Fit Brody model — fit_brody • rumenGP

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

Usage

fit_brody(data, start = NULL)

Arguments

data

A rumen_gp object.

start

Optional list of starting values. May contain any of:

Value

A brody_fit object containing:

Parameter estimates
Model diagnostics
Predicted values
Residuals

Details

Equation

$$ V(t) = A \left(1 - b e^{-kt}\right) $$

where:

$V(t)$ is cumulative gas production at time $t$
$A$ is asymptotic gas production
$b$ is an integration constant
$k$ is the fractional rate constant

Interpretation

The Brody model describes gas production as a monotonic increase toward an asymptotic value. The parameter $k$ controls the speed of fermentation, while $b$ controls the initial position of the curve.

Advantages

Simple and robust
Stable convergence
Easy biological interpretation
Useful as a baseline model

Limitations

No explicit lag parameter
Less flexible than sigmoidal models
May not adequately represent strongly sigmoidal fermentation profiles

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_brody(
  gp
)
#> Warning: Large negative pressure values detected. Minimum PSI = -1.274 . Please inspect the affected bottles.
#> rumenGP data validation passed.
#> Observations: 1752
#> Heads: 24
#> Treatments: 5

summary(fit_default)
#> 
#> Brody model summary
#> -------------------
#> Total bottles: 24
#> Successful fits: 23
#> Failed fits: 1
#> Low R-squared (< 0.90): 3
#> 

# Fit using custom starting values
fit_custom_start <- fit_brody(
  gp,
  start = list(
    A = 120,
    b = 0.9,
    k = 0.05
  )
)
#> Warning: Large negative pressure values detected. Minimum PSI = -1.274 . Please inspect the affected bottles.
#> rumenGP data validation passed.
#> Observations: 1752
#> Heads: 24
#> Treatments: 5

summary(fit_custom_start)
#> 
#> Brody model summary
#> -------------------
#> Total bottles: 24
#> Successful fits: 23
#> Failed fits: 1
#> Low R-squared (< 0.90): 3
#>