albatross (version 0.1-1)

feemife: Absorbance-based inner filter effect correction

Description

Use absorbance data to correct inner-filter effect in FEEM objects and collections of them.

Usage

feemife(x, …)
  # S3 method for feem
feemife(x, absorbance, abs.path = 1, …)
  # S3 method for feemcube
feemife(x, absorbance, abs.path, …)
  # S3 method for list
feemife(x, absorbance, abs.path, …)

Arguments

x

A FEEM object, a FEEM data cube, or a list of them.

absorbance

If x is a FEEM object: a two-column matrix-like object suitable for xy.coords containing the absorbance spectrum of the sample: the wavelengths in the first column and the unitless absorbance values in the second column.

Otherwise, this could be a list of such objects or a multi-column matrix-like objects. If x contains names of the samples (is a named list or had names specified when calling feemcube), absorbance is a named list or has named columns, and all samples from x can be looked up in absorbance, results of this lookup are used. If name lookup fails but (given \(N\)-sample x) absorbance has exactly \(N+1\) columns or is an \(N\)-element list, absorbances are supposed to be present in the same order as the samples in x.

abs.path

If x is a FEEM object, a number specifying the length of the optical path used when measuring the absorbance, cm.

Otherwise, a vector of them of exactly same length as the number of FEEMs in x.

If not set, assumed to be \(1\).

…

No parameters besides those described above are allowed.

Value

An object of the same kind as x, with inner filter effect corrected.

Details

The formula used is:

$$ I_{corr}(\lambda_{em}, \lambda_{ex}) = % I_{orig}(\lambda_{em}, \lambda_{ex}) 10^{ % \frac{A(\lambda{em}) + A(\lambda{ex})}{2 L_{abs}} % } $$

References

J.R. Lakowicz, Principles of Fluorescence Spectroscopy, 3rd ed., Springer US, 2006. https://www.springer.com/la/book/9780387312781

D.N. Kothawala, K.R. Murphy, C.A. Stedmon, G.A. Weyhenmeyer, L.J. Tranvik, Inner filter correction of dissolved organic matter fluorescence: Correction of inner filter effects, Limnology and Oceanography: Methods. 11 (2013) 616-630. 10.4319/lom.2013.11.616

Examples

# NOT RUN {
  data(feems)

  dataset <- feemcube(feems, FALSE)
  str(dataset)
  str(absorp)
  plot(feemife(dataset,absorp) / dataset)
# }