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Fit exponential model without lag (EXP0)

Source: R/fit_exp0.R
fit_exp0.Rd

Fits the exponential gas production model without an explicit lag phase.

Usage

fit_exp0(data, start = NULL)

Arguments

data

A rumen_gp object.

start

Optional list of starting values. May contain any of:

  • Vf

  • k

Value

An exp0_fit object containing:

  • Parameter estimates

  • Model diagnostics

  • Predicted values

  • Residuals

Details

Equation

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

where:

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

  • \(Vf\) is asymptotic gas production

  • \(k\) is the fractional rate constant

Interpretation

The EXP0 model assumes that gas production increases exponentially toward an asymptotic value without an explicit lag phase.

Advantages

  • Simple and computationally efficient

  • Stable convergence

  • Easy biological interpretation

Limitations

  • Does not model lag time

  • Limited flexibility for 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 defaults
fit_default <- fit_exp0(
  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)
#> 
#> Exponential model (EXP0) summary
#> --------------------------------
#> Total bottles: 24
#> Successful fits: 24
#> Failed fits: 0
#> Low R-squared (< 0.90): 4
#> 

# Fit using user-defined starting values
fit_custom_start <- fit_exp0(
  gp,
  start = list(
    Vf = 120,
    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)
#> 
#> Exponential model (EXP0) summary
#> --------------------------------
#> Total bottles: 24
#> Successful fits: 24
#> Failed fits: 0
#> Low R-squared (< 0.90): 4
#>