find_peaks {photobiology} | R Documentation |
Find local maxima or global maximum (peaks)
Description
These functions find peaks (local maxima) and valleys (local minima) in a
numeric vector, using a user selectable span and global and local size
thresholds, returning a logical
vector.
Usage
find_peaks(
x,
global.threshold = NULL,
local.threshold = NULL,
local.reference = "median",
threshold.range = NULL,
span = 3,
strict = FALSE,
na.rm = FALSE
)
find_valleys(
x,
global.threshold = NULL,
local.threshold = NULL,
local.reference = "median",
threshold.range = NULL,
span = 3,
strict = FALSE,
na.rm = FALSE
)
Arguments
x |
numeric vector. Hint: to find valleys, change the sign of the
argument with the unnary operator |
global.threshold |
numeric A value belonging to class |
local.threshold |
numeric A value belonging to class |
local.reference |
character One of |
threshold.range |
numeric vector If of length 2 or a longer vector
|
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 |
strict |
logical flag: if |
na.rm |
logical indicating whether |
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)
.
Passing 'strict = TRUE' ensures that multiple 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
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.
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
and fit_peaks
.
Value
A vector of logical values of the same length as x
. Values
that are TRUE correspond to local peaks in vector x
and can be used
to extract the rows corresponding to peaks from a data frame.
Note
The default for parameter strict
is FALSE
in functions
peaks()
and find_peaks()
, as in stat_peaks()
and in
stat_valleys()
, while the default in peaks
is strict = FALSE
.
See Also
Other peaks and valleys functions:
find_spikes()
,
get_peaks()
,
peaks()
,
replace_bad_pixs()
,
spikes()
,
valleys()
,
wls_at_target()
Examples
with(sun.data, which(find_peaks(s.e.irrad, span = NULL)))
with(sun.data, which(find_peaks(s.e.irrad, span = 51)))
with(sun.data, w.length[find_peaks(s.e.irrad, span = 51)])
with(sun.data, sum(find_peaks(s.e.irrad, span = NULL, strict = TRUE)))
with(sun.data, which(find_valleys(s.e.irrad, span = NULL)))
with(sun.data, which(find_valleys(s.e.irrad, span = 51)))