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.
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
)
A data frame with variables w.length and s.irrad with their values at the peaks or valleys plus a character variable of labels.
numeric
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.
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.
logical flag: if TRUE, an element must be strictly
greater than all other values in its window to be considered a peak.
character Vector of texts to be pasted at end of labels built from x value at peaks.
numeric Number of significant digits in wavelength label.
logical indicating whether NA values should be stripped
before searching for peaks.
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.
Other peaks and valleys functions:
find_peaks(),
find_spikes(),
peaks(),
replace_bad_pixs(),
spikes(),
valleys(),
wls_at_target()