peaks: Peaks or local maxima
In photobiology: Photobiological Calculations
peaks R Documentation
Peaks or local maxima
Description
Function that returns a subset of an R object with observations corresponding
to local maxima.
Usage
peaks(
x,
span,
global.threshold,
local.threshold,
local.reference,
threshold.range,
strict,
na.rm,
...
)
## Default S3 method:
peaks(
x,
span = NA,
global.threshold = NA,
local.threshold = NA,
local.reference = NA,
threshold.range = NA,
strict = NA,
na.rm = FALSE,
...
)
## S3 method for class 'numeric'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
...
)
## S3 method for class 'data.frame'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
x.var.name = NULL,
y.var.name = NULL,
var.name = y.var.name,
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'generic_spct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
var.name = NULL,
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'source_spct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
unit.out = getOption("photobiology.radiation.unit", default = "energy"),
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'response_spct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
unit.out = getOption("photobiology.radiation.unit", default = "energy"),
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'filter_spct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
filter.qty = getOption("photobiology.filter.qty", default = "transmittance"),
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'reflector_spct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'solute_spct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'cps_spct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
var.name = "cps",
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'raw_spct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
var.name = "counts",
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'generic_mspct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
var.name = NULL,
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
## S3 method for class 'source_mspct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
unit.out = getOption("photobiology.radiation.unit", default = "energy"),
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
## S3 method for class 'response_mspct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
unit.out = getOption("photobiology.radiation.unit", default = "energy"),
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
## S3 method for class 'filter_mspct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
filter.qty = getOption("photobiology.filter.qty", default = "transmittance"),
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
## S3 method for class 'reflector_mspct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
## S3 method for class 'solute_mspct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
## S3 method for class 'cps_mspct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
var.name = "cps",
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
## S3 method for class 'raw_mspct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
var.name = "counts",
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
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.
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.
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.
na.rm
logical indicating whether NA values should be stripped
before searching for peaks.
...
ignored
var.name, x.var.name, y.var.name
character Name of column where to look
for peaks.
refine.wl
logical Flag indicating if peak location should be refined
by fitting a function.
method
character String with the name of a method. Currently only
spline interpolation is implemented.
unit.out
character One of "energy" or "photon"
filter.qty
character One of "transmittance" or "absorbance"
.parallel
if TRUE, apply function in parallel, using parallel backend
provided by foreach
.paropts
a list of additional options passed into the foreach function
when parallel computation is enabled. This is important if (for example)
your code relies on external data or packages: use the .export and
.packages arguments to supply them so that all cluster nodes have the
correct environment set up for computing.
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 subset of x with rows corresponding to local maxima.
Methods (by class)
-
peaks(default): Default returning always NA.
-
peaks(numeric): Default function usable on numeric vectors.
-
peaks(data.frame): Method for "data.frame" objects.
-
peaks(generic_spct): Method for "generic_spct" objects.
-
peaks(source_spct): Method for "source_spct" objects.
-
peaks(response_spct): Method for "response_spct" objects.
-
peaks(filter_spct): Method for "filter_spct" objects.
-
peaks(reflector_spct): Method for "reflector_spct" objects.
-
peaks(solute_spct): Method for "solute_spct" objects.
-
peaks(cps_spct): Method for "cps_spct" objects.
-
peaks(raw_spct): Method for "raw_spct" objects.
-
peaks(generic_mspct): Method for "generic_mspct" objects.
-
peaks(source_mspct): Method for "source_mspct" objects.
-
peaks(response_mspct): Method for "cps_mspct" objects.
-
peaks(filter_mspct): Method for "filter_mspct" objects.
-
peaks(reflector_mspct): Method for "reflector_mspct" objects.
-
peaks(solute_mspct): Method for "solute_mspct" objects.
-
peaks(cps_mspct): Method for "cps_mspct" objects.
-
peaks(raw_mspct): Method for "raw_mspct" objects.
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 = TRUE.
See Also
Other peaks and valleys functions:
find_peaks(),
find_spikes(),
get_peaks(),
replace_bad_pixs(),
spikes(),
valleys(),
wls_at_target()
Examples
# default span = 5
peaks(sun.spct)
# global maximum
peaks(sun.spct, span = NULL)
peaks(sun.spct, span = NULL)$w.length
# fitted peak wavelength
peaks(sun.spct, span = NULL, refine.wl = TRUE)
peaks(sun.spct, span = NULL, refine.wl = TRUE)$w.length
# a wider window
peaks(sun.spct, span = 51)
# global threshold relative to the range of s.e.irrad values
peaks(sun.spct, global.threshold = 0.7)
peaks(sun.spct, global.threshold = -0.3)
# global threshold in actual s.e.irrad values
peaks(sun.spct, global.threshold = 0.7, threshold.range = c(0, 1))
# local threshold relative to the range of s.e.irrad values
peaks(sun.spct, local.threshold = 0.1)
# local threshold in actual s.e.irrad values
peaks(sun.spct, local.threshold = 0.1, threshold.range = c(0, 1))
# local threshold relative to the range of s.e.irrad values, using window
# median instead of window minimum
peaks(sun.spct, local.threshold = 0.05, local.reference = "median")
# minimum, the default.
peaks(sun.spct, local.threshold = 0.05, local.reference = "minimum")
peaks(sun.spct)
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| peaks | R Documentation |
Peaks or local maxima
Description
Function that returns a subset of an R object with observations corresponding to local maxima.
Usage
peaks(
x,
span,
global.threshold,
local.threshold,
local.reference,
threshold.range,
strict,
na.rm,
...
)
## Default S3 method:
peaks(
x,
span = NA,
global.threshold = NA,
local.threshold = NA,
local.reference = NA,
threshold.range = NA,
strict = NA,
na.rm = FALSE,
...
)
## S3 method for class 'numeric'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
...
)
## S3 method for class 'data.frame'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
x.var.name = NULL,
y.var.name = NULL,
var.name = y.var.name,
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'generic_spct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
var.name = NULL,
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'source_spct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
unit.out = getOption("photobiology.radiation.unit", default = "energy"),
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'response_spct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
unit.out = getOption("photobiology.radiation.unit", default = "energy"),
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'filter_spct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
filter.qty = getOption("photobiology.filter.qty", default = "transmittance"),
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'reflector_spct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'solute_spct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'cps_spct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
var.name = "cps",
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'raw_spct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
var.name = "counts",
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'generic_mspct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
var.name = NULL,
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
## S3 method for class 'source_mspct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
unit.out = getOption("photobiology.radiation.unit", default = "energy"),
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
## S3 method for class 'response_mspct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
unit.out = getOption("photobiology.radiation.unit", default = "energy"),
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
## S3 method for class 'filter_mspct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
filter.qty = getOption("photobiology.filter.qty", default = "transmittance"),
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
## S3 method for class 'reflector_mspct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
## S3 method for class 'solute_mspct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
## S3 method for class 'cps_mspct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
var.name = "cps",
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
## S3 method for class 'raw_mspct'
peaks(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
var.name = "counts",
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
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
|
global.threshold |
numeric A value between 0.0 and 1.0,
relative to |
local.threshold |
numeric A value between 0.0 and 1.0, relative to
|
local.reference |
character One of |
threshold.range |
numeric vector of length 2 or a longer vector or list
on which a call to |
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. |
na.rm |
logical indicating whether |
... |
ignored |
var.name, x.var.name, y.var.name |
character Name of column where to look for peaks. |
refine.wl |
logical Flag indicating if peak location should be refined by fitting a function. |
method |
character String with the name of a method. Currently only spline interpolation is implemented. |
unit.out |
character One of "energy" or "photon" |
filter.qty |
character One of "transmittance" or "absorbance" |
.parallel |
if TRUE, apply function in parallel, using parallel backend provided by foreach |
.paropts |
a list of additional options passed into the foreach function when parallel computation is enabled. This is important if (for example) your code relies on external data or packages: use the .export and .packages arguments to supply them so that all cluster nodes have the correct environment set up for computing. |
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 subset of x with rows corresponding to local maxima.
Methods (by class)
-
peaks(default): Default returning always NA. -
peaks(numeric): Default function usable on numeric vectors. -
peaks(data.frame): Method for "data.frame" objects. -
peaks(generic_spct): Method for "generic_spct" objects. -
peaks(source_spct): Method for "source_spct" objects. -
peaks(response_spct): Method for "response_spct" objects. -
peaks(filter_spct): Method for "filter_spct" objects. -
peaks(reflector_spct): Method for "reflector_spct" objects. -
peaks(solute_spct): Method for "solute_spct" objects. -
peaks(cps_spct): Method for "cps_spct" objects. -
peaks(raw_spct): Method for "raw_spct" objects. -
peaks(generic_mspct): Method for "generic_mspct" objects. -
peaks(source_mspct): Method for "source_mspct" objects. -
peaks(response_mspct): Method for "cps_mspct" objects. -
peaks(filter_mspct): Method for "filter_mspct" objects. -
peaks(reflector_mspct): Method for "reflector_mspct" objects. -
peaks(solute_mspct): Method for "solute_mspct" objects. -
peaks(cps_mspct): Method for "cps_mspct" objects. -
peaks(raw_mspct): Method for "raw_mspct" objects.
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 = TRUE.
See Also
Other peaks and valleys functions:
find_peaks(),
find_spikes(),
get_peaks(),
replace_bad_pixs(),
spikes(),
valleys(),
wls_at_target()
Examples
# default span = 5
peaks(sun.spct)
# global maximum
peaks(sun.spct, span = NULL)
peaks(sun.spct, span = NULL)$w.length
# fitted peak wavelength
peaks(sun.spct, span = NULL, refine.wl = TRUE)
peaks(sun.spct, span = NULL, refine.wl = TRUE)$w.length
# a wider window
peaks(sun.spct, span = 51)
# global threshold relative to the range of s.e.irrad values
peaks(sun.spct, global.threshold = 0.7)
peaks(sun.spct, global.threshold = -0.3)
# global threshold in actual s.e.irrad values
peaks(sun.spct, global.threshold = 0.7, threshold.range = c(0, 1))
# local threshold relative to the range of s.e.irrad values
peaks(sun.spct, local.threshold = 0.1)
# local threshold in actual s.e.irrad values
peaks(sun.spct, local.threshold = 0.1, threshold.range = c(0, 1))
# local threshold relative to the range of s.e.irrad values, using window
# median instead of window minimum
peaks(sun.spct, local.threshold = 0.05, local.reference = "median")
# minimum, the default.
peaks(sun.spct, local.threshold = 0.05, local.reference = "minimum")
peaks(sun.spct)
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