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Convert Volume Units to Match Concentration Denominator Units

Source: R/conversions.R
convert_volume_units.Rd

This function identifies rows associated with excretion samples (e.g., urine, feces, bile) and adjusts the VOLUME and VOLUMEU columns so that the volume unit matches the denominator unit in the corresponding concentration unit (AVALU). This is necessary for PKNCA calculation of excretion parameters.

Usage

convert_volume_units(
  df,
  avalu = "AVALU",
  volume = "VOLUME",
  volumeu = "VOLUMEU"
)

Arguments

df

A data frame containing pharmacokinetic data.

avalu

A character string specifying the column name for concentration values (default: "AVALU").

volume

A character string specifying the column name for volume or mass values (default: "VOLUME").

volumeu

A character string specifying the column name for volume or mass units (default: "VOLUMEU"). It must contain the following columns:

PCSPEC

Sample type (e.g., urine, feces, bile, plasma).

AVAL

Concentration values.

AVALU

Concentration units (e.g., "ug/mL", "mg/g").

VOLUME

Volume or mass values for integration.

VOLUMEU

Units for the VOLUME column (e.g., "mL", "g").

Value

A modified data frame with VOLUME and VOLUMEU converted (where necessary) so that multiplying AVAL * VOLUME results in a unit with consistent dimensionality (typically mass or moles). A new column AMOUNTU is created to represent the product of AVALU and VOLUMEU.

Details

It uses the units package to perform unit-safe conversions. If a direct conversion between volume and the concentration denominator is not possible (e.g., between mass and volume), a fallback conversion is attempted using a neutral density of 1 (target_unit / original_unit). The function modifies only the VOLUME and VOLUMEU columns when necessary and leaves all other data unchanged.

The function:

  1. Parses the denominator from AVALU (e.g., "ug/mL" → "mL").

  2. Attempts to convert the corresponding VOLUME to that unit.

  3. If direct conversion fails, assumes a neutral density of 1 (i.e., 1 unit_target / unit_original) and retries.

  4. Leaves units unchanged for non-excreta samples or already-valid combinations.

The function assumes that the AVALU column contains concentration units in the form of "x/y" (e.g., "ug/mL", "mg/g").

Examples

df <- data.frame(
  PCSPEC = c("urine", "feces", "plasma"),
  AVAL = c(100, 5, 70),
  AVALU = c("ug/mL", "mg/g", "ng/mL"),
  VOLUME = c(2, 1.5, 3),
  VOLUMEU = c("L", "mL", "mL"),
  stringsAsFactors = FALSE
)

df_converted <- convert_volume_units(df)
#> Row 1: Converted volume from 2 L to 2000 mL based on concentration unit ug/mL
#> Row 2: Converted volume from 1.5 mL to 1.5 g based on concentration unit mg/g