Archive for admixture

the new DIYABC-RF

Posted in Books, pictures, R, Statistics, Wines with tags , , , , , , , , , , , , , , , , on April 15, 2021 by xi'an

My friends and co-authors from Montpellier have released last month the third version of the DIYABC software, DIYABC-RF, which includes and promotes the use of random forests for parameter inference and model selection, in connection with Louis Raynal’s thesis. Intended as the earlier versions of DIYABC for population genetic applications. Bienvenue!!!

The software DIYABC Random Forest (hereafter DIYABC-RF) v1.0 is composed of three parts: the dataset simulator, the Random Forest inference engine and the graphical user interface. The whole is packaged as a standalone and user-friendly graphical application named DIYABC-RF GUI and available at https://diyabc.github.io. The different developer and user manuals for each component of the software are available on the same website. DIYABC-RF is a multithreaded software on three operating systems: GNU/Linux, Microsoft Windows and MacOS. One can use the program can be used through a modern and user-friendly graphical interface designed as an R shiny application (Chang et al. 2019). For a fluid and simplified user experience, this interface is available through a standalone application, which does not require installing R or any dependencies and hence can be used independently. The application is also implemented in an R package providing a standard shiny web application (with the same graphical interface) that can be run locally as any shiny application, or hosted as a web service to provide a DIYABC-RF server for multiple users.

Nature highlights

Posted in Books, Kids, pictures, Statistics with tags , , , , , , , on November 1, 2016 by xi'an

A mostly genetics issue of Nature this week (of October 13), as the journal contains an article on the genomes of 300 individuals from 142 diverse populations across the globe, and another one on the genetic history of Australia Aborigines, plus a third one of 483 individuals from 125 populations drawing genetic space barriers, leading to diverging opinions on the single versus multiple out-of-Africa scenario. As some of these papers are based on likelihood-based techniques, I wish I had more time to explore the statistics behind. Another paper builds a phylogeny of violence in mammals, rising as one nears the primates. I find the paper most interesting but I am not convinced by the genetic explanation of violence, in particular because it seems hard to believe that data about Palaeolithic, Mesolithic, and Neolithic periods can be that informative about the death rate due to intra-species violence. And to conclude on a “pessimistic” note, the paper that argues there is a maximum lifespan for humans, meaning that the 122 years enjoyed (?) by Jeanne Calment from France may remain a limit. However, the argument seems to be that the observed largest, second largest, &tc., ages at death reached a peak in 1997, the year Jeanne Calment died, and is declining since then. That does not sound super-convincing when considering extreme value theory, since 1997 is the extreme event and thus another extreme event of a similar magnitude is not going to happen immediately after.

ABC model choice via random forests [expanded]

Posted in Statistics, University life with tags , , , , , , , , , , , on October 1, 2014 by xi'an

outofAfToday, we arXived a second version of our paper on ABC model choice with random forests. Or maybe [A]BC model choice with random forests. Since the random forest is built on a simulation from the prior predictive and no further approximation is used in the process. Except for the computation of the posterior [predictive] error rate. The update wrt the earlier version is that we ran massive simulations throughout the summer, on existing and new datasets. In particular, we have included a Human dataset extracted from the 1000 Genomes Project. Made of 51,250 SNP loci. While this dataset is not used to test new evolution scenarios, we compared six out-of-Africa scenarios, with a possible admixture for Americans of African ancestry. The scenario selected by a random forest procedure posits a single out-of-Africa colonization event with a secondary split into a European and an East Asian population lineages, and a recent genetic admixture between African and European lineages, for Americans of African origin. The procedure reported a high level of confidence since the estimated posterior error rate is equal to zero. The SNP loci were carefully selected using the following criteria: (i) all individuals have a genotype characterized by a quality score (GQ)>10, (ii) polymorphism is present in at least one of the individuals in order to fit the SNP simulation algorithm of Hudson (2002) used in DIYABC V2 (Cornuet et al., 2014), (iii) the minimum distance between two consecutive SNPs is 1 kb in order to minimize linkage disequilibrium between SNP, and (iv) SNP loci showing significant deviation from Hardy-Weinberg equilibrium at a 1% threshold in at least one of the four populations have been removed.

In terms of random forests, we optimised the size of the bootstrap subsamples for all of our datasets. While this optimisation requires extra computing time, it is negligible when compared with the enormous time taken by a logistic regression, which is [yet] the standard ABC model choice approach. Now the data has been gathered, it is only a matter of days before we can send the paper to a journal