check_wl_stepsize: Check consistency of wavelength step size

In photobiology: Photobiological Calculations

Check consistency of wavelength step size

Description

Check consistency of wavelength step size

Usage

check_wl_stepsize(x, span = Inf)

Arguments

x	numeric vector. Hint: to find valleys, change the sign of the argument with the unary operator -.
span	odd integer A peak is defined as an element in a sequence which is greater than all other elements within a moving window of width span centred at that element. The default value is 5, meaning that a peak is taller than its four nearest neighbours. span = NULL extends the span to the whole length of x.

Details

As the search for peaks uses a window based on a fixed number of observations at neighbouring wavelengths, if the wavelength step between observations varies drastically, the window expressed in nanometres of wavelength becomes very irregular. With the default span = 5 in peaks(), valleys(), and wls_at_target() the search in most cases still works for "thinned" spectra, and the check is skipped. With spikes() and despike() methods the check is always done as these methods do not override span = Inf.

The typical case when the step can vary strongly are spectra returned by thin_wl(). As when using default arguments thin_wl() retains the original local maxima, and a reasonably narrow wavelength maximum step a call to peaks with span = NULL or span = 5 tends to discover the original peaks missing at most a few.

Value

logical TRUE if check is passed and otherwise FALSE with a warning.

photobiology documentation built on June 8, 2025, 10:14 a.m.