Function that returns a subset of an R object with observations corresponding to local maxima.
valleys(
x,
span,
global.threshold,
local.threshold,
local.reference,
threshold.range,
strict,
...
)# S3 method for default
valleys(
x,
span,
global.threshold = NA,
local.threshold = NA,
local.reference = NA,
threshold.range = NA,
strict,
...
)
# S3 method for numeric
valleys(
x,
span = 5,
global.threshold = 0,
local.threshold = 0,
local.reference = "minimum",
threshold.range = NULL,
strict = TRUE,
na.rm = FALSE,
...
)
# S3 method for data.frame
valleys(
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 generic_spct
valleys(
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 source_spct
valleys(
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 response_spct
valleys(
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 filter_spct
valleys(
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 reflector_spct
valleys(
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 solute_spct
valleys(
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 cps_spct
valleys(
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 raw_spct
valleys(
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 generic_mspct
valleys(
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 source_mspct
valleys(
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 response_mspct
valleys(
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 filter_mspct
valleys(
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 reflector_mspct
valleys(
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 solute_mspct
valleys(
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 cps_mspct
valleys(
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 raw_mspct
valleys(
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
)
A subset of x with rows corresponding to local minima or
global minimum.
numeric vector. Hint: to find valleys, change the sign of the
argument with the unary operator -.
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.
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.
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.
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.
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.
logical flag: if TRUE, an element must be strictly greater than all other values in its window to be considered a peak. Default: TRUE.
ignored
logical indicating whether NA values should be stripped
before searching for peaks.
character Name of column where to look for valleys.
logical Flag indicating if valley location should be refined by fitting a function.
character String with the name of a method. Currently only spline interpolation is implemented.
character One of "energy" or "photon"
character One of "transmittance" or "absorbance"
if TRUE, apply function in parallel, using parallel backend provided by foreach
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.
valleys(default): Default returning always NA.
valleys(numeric): Default function usable on numeric vectors.
valleys(data.frame): Method for "data.frame" objects.
valleys(generic_spct): Method for "generic_spct" objects.
valleys(source_spct): Method for "source_spct" objects.
valleys(response_spct): Method for "response_spct" objects.
valleys(filter_spct): Method for "filter_spct" objects.
valleys(reflector_spct): Method for "reflector_spct".
valleys(solute_spct): Method for "solute_spct" objects.
valleys(cps_spct): Method for "cps_spct" objects.
valleys(raw_spct): Method for "raw_spct" objects.
valleys(generic_mspct): Method for "generic_mspct" objects.
valleys(source_mspct): Method for "source_mspct" objects.
valleys(response_mspct): Method for "cps_mspct" objects.
valleys(filter_mspct): Method for "filter_mspct" objects.
valleys(reflector_mspct): Method for "reflector_mspct" objects.
valleys(solute_mspct): Method for "solute_mspct" objects.
valleys(cps_mspct): Method for "cps_mspct" objects.
valleys(raw_mspct): Method for "raw_mspct" objects.
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.
Other peaks and valleys functions:
find_peaks(),
find_spikes(),
get_peaks(),
peaks(),
replace_bad_pixs(),
spikes(),
wls_at_target()
# default span = 5
valleys(sun.spct)
# global minimum
valleys(sun.spct, span = NULL)
valleys(sun.spct, span = NULL, strict = FALSE)
# a wider window
valleys(sun.spct, span = 51)
# global threshold relative to the range of s.e.irrad values
valleys(sun.spct, global.threshold = -0.2)
# global threshold in actual s.e.irrad values
valleys(sun.spct, global.threshold = -0.2, threshold.range = c(0, 1))
# local threshold relative to the range of s.e.irrad values
valleys(sun.spct, local.threshold = 0.1)
# local threshold in actual s.e.irrad values
valleys(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
valleys(sun.spct, local.threshold = 0.1, local.reference = "median")
# minimum, the default.
valleys(sun.spct, local.threshold = 0.1, local.reference = "minimum")
valleys(sun.spct)
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