Importing Non-ANKOM Data

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

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title: "Importing Non-ANKOM Data" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Importing Non-ANKOM Data} %\VignetteEngine{knitr::rmarkdown} \usepackage[utf8]{inputenc}

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knitr::opts_chunk$set(
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Introduction

Not all rumen gas production experiments are conducted using the ANKOM RF Gas Production System.

rumenGP provides the function as_rumen_gp() for importing manually collected gas-volume data and pressure-based datasets into the standard rumen_gp format.

Once imported, the data can be analyzed using the same modeling, visualization, and model-comparison tools available for ANKOM experiments.

library(rumenGP)

Importing Gas Volume Data

The simplest workflow is to import cumulative gas production measurements directly.

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
  )

)

Convert the dataset into a rumen_gp object:

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

Inspect the resulting object:

gp

Verify the class:

class(gp)

Required Columns

At minimum, gas-volume datasets must contain:

Bottle identifier
Incubation time
Gas production

These columns can have any names as long as they are specified through the function arguments.

For example:

head_col = "Bottle"
time_col = "Time"
gas_col = "Gas"

Importing Pressure Data

rumenGP can also import pressure measurements and convert them to gas volume automatically.

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
  )

)

Convert pressure measurements:

gp_pressure <- as_rumen_gp(

  data = manual_pressure,

  head_col = "Bottle",

  time_col = "Time",

  pressure_col = "PSI",

  pressure_unit = "psi",

  headspace_volume = 60

)

Inspect the resulting gas volumes:

head(gp_pressure)

Pressure Units

Currently supported pressure units are:

psi
kpa

Examples:

pressure_unit = "psi"

or

pressure_unit = "kpa"

Headspace Volume

Pressure measurements require information about headspace volume.

Headspace volume is the gas volume available inside the bottle and is not necessarily the same as the total bottle volume.

Example:

Bottle volume = 125 mL

Liquid volume = 75 mL

Headspace volume = 50 mL

When pressure data are imported:

headspace_volume = 50

should represent the headspace volume, not the total bottle capacity.

Headspace Units

Supported headspace units:

mL
L

Examples:

headspace_unit = "mL"

headspace_unit = "L"

Negative Pressure Values

Pressure datasets occasionally contain slightly negative readings caused by sensor variation.

These values can be automatically corrected.

negative_pressure <- data.frame(

  Bottle = c(
    1,1,1
  ),

  Time = c(
    0,4,8
  ),

  PSI = c(
    -0.5,
    0.2,
    1.0
  )

)

gp_negative <- as_rumen_gp(

  data = negative_pressure,

  head_col = "Bottle",

  time_col = "Time",

  pressure_col = "PSI",

  pressure_unit = "psi",

  headspace_volume = 60,

  zero_negative_pressure = TRUE

)

Validation

Imported datasets can be validated using:

validate_ankom(
  gp
)

The function checks:

• Required columns
• Missing values
• Duplicate observations
• Time ordering
• Dataset consistency

Fitting a Model

Once imported, manually collected datasets can be analyzed exactly like ANKOM datasets.

fit <- fit_groot(
  gp
)

Inspect results:

summary(fit)

Compare Models

comparison <- compare_models(

  Groot = fit_groot(gp),

  Brody = fit_brody(gp),

  Gompertz = fit_gompertz(gp)

)

comparison

Common Errors

No gas or pressure supplied

as_rumen_gp(
  data = my_data,
  head_col = "Bottle",
  time_col = "Time"
)

Produces:

Provide either gas_col or pressure_col.

Both gas and pressure supplied

as_rumen_gp(
  data = my_data,
  gas_col = "Gas",
  pressure_col = "PSI"
)

Produces:

Provide only one of gas_col or pressure_col.

Missing headspace volume

as_rumen_gp(
  pressure_col = "PSI"
)

Produces:

headspace_volume must be supplied when pressure_col is used.

Summary

The as_rumen_gp() function makes it possible to use rumenGP with:

• Manual gas-volume datasets
• Pressure-based datasets
• Non-ANKOM experiments

Once imported, all datasets become standard rumen_gp objects and can be analyzed using the full modeling framework.

Next Steps

See:

?fit_custom

for information about fitting custom kinetic models.

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