Archive for China

COVID by numbers [not a book review]

Posted in Books, Kids, Statistics with tags , , , , , , , , , on October 13, 2021 by xi'an

David Spiegelhalter and Anthony Masters have made a book out of their COVID related columns in The Observer. Here are ten key figures extracted from that book:

  1. The UK was hit by more than 1,000 separate outbreaks (…) [with] far more imports of Sars-CoV-2 from France, Italy and Spain than from China
  2. Reported Covid deaths depend on the day of the week (due to delayed reporting, and a weekend effect, but smoothing is very rarely applied)
  3. In the first year of Covid, over-90s had 35,000 times the risk of dying of Covid-19 as young children (with no relevance of the figure per se since an extra death of a young child would have moved it from 35,000 to 32,000, since there were thankfully so few deaths of young children)
  4. 2020 saw the highest number of deaths since 1918 in England and Wales (even when correcting for population increase or population ageing)
  5. The UK has led the World in testing Covid treatments (like dexamethasone and hydroxychloroquine, thanks to the centralised NHS, making me wonder why France with another centralised and public health structure was not able to do the same)
  6. People who have died with Covid have on average lost about 10 years of life (contrary to the authors’ intial hunch, and mine as well, to oppose to the less relevant loss of life expectancy across the entire population)
  7. Most people died “of” Covid rather than “with” it, but most have also had other medical conditions (with 91% of pre-COVID conditions)
  8. Alcohol consumption stayed the same during lockdown (which came as a surprise, given the general feeling for the opposite, and still as a worrying indicator of alcoholism)
  9. Most people with Sars-CoV-2 don’t infect anyone (which would need more details, as the figure should be weighted by the base probability to infect someone)
  10. The pandemic has been a net lifesaver for young people (with 300 fewer deaths for 15-29 year old, but it also has had a potentially negative impact on their life expectancy).

The Shanghairen

Posted in pictures, Travel with tags , , , , , , on July 10, 2021 by xi'an

the pillar of shame [04 June 1989]

Posted in Kids, pictures with tags , , , , , , , , , on June 4, 2021 by xi'an

a journal of the plague year [post-december reviews]

Posted in Books, Kids, pictures, Travel with tags , , , , , , , , , , , , , , , , , , , , , , , , , , , , , on February 13, 2021 by xi'an

Read a (French) novel by Fred Vargas, Sous les Vents de Neptune, after finding it in the book depository near my office. And enjoyed it very much, partly because it was partly taking place near Ottawa [which I visited many times while my wife was completing her EE Master there] and partly because of the author’s ability to make us doubt the main character and to keep the suspense tight enough for most of the book. There are a trip to Montréal to attend a concert and a journey to Detroit and back to find a lost relation, both reminding me of drives on these roads more than 30 years ago. What annoyed me though was the caricaturesque depiction of the locals, with a Québecois French that sounded overdone. Checking for a local perspective on that aspect, I found a book review in Le Devoir of 2004 sharing the reservation on that aspect, if with humour.  (I would also have rather done without the super-hacker character à la Lisbeth Salander.)

Watched Still Life (三峡好人) a 2006 film by Jia Zhangke, as it was proposed in the list of my local cinema (which I support during the endless lockdown of cinemas and theatres in France). This is an amazing film, which at the same time feels incredibly remote or alien… It follows two characters arriving by boat on the at the Three Gorges Dam under construction in search of a runaway spouse. The search for their respective spouse takes place among the demolition of the old Fengjie, soon to be drowned under 150 meters of dam water. This demolition makes for a unique soundtrack, workers hammering in cadence as blurred black shades against the sky. The dialogues are full of long silences, except for the background hammering, and it often feels theatrical. But the characters maintain a strong dignity throughout the film and the depiction of the last days of Fengjie is gripping. The film received the 2006 Venezia Golden Lion.

Cooked a few Venetian dishes from a Venetian cookbook that was my Xmas gift. And finished that way past-the-date polenta boxes. Managed to escape unscathed from both the bûche and galette weeks! And found that cooking spelt bread with spelt yeast was unbelievably easy, taking less time to work on the dough than to reach the closest bakery!

Could not manage to achieve a coherent discussion with some anti-vaxxer relatives over the Xmas break. And gave up, still hoping they would change their mind.

Watched the first episodes of The Expanse, which started as a collection of eight novels and eight shorter works, before turning into a TV series which won the 2020 Hugo Award. Enjoyable if a rather conventional setting, with the usual disregard for space physics! Reminded me very much of the Takeshi Kovacs novels.  To quote from Wikipedia, “Ty Franck began developing the world of The Expanse initially as the setting for a MMORPG and, after a number of years, for a tabletop roleplaying game.” Some of the actors are terrific (even though Steven Strait’s Holden painfully reminds me of Kit Harrington’s Jon Snow, to the point I wondered for a while if they were the same actor…)

Bayesian phylogeographic inference of SARS-CoV-2

Posted in Books, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , on December 14, 2020 by xi'an

Nature Communications of 10 October has a paper by Philippe Lemey et al. (incl. Marc Suchard) on including travel history and removing sampling bias on the study of the virus spread. (Which I was asked to review for a CNRS COVID watch platform, Bibliovid.)

The data is made of curated genomes available in GISAID on March 10, that is, before lockdown even started in France. With (trustworthy?) travel history data for over 20% of the sampled patients. (And an unwelcome reminder that Hong Kong is part of China, at a time of repression and “mainlandisation” by the CCP.)

“we model a discrete diffusion process between 44 locations within China, including 13 provinces, one municipality (Beijing), and one special administrative area (Hong Kong). We fit a generalized linear model (GLM) parameterization of the discrete diffusion process…”

The diffusion is actually a continuous-time Markov process, with a phylogeny that incorporates nodes associated with location. The Bayesian analysis of the model is made by MCMC, since, contrary to ABC, the likelihood can be computed by Felsenstein’s pruning algorithm. The covariates are used to calibrate the Markov process transitions between locations. The paper also includes a posterior predictive accuracy assessment.

“…we generate Markov jump estimates of the transition histories that are averaged over the entire posterior in our Bayesian inference.”

In particular the paper describes “travel-aware reconstruction” analyses that track the spatial path followed by a virus until collection, as below. The top graph represents the posterior probability distribution of this path.Given the lack of representativity, the authors also develop an additional “approach that adds unsampled taxa to assess the sensitivity of inferences to sampling bias”, although it mostly reflects the assumptions made in producing the artificial data. (With a possible connection with ABC?). If I understood correctly, they added 458 taxa for 14 locations,

An interesting opening made in the conclusion about the scalability of the approach:

“With the large number of SARS-CoV-2 genomes now available, the question arises how scalable the incorporation of un-sampled taxa will be. For computationally expensive Bayesian inferences, the approach may need to go hand in hand with down-sampling procedures or more detailed examination of specific sub-lineages.”

In the end, I find it hard, as with other COVID-related papers I read, to check how much the limitations, errors, truncations, &tc., attached with the data at hand impact the validation of this philogeographic reconstruction, and how the model can help further than reconstructing histories of contamination at the (relatively) early stage.

%d bloggers like this: