admixr

admixr provides an R interface to ADMIXTOOLS for executing f3, D-statistics, f4, f4-ratio, qpWave, and qpAdm analyses and for automating configuration and output parsing to support reproducible population genetic inference on EIGENSTRAT-format data.

Key Features:

• ADMIXTOOLS integration: Integrates ADMIXTOOLS functionality into R to run f3, D-statistics, f4, f4-ratio, qpWave, and qpAdm analyses.
• Configuration and output automation: Automates generation of ADMIXTOOLS configuration files and parsing of program output.
• Reproducibility: Unifies analysis steps within an R framework to enable reproducible analytic workflows.
• EIGENSTRAT data manipulation: Provides R functions to process, filter, and manipulate datasets in EIGENSTRAT format.

Scientific Applications:

• Evolutionary biology: Detects admixture events and infers evolutionary relationships using f-statistics and qpAdm/qpWave analyses.
• Anthropology: Investigates population structure and migration patterns by applying D-statistics and related tests.
• Conservation genetics: Assesses gene flow and admixture in non-human populations to inform conservation and management decisions.

Methodology:

admixr integrates ADMIXTOOLS into R and automates configuration file generation and output parsing, and it provides functions to process, filter, and manipulate EIGENSTRAT-format datasets.