Archive for Africa

locusts in a random forest

Posted in pictures, Statistics, University life with tags , , , , , , , , , , , on July 19, 2019 by xi'an

My friends from Montpellier, where I am visiting today, Arnaud Estoup, Jean-Michel Marin, and Louis Raynal, along with their co-authors, have recently posted on biorXiv a paper using ABC-RF (Random Forests) to analyse the divergence of two populations of desert locusts in Africa. (I actually first heard of their paper by an unsolicited email from one of these self-declared research aggregates.)

“…the present study is the first one using recently developed ABC-RF algorithms to carry out inferences about both scenario choice and parameter estimation, on a real multi-locus microsatellite dataset. It includes and illustrates three novelties in statistical analyses (…): model grouping analyses based on several key evolutionary events, assessment of the quality of predictions to evaluate the robustness of our inferences, and incorporation of previous information on the mutational setting of the used microsatellite markers”.

The construction of the competing models (or scenarios) is built upon data of past precipitations and desert evolution spanning several interglacial periods, back to the middle Pleistocene, concluding at a probable separation in the middle-late stages of the Holocene, which corresponds to the last transition from humid to arid conditions in the African continent. The probability of choosing the wrong model is exploited to determine which model(s) lead(s) to a posterior [ABC] probability lower than the corresponding prior probability, and only one scenario stands this test. As in previous ABC-RF implementations, the summary statistics are complemented by pure noise statistics in order to determine a barrier in the collection of statistics, even though those just above the noise elements (which often cluster together) may achieve better Gini importance by mere chance. An aspect of the paper that I particularly like is the discussion of the various prior modellings one can derive from existing information (or lack thereof) and the evaluation of the impact of these modellings on the resulting inference based on simulated pseudo-data.


Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , on June 26, 2019 by xi'an

I found my (short) trip to Abdijan for the CISEA 2019 conference quite fantastic as it allowed me to meet with old friends, from the earliest days at CREST and even before, and to meet new ones. Including local students of ENSEA who had taken a Bayesian course out of my Bayesian Choice book. And who had questions about the nature of priors and the difficulty they had in accepting that several replies were possible with the same data! I wish I had had more time to discuss the relativity of Bayesian statements with them but this was a great and rare opportunity to find avid readers of my books! I also had a long chat with another student worried about the use or mis-use of reversible jump algorithms to draw inference  on time-series models in Bayesian Essentials, chat that actually demonstrated his perfect understanding of the matter. And it was fabulous to meet so many statisticians and econometricians from West Africa, most of them French-speaking. My only regret is not having any free time to visit Abidjan or the neighbourhood as the schedule of the conference did not allow for it [or even for a timely posting of a post!], especially as it regularly ran overtime. (But it did provide for a wide range of new local dishes that I definitely enjoyed tasting!) We are now discussing further opportunities to visit there, e.g. by teaching a short course at the Master or PhD levels.

green sunset [jatp]

Posted in pictures with tags , , , , , , , , , on June 17, 2019 by xi'an


Posted in pictures with tags , , , , , , on March 22, 2018 by xi'an

Bayesian maps of Africa

Posted in pictures, Statistics with tags , , , , , , on March 21, 2018 by xi'an

A rather special issue of Nature this week (1 March 2018) as it addresses Bayesian geo-cartography and mapping childhood growth failure and educational achievement (along with sexual differences) all across Africa! Including the (nice) cover of the journal, a preface by Kofi Annan, a cover article by Brian Reich and Murali Haran, and the first two major articles of the journal, one of which includes Ewan Cameron as a co-author. As I was reading this issue of Nature in the train back from Brussels, I could not access the supplementary material, so could not look at the specifics of the statistics, but the maps look quite impressive with a 5×5 km² resolution. And inclusion not only of uncertainty maps but also of predictive maps on the probability of achieving WHO 2025 goals. Surprisingly close to one in some parts of Africa. In terms of education, there are strong oppositions between different regions, with the south of the continent, including Madagascar, showing a positive difference for women in terms of years of education. While there is no reason (from my train seat) to doubt the statistical analyses, I take quite seriously the reservation of the authors that the quality of the prediction cannot be better than the quality of the data, which is “determined by the volume and fidelity of nationally representative surveys”. Which relates to an earlier post of mine about a similar concern with the deaths in Congo.

Nature snapshot [Volume 539 Number 7627]

Posted in Books, Statistics, University life with tags , , , , , , , , , , on November 15, 2016 by xi'an

A number of entries of interest [to me] in that Nature issue: from the Capuchin monkeys that break stones in a way that resembles early hominins biface tools, to the persistent association between some sounds and some meanings across numerous languages, to the use of infected mosquitoes in South America to fight Zika, to the call for more maths in psychiatry by the NIMH director, where since prevision is mentioned I presumed stats is included, to the potentially earthshaking green power revolution in Africa, to the reconstruction of the first HIV strains in North America, along with the deconstruction of the “Patient 0” myth, helped by Bayesian phylogenetic analyses, to a cover of the Open Syllabus Project, with Monte Carlo Statistical Methods arriving first [in the Monte Carlo list]….

“Observations should not converge on one model but aim to find anomalies that carry clues about the nature of dark matter, dark energy or initial conditions of the Universe. Further observations should be motivated by testing unconventional interpretations of those anomalies (such as exotic forms of dark matter or modified theories of gravity). Vast data sets may contain evidence for unusual behaviour that was unanticipated when the projects were conceived.” Avi Loeb

One editorial particularly drew my attention, Good data are not enough, by the astronomer Avi Loeb. as illustrated  by the quote above, Loeb objects to data being interpreted and even to data being collected towards the assessment of the standard model. While I agree that this model contains a lot of fudge factors like dark matter and dark energy, which apparently constitutes most of the available matter, the discussion is quite curious, in that interpreting data according to alternative theories sounds impossible and certainly beyond the reach of most PhD students [as Loeb criticises the analysis of some data in a recent thesis he evaluated].

“modern cosmology is augmented by unsubstantiated, mathematically sophisticated ideas — of the multiverse, anthropic reasoning and string theory.

The author argues to always allow for alternative interpretations of the data, which sounds fine at a primary level but again calls for the conception of such alternative models. When discrepancies are found between the standard model and the data, they can be due to errors in the measurement itself, in the measurement model, or in the theoretical model. However, they may be impossible to analyse outside the model, in the neutral way called and wished by Loeb. Designing neutral experiments sounds even less meaningful. Which is why I am fairly taken aback by the call to “a research frontier [that] should maintain at least two ways of interpreting data so that new experiments will aim to select the correct one”! Why two and not more?! And which ones?! I am not aware of fully developed alternative theories and cannot see how experiments designed under one model could produce indications about a new and incomplete model.

“Such simple, off-the-shelf remedies could help us to avoid the scientific fate of the otherwise admirable Mayan civilization.”

Hence I am bemused by the whole exercise, which deepest arguments seem to be a paper written by the author last year and an interdisciplinary centre on black holes also launched recently by the same author.


Posted in pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , on April 28, 2016 by xi'an