Calculates height, location and width of peak at the reflectance midpoint (FWHM).
Note: bounds should be set wide enough to incorporate all minima in spectra. Smoothing
procspec() is also recommended.
peakshape( rspecdata, select = NULL, lim = NULL, plot = TRUE, ask = FALSE, absolute.min = FALSE, ... )
(required) a data frame, possibly of class
contains a column containing a wavelength range, named 'wl', and spectra
data in remaining columns.
specification of which spectra to plot. Can be a numeric vector
or factor (e.g.,
sex == "male")
a vector specifying the wavelength range to analyze.
logical. Should plots indicating calculated parameters be returned?
logical, specifies whether user input needed to plot multiple plots
when number of spectra to analyze is greater than 1 (defaults to
TRUE, full width at half maximum will be
calculated using the absolute minimum reflectance of the spectrum, even if
that value falls outside the range specified by
lim. (defaults to
additional arguments to be passed to plot.
a data frame containing column names (id); peak height (max value, B3), location (hue, H1) and full width at half maximum (FWHM), as well as half widths on left (HWHM.l) and right side of peak (HWHM.r). Incl.min column indicates whether user-defined bounds incorporate the actual minima of the spectra. Function will return a warning if not.
data(teal) peakshape(teal, select = 3) #> id B3 H1 FWHM HWHM.l HWHM.r incl.min #> 1 Acrecca-02 56.4446 517 71 35 36 Yes peakshape(teal, select = 10) #> id B3 H1 FWHM HWHM.l HWHM.r incl.min #> 1 Acrecca-09 7.2747 307 NA NA 53 Yes # Use wavelength bounds to narrow in on peak of interest peakshape(teal, select = 10, lim = c(400, 550)) #> Warning: Consider fixing “lim” in spectra with “incl.min” marked “No” to incorporate all minima in spectral curves #> id B3 H1 FWHM HWHM.l HWHM.r incl.min #> 1 Acrecca-09 7.173 468 68 38 30 No