ADMIXTOOLS

This post covers using qpAdm in R to test ancestry models and estimate admixture proportions. qpAdm builds on f4-statistics and provides a framework for evaluating whether proposed source populations can explain a target population’s genetic makeup. For R and admixtools setup instructions on Debian/Ubuntu, see my previous post: Running f4-Statistics with Admixtools in R. Windows users can find R installation instructions on the R website. What is qpAdm? qpAdm is a method for testing ancestry models and estimating admixture proportions. It determines whether a target population can be modeled as a mixture of specified source populations (“left populations”), and if the model fits, calculates the contribution from each source. The method builds on f4-statistics (covered in my previous post) to evaluate these ancestry models. ...

In this post I’ll cover how to run f4-statistics using the admixtools package for R. While I do not typically use R for general-purpose programming, I prefer this implementation over the original one because working in a REPL environment is more practical than editing parameter files, especially when you’re testing different population combinations. The interactive workflow makes programmatic model testing straightforward. Beyond these workflow improvements, the R version is also significantly faster, not because of the language itself, but simply better implementation. You can work with the full AADR dataset without creating subsets. ...