ume (version 1.5.2)

calc_ideg: 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",
  ...
)

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.

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.

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"
)