Remove Raman and Rayleigh scattering lines from EEMs

Raman and Rayleigh scattering can interfere with sample fluorescence signals. Raman scattering is inelastic scattering caused by interaction with the solvent, shifting to longer wavelengths. Rayleigh scattering is elastic scattering, where light bounces off molecules without energy loss, appearing on the 1:1 line and often intense. Second-order Raman and Rayleigh scattering may also occur due to two-photon interactions doubling the excitation wavelength.

Usage

remove_scattering(
  eemlist,
  type = c(TRUE, TRUE, TRUE, TRUE),
  width = c(16, 3, 30, 10),
  interpolate = c(TRUE, TRUE, FALSE, FALSE),
  method = 1,
  cores = 1,
  arg_names = NULL
)

Arguments

eemlist

An eemlist object.

type

Logical vector of length four indicating which scattering lines to remove. The order is "raman1", "raman2", "rayleigh1", "rayleigh2". Set TRUE to remove.

width

Numeric vector of length four specifying the width (nm) of the scattering lines to remove. Order is "raman1", "raman2", "rayleigh1", "rayleigh2".

interpolate

Logical vector of length four indicating which scattering lines to interpolate. Order is "raman1", "raman2", "rayleigh1", "rayleigh2".

method

Numeric 0–4 specifying interpolation method (default = 1). See eem_interp().

cores

Number of cores for parallel interpolation computation.

arg_names

Optional list of arguments passed from higher-level functions for README generation.

Value

An eemlist object with specified scattering lines removed.

Note

This function is a modified version of staRdom::eem_rem_scat() from the staRdom package, allowing selective interpolation instead of all-or-nothing.

References

Gilchrist, J. R., & Reynolds, D. M. (2014). Optical Spectroscopy Instrumentation Design, Quality Assurance, and Control: Bench-Top Fluorimetry. In A. Baker, D. M. Reynolds, J. Lead, P. G. Coble, & R. G. M. Spencer (Eds.), Aquatic Organic Matter Fluorescence (pp. 147-189). Cambridge: Cambridge University Press. doi:10.1017/CBO9781139045452.009

Examples

# default settings (remove all, interpolate only raman lines)
eemlist <- remove_scattering(example_eems)
plot(eemlist[[6]])


# only remove only rayleigh lines
eemlist <- remove_scattering(example_eems, type = c(FALSE, FALSE, TRUE, TRUE))
plot(eemlist[[6]])


# change the width of the lines
eemlist <- remove_scattering(example_eems, width = c(16, 3, 100, 40))
plot(eemlist[[6]])