fit_groot: Fit Groot model

In rumenGP: Rumen Gas Production Modeling, Comparison, and Visualization

Fit Groot model

Description

Fits the Groot gas production model to each bottle in a rumen_gp dataset.

Usage

fit_groot(data, start = NULL)

Arguments

data	A rumen_gp object.
start	Optional list of starting values. May contain any of: VF b k

Details

Equation

V(t) = \frac{VF} { 1+\left(\frac{b}{t}\right)^k }

where:

• V(t) is cumulative gas production at time t

• VF is asymptotic gas production

• b is the half-time parameter

• k is the shape parameter

Interpretation

The Groot model is a flexible sigmoidal model widely used in rumen gas production studies.

The parameter b represents the time required to reach approximately half of the asymptotic gas production, while k controls curve shape and steepness.

Advantages

• Excellent flexibility

• Biologically interpretable parameters

• Often produces excellent fits

• Widely used in rumen fermentation studies

Limitations

• Requires positive incubation times

• Shape parameter may be less intuitive than simple exponential models

Notes

The Groot model is mathematically equivalent to the generalized Michaelis-Menten model implemented in fit_mm().

Parameter correspondence:

• VF = A

• b = K

• k = c

Both formulations produce identical fitted values, residuals, diagnostics, AIC, BIC, RMSE, and R-squared when convergence is achieved.

Researchers may choose either formulation according to the terminology commonly used in their field.

Value

A groot_fit object containing:

• Parameter estimates

• Model diagnostics

• Predicted values

• Residuals

Examples

files <- example_data()

raw_data <- read_ankom(
  files$ankom
)

metadata <- read_metadata(
  files$metadata
)

gp <- process_ankom(
  raw_data,
  metadata,
  headspace_ml = 210,
  temperature_c = 39
)

# Fit using package default starting values
fit_default <- fit_groot(
  gp
)

summary(fit_default)

# Fit using custom starting values
fit_custom_start <- fit_groot(
  gp,
  start = list(
    VF = 120,
    b = 10,
    k = 2
  )
)

summary(fit_custom_start)

rumenGP documentation built on Oct. 2, 2026, 5:09 p.m.