This repository contains R scripts to generate most of the figures and other results presented in Kobel et al. 2025.

The scripts are written as R Markdown documents that can be compiled with knitr to produce the figures and tables in the manuscript. The script RCT_definition.Rmd provides the computational definition for the two rumen community types (RCTs) compared in the manuscrip, based on Dirichlet Multinomial Mixtures (DMM) clustering of 16S rRNA gene amplicon data. The rest of the scripts are named according to the figure/table they correspond to.

Input data for the scripts is available through the Norwegian National Infrastructure for Research Data (NIRD) here.

Packages were managed with renv; see their documentation for how to use this.