photobiology (version 0.9.20)

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, ignore_threshold, strict, ...)
# S3 method for default
valleys(x, span, ignore_threshold, strict, ...)
# S3 method for numeric
valleys(x, span = 5, ignore_threshold, strict = TRUE, ...)
# S3 method for generic_spct
valleys(x, span = 5, ignore_threshold = 0,
  strict = TRUE, ...)
# S3 method for source_spct
valleys(x, span = 5, ignore_threshold = 0,
  strict = TRUE, unit.out = getOption("photobiology.radiation.unit", default
  = "energy"), ...)
# S3 method for response_spct
valleys(x, span = 5, ignore_threshold = 0,
  strict = TRUE, unit.out = getOption("photobiology.radiation.unit", default
  = "energy"), ...)
# S3 method for filter_spct
valleys(x, span = 5, ignore_threshold = 0,
  strict = TRUE, filter.qty = getOption("photobiology.filter.qty", default =
  "transmittance"), ...)
# S3 method for reflector_spct
valleys(x, span = 5, ignore_threshold = 0,
  strict = TRUE, ...)
# S3 method for cps_spct
valleys(x, span = 5, ignore_threshold = 0,
  strict = TRUE, ...)
# S3 method for generic_mspct
valleys(x, span = 5, ignore_threshold = 0,
  strict = TRUE, ..., .parallel = FALSE, .paropts = NULL)

Arguments

x

an R object

span

a peak is defined as an element in a sequence which is greater than all other elements within a window of width span centered at that element. The default value is 3, meaning that a peak is bigger than both of its neighbors. Default: 3.

ignore_threshold

numeric value between 0.0 and 1.0 indicating the relative size compared to tallest peak threshold below which valleys will be ignored.

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.

...

ignored

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.

Value

A subset of x with rows corresponding to local minima.

Methods (by class)

• default: Default function usable on numeric vectors.

• numeric: Default function usable on numeric vectors.

• generic_spct: Method for "generic_spct" objects.

• source_spct: Method for "source_spct" objects.

• response_spct: Method for "response_spct" objects.

• filter_spct: Method for "filter_spct" objects.

• reflector_spct: Method for "reflector_spct".

• cps_spct: Method for "cps_spct" objects.

• generic_mspct: Method for "generic_mspct" objects.

See Also

Other peaks and valleys functions: find_peaks, get_peaks, peaks

Examples

# NOT RUN {
valleys(sun.spct)

# }