procspec: Process spectra

Description

Applies normalization and/or smoothing to spectra for further analysis or plotting

Usage

procspec(rspecdata,
    opt = c("none", "smooth", "maximum", "minimum", "bin", "sum", "center"),
    fixneg = c("none", "addmin", "zero"), span = 0.25,
    bins = 20)

Arguments

rspecdata

(required) a data frame, possibly an object of class rspec, with a column with wavelength data, named 'wl', and the remaining column containing spectra to process.

opt

what type of processing options to apply. User can select multiple options by providing a vector. Possibilites are:

"none"does not perform any processing (default).
"smooth"applies LOESS smoothing to each sp

fixneg

how to handle negative values. Possibilities are:

"none"does not perform negative value correction (default).
"zero"sets all negative values to zero.
"addmin"adds the absolute value of the

span

sets the smoothing parameter used by loess.smooth

bins

sets the number of equally sized wavelength bins for opt="bin"

Value

A data frame of class rspec with the processed data.

References

Cuthill, I., Bennett, A. T. D., Partridge, J. & Maier, E. 1999. Plumage reflectance and the objective assessment of avian sexual dichromatism. The American Naturalist, 153, 183-200.

Montgomerie R. 2006. Analyzing colors. In Hill, G.E, and McGraw, K.J., eds. Bird Coloration. Volume 1 Mechanisms and measuremements. Harvard University Press, Cambridge, Massachusetts.

Examples

Run this code

data(teal)
plot(teal, select = 10)
# Smooth data to remove noise
teal.sm <- procspec(teal, opt = 'smooth', span = 0.25)
plot(teal.sm, select = 10)
# Normalize to max of unity
teal.max <- procspec(teal, opt = c('max'), span = 0.25)
plot(teal.max, select = 10)