Compute humification indices from mid infrared spectra

irp_hi computes either custom humification indices or a predefined set of humification indices as reported by Broder et al. (2012) for mid infrared spectra with the x values representing wavenumber values (no checks are performed) (see the details section for the humification indices computed by default). A humification index is the ratio of the intensity values at two different x axis values (e.g. wavenumbers) and defined as: $$ HI = \frac{y_x1}{y_x2} $$, where \(y_x1\) is the intensity of the spectrum at x axis value \(x1\) and \(y_x2\) is the intensity of the spectrum at x axis value \(x2\).

Usage

irp_hi(x, x1 = NULL, x2 = NULL)

Arguments

x

An object of class ir.

x1

A numeric vector with values representing x axis values in the spectra of x. This is \(x1\) in the equation displayed above. If multiple humification indices for the same x2 should be computed, x1 can contain multiple values. If x1 = NULL, the default humification indices will be computed (see details section).

x2

A numeric value representing an x axis value in the spectra of x. This is \(x2\) in the equation displayed above. If x2 = NULL, the default humification indices will be computed (see details section).

Value

An object of class ir with additional columns for additional humification indices. If x1 = NULL and x2 = NULL, these are four new columns (hi1, hi2, hi3 and hi4) that correspond to the humification indices defined in the details section. If x1 and x2 are not NULL, the columns have names "hi_x1_x2" where x1 and x2 are replaced by the respective values.

Details

The following humification indices are computed by default (if x1 = NULL and x2 = NULL) (values represent wavenumbers [cm\(^{-1}\)]) (Broder et al. 2012) :

hi1: 1420/1090

OH and CO of phenols or CH of CH_1 and CH_3 groups (phenolic and aliphatic structures)/polysaccharides

hi2: 1510/1090

Aromatic C=C or C=O of amides/polysaccharides

hi3: 1630/1090

Aromatic C=C and COO\(^{-1}\) (aromatics and aromatic or aliphatic carboxylates)/polysaccharides

hi4: 1720/1090

carbonylic and carboxylic C=O (carboxylic acids and aromatic esters)/polysaccharides

References

Broder T, Blodau C, Biester H, Knorr KH (2012). “Peat decomposition records in three pristine ombrotrophic bogs in southern Patagonia.” Biogeosciences, 9(4), 1479--1491. doi:10.5194/bg-9-1479-2012 .

Examples

# get sample data
library(ir)

# compute default humification indices
d <- ir_sample_data[1:5, ]
d <- irp_hi(d)

# compute custom humification index
d <- ir_sample_data
d <- irp_hi(d, x1 = 2900, x2 = 1090)

# compute custom humification indices
d <- ir_sample_data
d <- irp_hi(d, x1 = c(2900, 1630), x2 = 1090)