Get peaks and valleys from a spectrum

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,
  span = 5,
  strict = TRUE,
  x_unit = "",
  x_digits = 3,
  na.rm = FALSE
)

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

Arguments

x, y

numeric

global.threshold

numeric A value belonging to class "AsIs" is interpreted as an absolute minimum height or depth expressed in data units. A bare numeric value (normally between 0.0 and 1.0), is interpreted as relative to threshold.range. In both cases it sets a global height (depth) threshold below which peaks (valleys) are ignored. A bare negative numeric value indicates the global height (depth) threshold below which peaks (valleys) are be ignored. If global.threshold = NULL, no threshold is applied and all peaks returned.

span

odd positive 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.

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.

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.

Details

As find_valleys, peaks and valleys call find_peaks to search for peaks and valleys, this explanation applies to the four functions. It also applies to stat_peaks and stat_valleys. 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). Passing strict = TRUE ensures that non-unique global and within window maxima are ignored, and can result in no peaks being returned.

Two tests make it possible to ignore irrelevant peaks. One test (global.threshold) is based on the absolute height of the peaks and can be used in all cases to ignore globally low peaks. A second test (local.threshold) is available when the window defined by `span` does not include all observations and can be used to ignore peaks that are not locally prominent. In this second approach the height of each peak is compared to a summary computed from other values within the window of width equal to span where it was found. In this second case, the reference value used within each window containing a peak is given by the argument passed to 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 threshold values can in some cases result in no peaks being returned.

The local.threshold argument is used as is when local.reference is "median" or "farthest", i.e., the same distance between peak and reference is used as cut-off irrespective of the value of the reference. In cases when the prominence of peaks is positively correlated with the baseline, a local.threshold that increases together with increasing computed within window median or farthest value applies apply a less stringent height requirement in regions with overall low height. In this case, natural logarithm or square root weighting can be requested with local.reference arguments "median.log", "farthest.log", "median.sqrt", and "farthest.sqrt" as arguments for local.reference.

While functions find_peaks and find_valleys accept as input a numeric vector and return 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, find_valleys and fit_peaks.

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()