get_peaks: Get peaks and valleys from a spectrum

In photobiology: Photobiological Calculations

Get peaks and valleys from a spectrum

Description

These functions "get" (or extract) peaks (maxima) and valleys (minima) in two vectors, usually a spectral quantity and wavelength, using a user selectable span for window width and global and local (within moving window) size thresholds. They also generate character values for x.

Usage

get_peaks(
  x,
  y,
  global.threshold = 0,
  local.threshold = 0,
  local.reference = "minimum",
  threshold.range = NULL,
  span = 5,
  strict = TRUE,
  x_unit = "",
  x_digits = 3,
  na.rm = FALSE
)

get_valleys(
  x,
  y,
  global.threshold = 0,
  local.threshold = 0,
  local.reference = "minimum",
  threshold.range = NULL,
  span = 5,
  strict = TRUE,
  x_unit = "",
  x_digits = 3,
  na.rm = FALSE
)

Arguments

x, y	numeric
global.threshold	numeric A value between 0.0 and 1.0, relative to threshold.range indicating the global height (depth) threshold below which peaks (valleys) will be ignored, or a negative value, between 0.0 and -1.0 indicating the global height (depth) threshold above which peaks (valleys) will be ignored. If threshold.range = 0 or the value passed as argument belongs to class "AsIs" the value is interpreted as an absolute value expressed in data units.
local.threshold	numeric A value between 0.0 and 1.0, relative to threshold.range, indicating the within-window height (depth) threshold below which peaks (valleys) will be ignored. If threshold.range = 0 or the value passed as argument belongs to class "AsIs" the value is interpreted as an absolute value expressed in data units.
local.reference	character One of "minimum" (eqv. "maximum") or "median". The reference used to assess the height of the peak, either the minimum (maximum) value within the window or the median of all values in the window.
threshold.range	numeric vector of length 2 or a longer vector or list on which a call to range() returns a numeric vector of length 2. If NULL, the default, range(x) is used.
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.
strict	logical flag: if TRUE, an element must be strictly greater than all other values in its window to be considered a peak. Default: TRUE.
x_unit	character Vector of texts to be pasted at end of labels built from x value at peaks.
x_digits	numeric Number of significant digits in wavelength label.
na.rm	logical indicating whether NA values should be stripped before searching for peaks.

Details

Function find_peaks is a wrapper built onto function peaks from splus2R, adds support for peak height thresholds and handles span = NULL and non-finite (including NA) values differently than splus2R::peaks. Instead of giving an error when na.rm = FALSE and x contains NA values, NA values are replaced with the smallest finite value in x. span = NULL is treated as a special case and selects max(x). Two tests are optional, one based on the absolute height of the peaks (global.threshold) and another based on the height of the peaks compared to other values within the window of width equal to span (local.threshold). The reference value used within each window containing a peak is given by local.reference. Parameter threshold.range determines how the values passed as argument to global.threshold and local.threshold are scaled. The default, NULL uses the range of x. Thresholds for ignoring too small peaks are applied after peaks are searched for, and negative threshold values can in some cases result in no peaks being returned.

While function find_peaks accepts as input a numeric vector and returns a logical vector, methods peaks and valleys accept as input different R objects, including spectra and collections of spectra and return a subset of the object. These methods are implemented using calls to functions find_peaks and fit_peaks.

Value

A data frame with variables w.length and s.irrad with their values at the peaks or valleys plus a character variable of labels.

Note

The use of these two functions is deprecated. They are retained for backwards compatibility and will be removed in the near future.

See Also

Other peaks and valleys functions: find_peaks(), find_spikes(), peaks(), replace_bad_pixs(), spikes(), valleys(), wls_at_target()

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