peaks | R Documentation |
Function that returns a subset of an R object with observations corresponding to local maxima.
peaks(x, span, ignore_threshold, strict, na.rm, ...)
## Default S3 method:
peaks(x, span = NA, ignore_threshold = NA, strict = NA, na.rm = FALSE, ...)
## S3 method for class 'numeric'
peaks(x, span = 5, ignore_threshold = NA, strict = TRUE, na.rm = FALSE, ...)
## S3 method for class 'data.frame'
peaks(
x,
span = 5,
ignore_threshold = 0,
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,
ignore_threshold = 0,
strict = TRUE,
na.rm = FALSE,
var.name = NULL,
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'source_spct'
peaks(
x,
span = 5,
ignore_threshold = 0,
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,
ignore_threshold = 0,
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,
ignore_threshold = 0,
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,
ignore_threshold = 0,
strict = TRUE,
na.rm = FALSE,
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'solute_spct'
peaks(
x,
span = 5,
ignore_threshold = 0,
strict = TRUE,
na.rm = FALSE,
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'cps_spct'
peaks(
x,
span = 5,
ignore_threshold = 0,
strict = TRUE,
na.rm = FALSE,
var.name = "cps",
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'raw_spct'
peaks(
x,
span = 5,
ignore_threshold = 0,
strict = TRUE,
na.rm = FALSE,
var.name = "counts",
refine.wl = FALSE,
method = "spline",
...
)
## S3 method for class 'generic_mspct'
peaks(
x,
span = 5,
ignore_threshold = 0,
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,
ignore_threshold = 0,
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,
ignore_threshold = 0,
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,
ignore_threshold = 0,
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,
ignore_threshold = 0,
strict = TRUE,
na.rm = FALSE,
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
## S3 method for class 'solute_mspct'
peaks(
x,
span = 5,
ignore_threshold = 0,
strict = TRUE,
na.rm = FALSE,
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
## S3 method for class 'cps_mspct'
peaks(
x,
span = 5,
ignore_threshold = 0,
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,
ignore_threshold = 0,
strict = TRUE,
na.rm = FALSE,
var.name = "counts",
refine.wl = FALSE,
method = "spline",
...,
.parallel = FALSE,
.paropts = NULL
)
x |
an R object |
span |
integer A peak is defined as an element in a sequence which is
greater than all other elements within a window of width |
ignore_threshold |
numeric Value between 0.0 and 1.0 indicating the relative size compared to tallest peak threshold below which peaks will be ignored. Negative values set a threshold so that the tallest peaks are ignored, instead of the shortest. |
strict |
logical If |
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. |
A subset of x
with rows corresponding to local maxima.
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.
Thresholds for ignoring peaks are applied after peaks are searched for, and negative threshold values can in some cases result in no peaks being returned.
Other peaks and valleys functions:
find_peaks()
,
find_spikes()
,
get_peaks()
,
replace_bad_pixs()
,
spikes()
,
valleys()
,
wls_at_target()
peaks(sun.spct, span = 51)
peaks(sun.spct, span = NULL)
peaks(sun.spct, span = 51, refine.wl = TRUE)
peaks(sun.spct)
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