as_rumen_gp: Convert data to a rumen_gp object

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

Convert data to a rumen_gp object

Description

Converts gas production data from any source into the internal rumenGP format.

Usage

as_rumen_gp(
  data,
  head_col,
  time_col,
  gas_col = NULL,
  pressure_col = NULL,
  treatment_col = NULL,
  bottle_col = NULL,
  rep_col = NULL,
  pressure_unit = c("psi", "kpa"),
  headspace_volume = NULL,
  headspace_unit = c("mL", "L"),
  temperature = 39,
  zero_negative_pressure = FALSE
)

Arguments

data	A data frame.
head_col	Column identifying bottles.
time_col	Column containing incubation time.
gas_col	Optional column containing cumulative gas production (mL).
pressure_col	Optional column containing pressure measurements.
treatment_col	Optional treatment column.
bottle_col	Optional bottle column.
rep_col	Optional replicate column.
pressure_unit	Pressure unit. Either "psi" or "kpa".
headspace_volume	Headspace volume. Required when pressure_col is supplied.
headspace_unit	Headspace unit. Either "mL" or "L".
temperature	Incubation temperature in degC.
zero_negative_pressure	Logical. If TRUE, negative pressure values are converted to zero before gas-volume calculations.

Details

The function accepts either cumulative gas volume or gas pressure measurements.

When pressure is supplied, gas volume is estimated using the same conversion used by process_ankom().

Value

A rumen_gp object.

Examples

# ----------------------------
# Example 1: Gas volume data
# ----------------------------

manual_volume <- data.frame(
  Bottle = c(
    1, 1, 1,
    2, 2, 2
  ),
  Treatment = c(
    "Control", "Control", "Control",
    "Corn", "Corn", "Corn"
  ),
  Time = c(
    0, 4, 8,
    0, 4, 8
  ),
  Gas = c(
    0, 20, 40,
    0, 35, 60
  )
)

gp <- as_rumen_gp(
  data = manual_volume,
  head_col = "Bottle",
  treatment_col = "Treatment",
  time_col = "Time",
  gas_col = "Gas"
)

head(gp)

# ----------------------------
# Example 2: Pressure data
# ----------------------------

manual_pressure <- data.frame(
  Bottle = rep(
    1,
    10
  ),
  Time = c(
    0, 2, 4, 6, 8,
    12, 16, 24, 36, 48
  ),
  PSI = c(
    0,
    0.2,
    0.5,
    0.8,
    1.2,
    1.8,
    2.5,
    3.2,
    4.0,
    4.5
  )
)

gp <- as_rumen_gp(
  data = manual_pressure,
  head_col = "Bottle",
  time_col = "Time",
  pressure_col = "PSI",
  pressure_unit = "psi",
  headspace_volume = 60
)

head(gp)

# Example model fit
fit <- fit_groot(gp)

summary(fit)

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