Computes contents of Klason lignin and holocellulose of peat from mid infrared spectra

irp_content_klh_hodgkins computes the mass fraction of Klason lignin and holocellulose in peat from mid infrared spectra of the peat samples. This function may also work for organic matter in general. Note that the models have been shown to be biased for peat samples (Teickner and Knorr 2022) .

Usage

irp_content_klh_hodgkins(x, export = NULL, verbose = FALSE, make_plots = FALSE)

Source

irp_content_klh_hodgkins is a wrapper function to a script written by Suzanne Hodgkins (https://github.com/shodgkins/FTIRbaselines/blob/master/FTIRbaselines.R). and distributed under the GPL-3 (https://www.gnu.org/licenses/gpl-3.0.html) license. The original script was modified for this purpose.

Arguments

x

An object of class ir.

export

Either a valid path to an existing directory where to store the results of the original script (see section "Source") irp_content_klh_hodgkins is based on (if this output should be exported) or NULL (if nothing should be exported). Note that export has to be specified in order to analyze any issues with the data (e.g. high clay content) that may confound the computed values. Refer to the original publication ((Hodgkins et al. 2018) ) to get information on the meaning of the exported objects.

verbose

A logical value indicating if messages should be printed (verbose = TRUE) or not (verbose = FALSE).

make_plots

logical value indicating if plots should be printed (make_plots = TRUE) or not (make_plots = FALSE).

Value

An object of class ir with additional columns containing the computed mass fractions of Klason lignin and holocellulose for the spectra in x.

Note

Note that the models have been shown to be biased for peat samples (Teickner and Knorr 2022) .

References

Hodgkins SB, Richardson CJ, Dommain R, Wang H, Glaser PH, Verbeke B, Winkler BR, Cobb AR, Rich VI, Missilmani M, Flanagan N, Ho M, Hoyt AM, Harvey CF, Vining SR, Hough MA, Moore TR, Richard PJH, De La Cruz, Florentino B., Toufaily J, Hamdan R, Cooper WT, Chanton JP (2018). “Tropical peatland carbon storage linked to global latitudinal trends in peat recalcitrance.” Nature communications, 9(1), 3640. doi:10.1038/s41467-018-06050-2 .

Teickner H, Knorr K (2022). “Improving Models to Predict Holocellulose and Klason Lignin Contents for Peat Soil Organic Matter with Mid Infrared Spectra.” Soil and methods. doi:10.5194/soil-2022-27 .

Examples

library(ir)

irp_content_klh_hodgkins(
  ir::ir_sample_data[1:5, ],
  export = NULL,
  verbose = TRUE,
  make_plots = FALSE
)
#> Processing 1 (1 of 5)
#> Processing 2 (2 of 5)
#> Processing 3 (3 of 5)
#> Processing 4 (4 of 5)
#> Processing 5 (5 of 5)
#> Spectra with baselines and peak locations will be shown for all 5 samples.
#> Computing Klason lignin and holocellulose contents.
#> # A tibble: 5 × 9
#>   id_measurement id_sample sample_type sample_comment              klason_lignin
#> *          <int> <chr>     <chr>       <chr>                                 [1]
#> 1              1 GN 11-389 needles     Abies Firma Momi fir                0.360
#> 2              2 GN 11-400 needles     Cupressocyparis leylandii …         0.339
#> 3              3 GN 11-407 needles     Juniperus chinensis Chines…         0.268
#> 4              4 GN 11-411 needles     Metasequoia glyptostroboid…         0.350
#> 5              5 GN 11-416 needles     Pinus strobus Torulosa              0.331
#> # … with 4 more variables: holocellulose [1], spectra <named list>,
#> #   holocellulose_hodgkins (err) [g/g], klason_lignin_hodgkins (err) [g/g]