Peak shape descriptors

Source: R/peakshape.R

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 spectra using procspec() is also recommended.

peakshape(
  rspecdata,
  select = NULL,
  lim = NULL,
  plot = TRUE,
  ask = FALSE,
  absolute.min = FALSE,
  ...
)

Arguments

rspecdata

(required) a data frame, possibly of class rspec, which contains a column containing a wavelength range, named 'wl', and spectra data in remaining columns.

select

specification of which spectra to plot. Can be a numeric vector or factor (e.g., sex == "male")

lim

a vector specifying the wavelength range to analyze.

plot

logical. Should plots indicating calculated parameters be returned? (Defaults to TRUE).

ask

logical, specifies whether user input needed to plot multiple plots when number of spectra to analyze is greater than 1 (defaults to FALSE).

absolute.min

logical. If 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 FALSE)

...

additional arguments to be passed to plot.

Value

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.

See also

procspec()

Author

Chad Eliason cme16@zips.uakron.edu

Rafael Maia rm72@zips.uakron.edu

Hugo Gruson hugo.gruson+R@normalesup.org

Examples

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