This repository hosts the source files for the Bookdown guide “Genome polarisation with diemr” published at https://nmartinkova.github.io/genome-polarisation/.

The book provides a practical guide to genome polarisation using the diemr R package. It explains how to:

• import and polarise genotypes,
• filter markers by diagnostic index,
• smooth polarised genomic states along chromosomes,
• compute hybrid indices and visualise genomic structure.

Each chapter includes example code and interpretation notes based on the diagnostic index expectation maximisation (diem) algorithm described in Baird et al. (2023).

• .Rmd files — source text for each chapter
• _bookdown.yml, _output.yml — build configuration
• docs/ — rendered HTML files for GitHub Pages
• figs/ — pre-rendered figures included in the book

To render locally:

bookdown::render_book("index.Rmd")