] to statistics.

This limitation is somewhat my difficulty with [adhering to] the global message proposed by the book. It is great to construct such tools that monitor and archive successive versions of code and research, as anyone can trace back the research steps conducting to the published result(s). Using some of the platforms covered by the book establishes for instance a superb documentation principle, going much further than just providing an “easy” verification tool against fraudulent experiments. The notion of a super-wiki where notes and preliminary versions and calculations (and dead ends and failures) would be preserved for open access is just as great. However this type of research processing and discipline takes time and space and human investment, i.e. resources that are sparse and costly. Complex studies may involve enormous amounts of data and, neglecting the notions of confidentiality and privacy, the cost of storing such amounts is significant. Similarly for experiments that require days and weeks of huge clusters. I thus wonder where those resources would be found (journals, universities, high tech companies, …?) for the principle to hold in full generality and how transient they could prove. One cannot expect the research time to garantee availability of those meta-documents for remote time horizons. Just as a biased illustration, checking the available Bayes’ notebooks meant going to a remote part of London at a specific time and with a preliminary appointment. Those notebooks are not available on line for free. But for how long?

“So far, Bob has been using Charlie’s old computer, using Ubuntu 10.04. The next day, he is excited to find the new computer Alice has ordered for him has arrived. He installs Ubuntu 12.04″ A. Davison et al.

Putting their principles into practice, the authors of Implementing reproducible research have made all chapters available for free on the Open Science Framework. I thus encourage anyone interesting in those principles (and who would not be?!) to peruse the chapters and see how they can benefit from and contribute to open and reproducible research.

revenge of the pigeons

Posted in Books, Kids, pictures, R, Statistics, Travel, University life with tags , , , , , , on June 24, 2014 by xi'an

pigeonpooWhile I had not had kamikaze pigeons hitting my windows for quite a while…, it may be that one of them decided to move to biological warfare: when I came back from Edinburgh, my office at the University was in a terrible state as a bird had entered through a tiny window opening and wrecked havoc on the room, dropping folders and rocks from my shelves and… leaving a most specific proof of its visit. This bird was particularly attracted by and aggressive against the above book, Implementing Reproducible Research, standing on top of my books to review for CHANCE. Obvious disclaimer: this reflects neither my opinion nor the University opinion about the book contents, but only the bird’s, which is solely responsible for its action!

Nonlinear Time Series just appeared

Posted in Books, R, Statistics, University life with tags , , , , , , , , , , , , , , , on February 26, 2014 by xi'an

My friends Randal Douc and Éric Moulines just published this new time series book with David Stoffer. (David also wrote Time Series Analysis and its Applications with Robert Shumway a year ago.) The books reflects well on the research of Randal and Éric over the past decade, namely convergence results on Markov chains for validating both inference in nonlinear time series and algorithms applied to those objects. The later includes MCMC, pMCMC, sequential Monte Carlo, particle filters, and the EM algorithm. While I am too close to the authors to write a balanced review for CHANCE (the book is under review by another researcher, before you ask!), I think this is an important book that reflects the state of the art in the rigorous study of those models. Obviously, the mathematical rigour advocated by the authors makes Nonlinear Time Series a rather advanced book (despite the authors’ reassuring statement that “nothing excessively deep is used”) more adequate for PhD students and researchers than starting graduates (and definitely not advised for self-study), but the availability of the R code (on the highly personal page of David Stoffer) comes to balance the mathematical bent of the book in the first and third parts. A great reference book!

Philosophy of Science, a very short introduction (and review)

Posted in Books, Kids, Statistics, Travel with tags , , , , , , , , , , , on November 3, 2013 by xi'an

When visiting the bookstore on the campus of the University of Warwick two weeks ago, I spotted this book, Philosophy of Science, a very short introduction, by Samir Okasha, and the “bargain” offer of getting two books for £10 enticed me to buy it along with a Friedrich Nietzsche, a very short introduction… (Maybe with the irrational hope that my daughter would take a look at those for her philosophy course this year!)

Popper’s attempt to show that science can get by without induction does not succeed.” (p.23)

Since this is [unsusrprisingly!] a very short introduction, I did not get much added value from the book. Nonetheless, it was an easy read for short trips in the metro and short waits here and there. And would be a good [very short] introduction to any one newly interested in the philosophy of sciences. The first chapter tries to define what science is, with reference to the authority of Popper (and a mere mention of Wittgenstein), and concludes that there is no clear-cut demarcation between science and pseudo-science. (Mathematics apparently does not constitute a science: “Physics is the most fundamental science of all”, p.55) I would have liked to see the quote from Friedrich Nietzsche

“It is perhaps just dawning on five or six minds that physics, too, is only an interpretation and exegesis of the world (to suit us, if I may say so!) and not a world-explanation.”

in Beyond Good and Evil. as it illustrates the main point of the chapter and maybe the book that scientific theories can never be proven true, Plus, it is often misinterpreted as a anti-science statement by Nietzsche. (Plus, it links both books I bought!) Continue reading

micro

Posted in Books, Kids with tags , , , , on May 18, 2013 by xi'an

“Indoctrinating children in proper environmental thought was a hallmark of the green movement.” M. Crichton, micro, p. ix

I believe I read most of Michael Crichton‘s novels and this posthumous version (completed by Richard Preston) is not very different in its style and pattern from the previous ones. micro delivers an efficient fast-paced techno-thriller that filled most of one afternoon when convalescing at home.  In that respect, it fills its intended role. I however feel this is one of the weakest novels in that the technological and scientific background is very poor. (The best Crichton’s novels are in my opinion The Andromeda Strain and Airframe. One of the last novels, State of Fear, carries a very anti-environmentalist and climatoskeptic  message similar to the above quote.)

“Perhaps the most important lesson to be learned by direct experience is that the natural world (…) represents a complex system and therefore we cannot understand it and we cannot predict its behavior. “ M. Crichton, micro, p. x

Indeed, the plot of micro is based on the assumption that there exists a technology that can miniaturise living and non-living objects to 1/100th of their original size without any short-term impact. I remember watching as a child Fantastic Voyage, where a miniaturised submarine goes inside a blood vessel to remove a tumor, and I sat in front of a neighbour’s TV, mesmerised by the idea more than by the (weak) plot. This was in the laste 60′s. I also remember a sci’fi’ book I read when a pre-teen, with a great cover, called The Forgotten Planet: nothing truly memorable, apart from the cover, but hey this was a 1954 book. Now, micro does not use a deeper theory to justify this miniaturisation and the remainder of the plot is just as weak: I cannot imagine  1/100th humans surviving more than a few minutes in a rain forest environment! The place is crawling with insects, all way faster and far more deadly than tiny humans with a pocket knife, but the heroes conveniently meet only one dangerous insect at a time, loosing only at most one member of the group each time (sorry for the spoiler!). (In fact, the earlier Prey was much better at involving nanotechnologies. ) The grad students are very charicaturesque as well, providing biological infodump at times when they should be frozen solid with fright. Provided they had not been eaten already. The final resolution of the thriller is just… grotesque! So wait until you are sick or recovering from being sick before embarking upon this micro and no so fantastic trip!

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