photobiology (version 0.13.1)

valleys: Valleys or local minima

Description

Function that returns a subset of an R object with observations corresponding to local maxima.

Usage

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 = NULL,
  local.threshold = NULL,
  local.reference = "median",
  threshold.range = NULL,
  strict = FALSE,
  na.rm = FALSE,
  ...
)
# S3 method for data.frame
valleys(
  x,
  span = 5,
  global.threshold = NULL,
  local.threshold = NULL,
  local.reference = "median",
  threshold.range = NULL,
  strict = FALSE,
  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 = NULL,
  local.threshold = NULL,
  local.reference = "median",
  threshold.range = NULL,
  strict = FALSE,
  na.rm = FALSE,
  var.name = NULL,
  refine.wl = FALSE,
  method = "spline",
  ...
)
# S3 method for source_spct
valleys(
  x,
  span = 5,
  global.threshold = NULL,
  local.threshold = NULL,
  local.reference = "median",
  threshold.range = NULL,
  strict = FALSE,
  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 = NULL,
  local.threshold = NULL,
  local.reference = "minimum",
  threshold.range = NULL,
  strict = FALSE,
  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 = NULL,
  local.threshold = NULL,
  local.reference = "minimum",
  threshold.range = NULL,
  strict = FALSE,
  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 = NULL,
  local.threshold = NULL,
  local.reference = "minimum",
  threshold.range = NULL,
  strict = FALSE,
  na.rm = FALSE,
  refine.wl = FALSE,
  method = "spline",
  ...
)
# S3 method for solute_spct
valleys(
  x,
  span = 5,
  global.threshold = NULL,
  local.threshold = NULL,
  local.reference = "minimum",
  threshold.range = NULL,
  strict = FALSE,
  na.rm = FALSE,
  refine.wl = FALSE,
  method = "spline",
  ...
)
# S3 method for cps_spct
valleys(
  x,
  span = 5,
  global.threshold = NULL,
  local.threshold = NULL,
  local.reference = "minimum",
  threshold.range = NULL,
  strict = FALSE,
  na.rm = FALSE,
  var.name = "cps",
  refine.wl = FALSE,
  method = "spline",
  ...
)
# S3 method for raw_spct
valleys(
  x,
  span = 5,
  global.threshold = NULL,
  local.threshold = NULL,
  local.reference = "minimum",
  threshold.range = NULL,
  strict = FALSE,
  na.rm = FALSE,
  var.name = "counts",
  refine.wl = FALSE,
  method = "spline",
  ...
)
# S3 method for generic_mspct
valleys(
  x,
  span = 5,
  global.threshold = NULL,
  local.threshold = NULL,
  local.reference = "minimum",
  threshold.range = NULL,
  strict = FALSE,
  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 = NULL,
  local.threshold = NULL,
  local.reference = "minimum",
  threshold.range = NULL,
  strict = FALSE,
  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 = NULL,
  local.threshold = NULL,
  local.reference = "minimum",
  threshold.range = NULL,
  strict = FALSE,
  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 = NULL,
  local.threshold = NULL,
  local.reference = "minimum",
  threshold.range = NULL,
  strict = FALSE,
  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 = NULL,
  local.threshold = NULL,
  local.reference = "minimum",
  threshold.range = NULL,
  strict = FALSE,
  na.rm = FALSE,
  refine.wl = FALSE,
  method = "spline",
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for solute_mspct
valleys(
  x,
  span = 5,
  global.threshold = NULL,
  local.threshold = NULL,
  local.reference = "minimum",
  threshold.range = NULL,
  strict = FALSE,
  na.rm = FALSE,
  refine.wl = FALSE,
  method = "spline",
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for cps_mspct
valleys(
  x,
  span = 5,
  global.threshold = NULL,
  local.threshold = NULL,
  local.reference = "minimum",
  threshold.range = NULL,
  strict = FALSE,
  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 = NULL,
  local.threshold = NULL,
  local.reference = "minimum",
  threshold.range = NULL,
  strict = FALSE,
  na.rm = FALSE,
  var.name = "counts",
  refine.wl = FALSE,
  method = "spline",
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

Value

A subset of x with rows corresponding to local minima or global minimum.

Arguments

x

numeric vector. Hint: to find valleys, change the sign of the argument with the unnary operator -.

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 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 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.

local.threshold

numeric A value belonging to class "AsIs" is interpreted as an absolute minimum height (depth) expressed in data units relative to a within-window computed reference value. A bare numeric value (normally between 0.0 and 1.0), is interpreted as expressed in units relative to threshold.range. In both cases local.threshold sets a local height (depth) threshold below which peaks (valleys) are ignored. If local.threshold = NULL or if span spans the whole of x, no threshold is applied.

local.reference

character One of "median" or "farthest". 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 If of length 2 or a longer vector range(threshold.range) is used to scale both thresholds. With NULL, the default, range(x) is used, and with a vector of length one range(threshold.range, x) is used, i.e., the range is expanded.

strict

logical flag: if TRUE, an element must be strictly greater than all other values in its window to be considered a peak. Default: FALSE (since version 0.13.1).

...

ignored

na.rm

logical indicating whether NA values should be stripped before searching for peaks.

var.name, x.var.name, y.var.name

character Name of column where to look for valleys.

refine.wl

logical Flag indicating if valley 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.

Methods (by class)

• 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.

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.

See Also

Other peaks and valleys functions: find_peaks(), find_spikes(), get_peaks(), peaks(), replace_bad_pixs(), spikes(), wls_at_target()

Examples

# 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 = "farthest")

valleys(sun.spct)