calc_ideg: Calculate Degradation Index (Ideg)

In ume: Ultrahigh-Resolution Mass Spectrometry Data Evaluation for Complex Organic Matter

Calculate Degradation Index (Ideg)

Description

This function calculates the degradation index ('Ideg') following Flerus et al. (2012). High Ideg values indicate 'older' marine DOM (i.e., a higher contribution of peaks that correlate negatively with delta14C), while low values indicate 'younger' DOM (i.e., a higher contribution of peaks that correlate positively with delta14C)./

Ideg is computed as the ratio of summed magnitudes for five negative (NEG) molecular formulas to the total summed magnitudes of five positive (POS) and five negative (NEG) molecular formulas:

Ideg = \frac{\sum{NEG}}{\sum{NEG} + \sum{POS}}

The index ranges from 0 to 1 and is valid only if all required formulas (n = 10) are present. Ideg depends strongly on the type of sample preparation, ionization method, and instrument settings, and should only be interpreted for relative changes within the same dataset.

Usage

calc_ideg(
  mfd,
  mf_col = "mf",
  magnitude_col = "i_magnitude",
  grp = "file_id",
  ...
)

Arguments

mfd	data.table with molecular formula data as derived from ume::assign_formulas. Column names of elements/isotopes must match names in the isotope column of ume::masses; values are integers representing counts per formula.
mf_col	Character. The name of the column containing molecular formulas. Default is "mf".
magnitude_col	Character. The name of the column containing magnitude values (absolute or relative). Default is "i_magnitude".
grp	Character vector. Names of columns (e.g., sample or file identifiers) used to aggregate results.
...	Additional arguments passed to methods.

Value

A data.table with columns:

• grp: Grouping variable.

• ideg: Calculated degradation index (rounded to 3 decimals).

• ideg_n: Number of assigned formulas used in the calculation.

See Also

Other calculations: calc_data_summary(), calc_dbe(), calc_eval_params(), calc_exact_mass(), calc_ma(), calc_neutral_mass(), calc_nm(), calc_norm_int(), calc_number_assignment(), calc_number_occurrence(), calc_recalibrate_ms()

Examples

# Create a minimal dataset containing all required POS and NEG formulas
library(data.table)

demo_ideg <- data.table(
  file_id = 1,
  mf = c(
    "C17H20O9", "C19H22O10", "C20H22O10", "C20H24O11", "C21H26O11",   # NEG
    "C13H18O7", "C14H20O7", "C15H22O7", "C15H22O8", "C16H24O8"        # POS
  ),
  i_magnitude = c(
    1200, 900, 1500, 700, 800,     # NEG intensities
    2000, 1800, 2200, 1600, 1900   # POS intensities
  )
)

calc_ideg(
  mfd = demo_ideg,
  mf_col = "mf",
  magnitude_col = "i_magnitude",
  grp = "file_id"
)

ume documentation built on Dec. 13, 2025, 1:06 a.m.