Calculate isotope ratios

Calculate intensity ratios of each mass relative to a base mass for every measurement in an ir_aggregate_isofiles() result. Ratios are added directly to the traces (continuous flow), cycles (dual inlet), and/or scans data present in the aggregated data as two extra columns: ratio_name (e.g. "29/28") and ratio. The ratio at each time.s/cycle/x position (within every uidx and analysis) is

Usage

ir_calculate_ratios(
  aggregated_data,
  ...,
  num_add.V = 100,
  denom_add.V = num_add.V,
  num_add.nA = 0,
  denom_add.nA = num_add.nA,
  num_add.cps = 0,
  denom_add.cps = num_add.cps,
  normalize_ratios = NULL
)

Arguments

aggregated_data

datasets aggregated from ir_aggregate_isofiles() (must include at least one of traces, cycles, or scans)

...

named base masses for individual species, e.g. SO2 = 64, N2 = 28. Species not listed here use their numerically lowest measured mass as the base mass.

num_add.V, denom_add.V

additive offset (in volts) for the numerator and denominator intensities of voltage-unit data (V/mV). Applies to traces and scans only, not to cycles (dual inlet). Default num_add.V = 100, denom_add.V = num_add.V.

num_add.nA, denom_add.nA

additive offset (in nanoamperes) for the numerator and denominator intensities of current-unit data (A/mA/µA/nA/pA/fA). Applies to traces and scans only, not to cycles (dual inlet). Default num_add.nA = 0, denom_add.nA = num_add.nA.

num_add.cps, denom_add.cps

additive offset (in cps) for the numerator and denominator intensities of count-unit data (cps). Applies to traces and scans only, not to cycles (dual inlet). Default num_add.cps = 0, denom_add.cps = num_add.cps.

normalize_ratios

NULL (default) for no normalization, or a function (e.g. mean, median, min, max) applied per uidx/analysis/ratio_name group; each ratio is divided by the value the function returns for its group's non-NA ratios.

Value

the aggregated_data with ratio_name and ratio columns added to each of the traces, cycles, and/or scans datasets that is present. Both columns are NA for base mass rows (and for any species whose requested base mass could not be found).

Details

$$ratio = (I_{mass} + num\_add) / (I_{base} + denom\_add)$$

i.e. the intensity of the mass divided by the intensity of the base mass of the same species, after adding an additive offset to numerator and denominator (see below). Base mass rows are kept and have NA in both columns. Calling this function again recomputes (overwrites) the ratio_name/ratio columns. The resulting ratios are not constrained in any way (they can be any value).

The base mass for a species is, by default, the numerically lowest mass measured for that species. Override it for individual species via ... (e.g. SO2 = 64, N2 = 28).

Additive offsets

The additive offsets apply to continuous-flow (traces) and scans data only. Dual inlet (cycles) data is not offset and always uses the plain ratio I_mass / I_base regardless of the num_add.*/denom_add.* settings.

For traces and scans, which pair of additive offsets is used depends on the intensity unit family of the data: voltage (V, mV) uses num_add.V/denom_add.V, current (A, mA, µA, nA, pA, fA) uses num_add.nA/denom_add.nA, and counts (cps) uses num_add.cps/denom_add.cps. The offsets are specified in their family's reference unit (volts, nanoamperes, cps) and are automatically scaled to the data's actual intensity unit before being added. For example, with intensity.mV data the default num_add.V = 100 (volts) is multiplied by 1000 and 100000 mV are added; with intensity.pA data the default num_add.nA = 0 would be multiplied by 1000 (1 nA = 1000 pA).

Normalization

normalize_ratios is NULL by default (no normalization). Pass a function to divide every ratio by the value that function returns for its uidx/analysis/ratio_name group (the function receives the group's non-NA ratios). For example normalize_ratios = mean centers each ratio around 1, while median, min, or max normalize to the group median, minimum, or maximum, respectively.