packed off!!!

Deliverance!!! We have at last completed our book! Bayesian Essentials with R is off my desk! In a final nitty-gritty day of compiling and recompiling the R package bayess and the LaTeX file, we have reached versions that were in par with our expectations. The package has been submitted to CRAN (it has gone back and forth a few times, with requests to lower the computing time in the examples: each example should take less than 10s, then 5s…), then accepted by CRAN, incl. a Windows version, and the book has be sent to Springer-Verlag. This truly is a deliverance for me as this book project has been on my work horizon almost constantly for more than the past two years, led to exciting times in Luminy, Carnon and Berlin, has taken an heavy toll on my collaborations and research activities, and was slowly turning into a unsavoury chore! I am thus delighted Jean-Michel and I managed to close the door before any disastrous consequence on either the book or our friendship could develop. Bayesian Essentials with R is certainly an improvement compared with Bayesian Core, primarily by providing a direct access to the R code. We dearly hope it will attract a wider readership by reducing the mathematical requirements (even though some parts are still too involved for most undergraduates) and we will keep testing it with our own students in Montpellier and Paris over the coming months. In the meanwhile, I just enjoy this feeling of renewed freedom!!!

local package delays

When Jean-Michel and I left Berlin, a month ago, I really thought we were that close to sending the new edition of Bayesian Core. Alas, we are not done yet for a series of reasons: leaving for India did not give me enough time to complete the help manual, some codes from the original version did not seem to work any longer, apparently jeopardising a whole chapter!, and the package did not seem to compile. Yesterday, we met again and made progress that makes me much more confident. For one thing, the R code that “did not work” was an original spreadsheet of Bayesian Core that we turned into functions towards the completion of the bayess package. However, due to sloppy programming at the time, we had used global variables that were called inside functions without being (explicitly) declared as variables. When those R codes got turned into functions, variables defined inside those functions were no longer global and recognised by the other functions defined within those same functions… Silly me! Once this issue got spotted by Jean-Michel, as well as the use of a few && instead of &’s, the whole problem unravelled rather quickly and we got a compiled package by the end of the day, even though some of the demos (reproducing the outcome found in the text) are still bugged. Stay tuned!

Core [still] minus one…

Another full day spent working with Jean-Michel Marin on the new edition of Bayesian Core (soon to be Bayesian Essentials with R!) and the remaining hierarchical Bayes chapter… I have reread and completed the regression and GLM chapters, sent to very friendly colleagues for a last round of comments. Now, I am essentially idle, waiting for Jean-Michel to finish his part on the hierarchical Bayes chapter, so that I can do the final editing.round. Jean-Michel had a very long day on that chapter, leaving Montpellier at 5am to return only at half past midnight, due to massive delays in the train schedule (which is why I always fly to Montpellier…)

Core minus one!

Jean-Michel Marin visited me in Paris last week and, besides taking part in Pierre’s PhD defence, we made enough progress to close two more chapters of the new edition of Bayesian Core (soon to be Bayesian Essentials with R!) This follows the good work session we had in Carnon where we also completed two chapters (although it was hard to convince anyone that renting a flat by the Mediterranean sea was at all connected with…work! While it was: the only breaks I took were my morning runs…). There just remains one single chapter to complete, now, the one on hierarchical Bayes models. By all means, I dearly want to see it done by November 1!!!

Core not in CiRM

Despite not enjoying this year the optimal environment of CiRM, we are still making good progress on the revision (or the R vision) of Bayesian Core. In the past two days, we went over Chapters 1 (Introduction), 2 (Normal Models), 5 (Capture-Recapture Experiments), and 6 (Mixture Models), with Chapters 3 (Regression), 4 (Generalised Linear Models) and 9 (Image Analysis) being close to completion. While having a “last”go at the R tutorial part of Chapter 1, I came across this paragraph

One of the most frustrating features of R is that the graphical device is not refreshed while a program is executed in the main window. This implies that, if you switch from one terminal to another or if the screen saver starts, the whole or parts of the graph currently on the graphical device will not be visible until the completion of the program. Conversely, refreshing very large graphs will delay the activation of the prompt >.

that I very gladly deleted, as the current 2.11.1 version of R does no longer suffer from this painful freeze in the graphics (at least on my Kubuntu 10.10 version).

Actually, I do not think I mentioned it in a previous post: our new edition will be called Bayesian Essentials with R. Both to distinguish it from Bayesian Core (as it should be published in the Use R! series) and because it appeared (thanks to colleagues and readers) that core did not sound very appealing to English-speaking audiences looking for a statistics book…