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…

Móskarðshnjúkar [hiking near Reykjavik]

Posted in Mountains, pictures, Running, Travel with tags , , , , , , , on June 7, 2015 by xi'an

moskard1Today, as I had a free day (with 24 hour daylight!) in Reykjavik before the NBBC15 conference started, thanks to the crazy schedules of the low cost sister of Air France, Transavia (!), I went in search of a hike… Which is not very difficult in Iceland! moskard2I had originally planned to stop near Geysir as the dirt road beyond Gullfoss is off-limit for rental cars. Especially small 2WD like mine.

As I was driving the first kms of the Þingvellir road, I admired the Esjan range starting with the Esja mountain that we had climbed during our previous visit to Iceland. Especially the “last” peak that glowed with a warm yellow (and apparently no snow at all). More especially, because it had a top reminding me of the Old Man of Storr on its slope. (Not that I could spot it while driving!) And quickly decided this was a great opportunity for a nice hikemoskard4 and a minimum of driving as I was about 20 mn from down-town Reykjavik.

I thus took a dirt road that seemed to get closer to my goal and after 500m came to a farm yard where I parked the car and went hiking, aiming at this peak,  which name is Móskarðshnjúkar. Despite a big cut due to a torrent after the first hill, I managed to keep enough to high ground not to loose any altitude and sticking to the side of the ski station Skálafellmoskard5 (where a few people were still skiing with the noisy help of two snowmobiles), I crossed the brook easily as it was covered by snow and started moving to steeper if manageable slopes. I moskard6reached the bottom of the main peak rather quickly and then understood both its colour and the absence of snow.

As maybe visible from some of my pictures (?), the Móskarðshnjúkar peak is covered with gravel in a bright yellow stone that seems to accumulate heat very well. Climbing stramoskard3ight on the loose gravel was then impossible and I had to zigzag mostly up, trying to not lose too much ground to micro-avalanches. As I reached the tor I spotted two hikers above me and when I reached the top I realised there was a path coming from the west, connecting this peak with its neighbours. The normal route seems to come from a gravel road that starts close to Mount Esja, to the west, and as I followed the path down to the saddle between Móskarðshnjúkar and the rest of the range, I saw this path winding down to the valley with further hikers coming up. Before I crossed them, I went up again to the next peak, which was an easy if beautiful ridge walk, with moskard7still a fair amount of snow remaining on the north face (heavy enough to bear tracks of snowmobiles!). After following the ridge track for a while, it branched north to reach the main Esja plateau and I left the track to get down a rocky shoulder towards my starting point. However, I had forgotten about the torrent cut between the two ranges and this forced me to take a further detour. And to cross the torrent barefooted, as there was no stone ford on this off-path section. No big drama as the melted snow water was not that cold…

moskard8A last sight was provided by the final rocky outcrop, which enjoyed basaltic volcanic columns as on the picture above. A terrific hiking half-day with a sharp sunny weather and not too much wind except at the top. It was very pleasant to walk part of the way on moss and last year grass, with a surprising absence of bogs and mud when compared with Scotland.

moon under the midnight sun

Posted in Mountains, pictures, Travel, University life with tags , , , , , on June 6, 2015 by xi'an

moon

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