ume (version 1.5.2)

calc_iterr: Calculate terrestrial indeces Iterr and Iterr2 (after Medeiros et al. 2016)

Description

Calculate a degradation index 'Iterr' and modified index 'iterr2' after Medeiros et al. (2016). High Iterr values represent higher contribution of terrestrial material (i.e. higher contribution of peaks that correlate positively with delta13C) while low values represent less terrestrial material (i.e. higher contribution of peaks that correlate negatively with delta13C). Iterr / Iterr2 are calculated from a peak magnitude ratio of 50 or 5 POS and NEG formulas, respectively: sum(POS) / (sum(POS) + sum(NEG)) Therefore Iterr / Iterr2 range between 1 and 0. It should be noted that absolute values strongly depend on factors such as type of solid phase extraction, ionization method, instrument settings etc. Therefore values can only be interpreted as relative changes. It should also be noted that for an appropriate evaluation ALL index formulas must be present.

Usage

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

Value

Iterr and iterr2 values

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

Name of the column containing molecular formulas (string)

magnitude_col

Name of the column containing absolute or relative mass peak magnitudes (string).

grp

Character vector. Names of columns (e.g., sample or file identifiers) used to aggregate results.

...

Additional arguments passed to methods.

Examples

library(data.table)

# Create a minimal dataset containing all required
# POS, NEG, POS2, and NEG2 formulas for demonstration

demo_iterr <- data.table(
  file_id = 1,
  mf = c(
    # NEG (Iterr)
    'C13H12O5','C15H14O4','C14H12O5','C14H14O5','C13H12O6',
    'C16H16O4','C15H14O5','C14H12O6','C15H16O5','C14H14O6',
    'C16H14O5','C16H16O5','C15H14O6','C15H16O6','C14H14O7',
    'C17H16O5','C16H14O6','C17H18O5','C16H16O6','C15H14O7',
    'C17H16O6','C16H14O7','C18H18O6','C17H16O7','C17H18O7',
    'C18H16O7','C18H18O7','C17H16O8','C19H18O7','C20H20O7',
    'C19H18O8','C20H18O9','C19H16O10','C21H20O9','C20H18O10',
    'C22H22O9','C21H20O10','C23H22O10','C24H24O10','C25H26O10',

    # POS (Iterr)
    'C15H19NO6','C15H21NO6','C17H21NO7','C17H23NO7','C17H22O8',
    'C16H21NO8','C17H20N2O7','C17H19NO8','C18H23NO7','C17H21NO8',
    'C18H24O8','C16H19NO9','C17H23NO8','C17H22O9','C17H24O9',
    'C18H21NO8','C17H19NO9','C18H23NO8','C18H22O9','C17H21NO9',
    'C18H24O9','C18H20N2O8','C18H21NO9','C19H24O9','C18H23NO9',
    'C18H22O10','C18H24O10','C20H24O9','C19H22O10','C20H26O9',
    'C19H24O10','C19H26O10','C20H24O10','C20H26O10','C19H24O11',
    'C20H24O11','C20H26O11','C20H26O12','C22H28O11','C21H28O12',

    # NEG2 (Iterr2)
    'C17H18O7','C18H18O7','C17H16O7','C17H16O8','C15H16O6',

    # POS2 (Iterr2)
    'C20H24O9','C20H24O10','C19H22O10','C17H21NO8','C20H26O9'
  ),

  # Assign magnitude values (arbitrary but valid)
  i_magnitude = c(
    rep(1000, 40),  # NEG
    rep(2000, 40),  # POS
    rep(1500, 5),   # NEG2
    rep(1800, 5)    # POS2
  )
)

calc_iterr(
  mfd = demo_iterr,
  mf_col = "mf",
  magnitude_col = "i_magnitude",
  grp = "file_id"
)