photobiology (version 0.9.25)

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

na.rm

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

var.name

Name of column where to look for peaks.

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.

• default: Default returning always NA.

• numeric: Default function usable on numeric vectors.

• data.frame: Method for "data.frame" objects.

• 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, wls_at_target

Examples

# NOT RUN {
valleys(sun.spct, span = 50)

valleys(sun.spct)

# }