GnG1 Models: Generalized compartmental models to estimate the rates of fiber digestion and passage in ruminants: History, science, and user guide

This document covers the history, science, and user guide for GnG1 Models, version 3.0, a Windows program that fits generalized compartmental models to two kinds of data from ruminant nutrition experiments: the residue of fiber left after increasing times of incubation, in vitro or in situ, which gives the fractional rate of digestion (kd), and the concentration of a marker in the feces after a single dose, which gives the fractional rate of passage (kp). In its central model, GnG1, fiber passes through a chain of n age-dependent stages before reaching a stage it leaves at a constant fractional rate. Instead of fitting a single model, GnG1 Models fits nine models to each digestion profile, from the exponential, the exponential with a discrete lag, and the logistic to GnG1 of orders one to six, and eight models to each passage profile: GnG1 of orders one to six, the two-compartment model of Grovum and Williams, and the multicompartment model of Dhanoa. It then selects the best-fitting model for each profile by AIC, BIC, or SSE, and derives from the selected curve the potentially digestible and indigestible fractions, the lag or mean delay, the effective digestibility, and the equivalent first-order kd, or the transit time, the mean retention times, and the ruminal kp. The modeling is done in R, behind a graphical interface for users unfamiliar with R, and each run writes a report and a page documenting how each result is computed. The first chapter traces the model from the age-dependent compartments of Blaxter, Matis, and Pond to the companion papers of 2007 and the papers of 2008 in the Journal of Theoretical Biology by Vieira, Tedeschi, and Cannas. It continues through the 2008 R scripts, the 2009 Windows program and its versions through 2025, and ends with GnG1 Models 3, rewritten in 2026. The second chapter summarizes the science: the data; the models of digestion; GnG1 as an age-dependent model of digestion; effective digestibility; the models of passage; retention times and the rate of passage; fitting and choosing the model; digestion and passage together; and a worked example. The third chapter revisits the first evaluation of the models, on 199 in vitro NDF degradation profiles and on the mass of NDF in the ruminoreticulum of cattle and sheep. The fourth is a user guide to the main window, the dataset and the parameter file, the options, running, the results, projects, and the menus. The fifth works through the sample datasets: a passage run, a digestion run, and a digestion run that takes its rate of passage from the passage run.