Archive for Reykjavik

Mýrin aka Jar City [book review]

Posted in Books, Mountains, pictures, Travel with tags , , , , , , , , , , on July 26, 2015 by xi'an

Mýrin (“The Bog”) is the third novel in the Inspector Erlendur series written by Arnaldur Indridason. It contains the major themes of the series, from the fascination for unexplained disappearances in Iceland to Elendur’s inability to deal with his family responsibilities, to domestic violence, to exhumations. The death that starts the novel takes place in the district of Norðurmýri, “the northern marsh”, not far from the iconic Hallgrimskirkja, and not far either from DeCODE, the genetic company I visited last June and which stores genetic information about close to a million Icelanders, the Íslendingabók. And which plays an important and nefarious role in the current novel. While this episode takes place mostly between Reykjavik and Keflavik, hence does not offer any foray into Icelandic landscapes, it reflects quite vividly on the cultural pressure still present in the recent years to keep rapes and sexual violence a private matter, hidden from an indifferent or worse police force. It also shows how the police misses (in 2001) the important genetic clues for being yet unaware of the immense and frightening possibilities of handling the genetic code of an entire population. (The English and French titles refer to the unauthorised private collections of body part accumulated [in jars] by doctors after autopsies, families being unaware of the fact.) As usual, solving the case is the least important part of the story, which tells about broken lifes and survivors against all odds.

Einstök

Posted in pictures, Travel, Wines with tags , , , , , , on July 12, 2015 by xi'an

einstok

dynamic mixtures [at NBBC15]

Posted in R, Statistics with tags , , , , , , , , , , , , on June 18, 2015 by xi'an

KleifarvatnA funny coincidence: as I was sitting next to Arnoldo Frigessi at the NBBC15 conference, I came upon a new question on Cross Validated about a dynamic mixture model he had developed in 2002 with Olga Haug and Håvård Rue [whom I also saw last week in Valencià]. The dynamic mixture model they proposed replaces the standard weights in the mixture with cumulative distribution functions, hence the term dynamic. Here is the version used in their paper (x>0)

(1-w_{\mu,\tau}(x))f_{\beta,\lambda}(x)+w_{\mu,\tau}(x)g_{\epsilon,\sigma}(x)

where f is a Weibull density, g a generalised Pareto density, and w is the cdf of a Cauchy distribution [all distributions being endowed with standard parameters]. While the above object is not a mixture of a generalised Pareto and of a Weibull distributions (instead, it is a mixture of two non-standard distributions with unknown weights), it is close to the Weibull when x is near zero and ends up with the Pareto tail (when x is large). The question was about simulating from this distribution and, while an answer was in the paper, I replied on Cross Validated with an alternative accept-reject proposal and with a somewhat (if mildly) non-standard MCMC implementation enjoying a much higher acceptance rate and the same fit.

capture mark recapture with no mark and no recapture [aka 23andmyfish]

Posted in Mountains, pictures, Statistics, Travel, University life with tags , , , , , , , , on June 11, 2015 by xi'an

moonA very exciting talk today at NBBC15 here in Reykjavik was delivered by Mark Bravington yesterday on Close-kin mark recapture by modern magic (!). Although Mark is from Australia, being a Hobart resident does qualify him for the Nordic branch of the conference! The exciting idea is to use genetic markers to link catches in a (fish) population as being related as parent-offspring or as siblings. This sounds like science-fantasy when you first hear of it!, but it is actually working better than standard capture-mark-recapture methods for populations of a certain size (so that the chances to find related animals are not the absolute zero!, as, e.g., krill populations). The talk was focussed on bluefin tuna, whose survival is unlikely under the current fishing pressure… Among the advantages, a much more limited impact of the capture on the animal, since only a small amount of genetic material is needed, no tag loss, tag destruction by hunters, or tag impact of the animal survival, no recapture, a unique identification of each animal, and the potential for a detailed amount of information through the genetic record. Ideally, the entire sample could lead to a reconstruction of its genealogy all the way to the common ancestor, a wee bit like what 23andme proposes for humans, but this remains at the science-fantasy level given what is currently know about the fish species genomes.

visiting deCODE [Íslensk erfðagreining]

Posted in Books, Kids, pictures, Statistics, Travel, University life with tags , , , , on June 9, 2015 by xi'an

Tonight, we [participants to the NBBC15 conference] got invited [and bused] to deCODE, the Icelandic genetic company that has worked on the human genome since 1996, taking advantage of the uniquely homogeneous features of the Icelandic population. Which overwhelmingly descends from the few originals settlers to populate Iceland in the late 800’s.  deCODE is located in downtown Reyjavik next to the regional airport and to Hallgrímskirkja, the iconic church overlooking the city. The genetic company has gathered genotypic and phenotypic information about half the population of Iceland and, thanks to extensive genealogical sources, has also put together the Íslendingabók that covers the entire current population and runs back to the origins of the country. Despite being a company (and now a subsidiary of Amgen), deCODE appears to operate just like another research institution, searching for genetic explanations of diseases and genotyping more and more individuals towards that goal, with a startup atmosphere in a well-designed building… A most unusual and enjoyable evening at a conference! Making me wonder if they have visiting positions…