clean: Clean (=replace) off-range values in a spectrum

Description

These functions implement the equivalent of replace() but for spectral objects instead of vectors.

Usage

clean(x, range, range.s.data, fill, ...)
# S3 method for default
clean(x, range, range.s.data, fill, ...)
# S3 method for source_spct
clean(
  x,
  range = x,
  range.s.data = c(0, NA),
  fill = range.s.data,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...
)
# S3 method for filter_spct
clean(
  x,
  range = x,
  range.s.data = NULL,
  fill = range.s.data,
  qty.out = getOption("photobiology.filter.qty", default = "transmittance"),
  ...
)
# S3 method for reflector_spct
clean(x, range = x, range.s.data = c(0, 1), fill = range.s.data, ...)
# S3 method for solute_spct
clean(x, range = x, range.s.data = c(0, NA), fill = range.s.data, ...)
# S3 method for object_spct
clean(
  x,
  range = x,
  range.s.data = c(0, 1),
  fill = range.s.data,
  min.Afr = NULL,
  ...
)
# S3 method for response_spct
clean(
  x,
  range = x,
  range.s.data = c(0, NA),
  fill = range.s.data,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...
)
# S3 method for cps_spct
clean(x, range = x, range.s.data = c(0, NA), fill = range.s.data, ...)
# S3 method for raw_spct
clean(
  x,
  range = x,
  range.s.data = c(NA_real_, NA_real_),
  fill = range.s.data,
  ...
)
# S3 method for generic_spct
clean(
  x,
  range = x,
  range.s.data = c(NA_real_, NA_real_),
  fill = range.s.data,
  col.names,
  ...
)
# S3 method for source_mspct
clean(
  x,
  range = NULL,
  range.s.data = c(0, NA),
  fill = range.s.data,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for filter_mspct
clean(
  x,
  range = NULL,
  range.s.data = NULL,
  fill = range.s.data,
  qty.out = getOption("photobiology.filter.qty", default = "transmittance"),
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for reflector_mspct
clean(
  x,
  range = NULL,
  range.s.data = c(0, 1),
  fill = range.s.data,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for object_mspct
clean(
  x,
  range = NULL,
  range.s.data = c(0, 1),
  fill = range.s.data,
  min.Afr = NULL,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for solute_mspct
clean(
  x,
  range = NULL,
  range.s.data = c(0, NA),
  fill = range.s.data,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for response_mspct
clean(
  x,
  range = NULL,
  range.s.data = c(0, NA),
  fill = range.s.data,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for cps_mspct
clean(
  x,
  range = NULL,
  range.s.data = c(0, NA),
  fill = range.s.data,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for raw_mspct
clean(
  x,
  range = NULL,
  range.s.data = c(0, NA),
  fill = range.s.data,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for generic_mspct
clean(
  x,
  range = x,
  range.s.data = c(NA_real_, NA_real_),
  fill = range.s.data,
  col.names,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

Value

A copy of x, possibly with some of the spectral data values replaced by the value passed to fill.

Arguments

x: an R object
range: numeric vector of wavelengths
range.s.data: numeric vector of length two giving the allowable range for the spectral data.
fill: numeric vector of length 1 or 2, giving the replacement values to use at each extreme of the range.
...: currently ignored
unit.out: character string with allowed values "energy", and "photon", or its alias "quantum"
qty.out: character string with allowed values "energy", and "photon", or its alias "quantum"
min.Afr: numeric Gives the minimum value accepted for the computed absorptance. The default NULL sets a valid value (Afr >= 0) with a warning. If an integer value is passed to digits values are adjusted silently.
col.names: character The name of the variable to clean
.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)

clean(default): Default for generic function
clean(source_spct): Replace off-range values in a source spectrum
clean(filter_spct): Replace off-range values in a filter spectrum
clean(reflector_spct): Replace off-range values in a reflector spectrum
clean(solute_spct): Replace off-range values in a solute spectrum
clean(object_spct): Replace off-range values in an object spectrum
clean(response_spct): Replace off-range values in a response spectrum
clean(cps_spct): Replace off-range values in a counts per second spectrum
clean(raw_spct): Replace off-range values in a raw counts spectrum
clean(generic_spct): Replace off-range values in a generic spectrum
clean(source_mspct):
clean(filter_mspct):
clean(reflector_mspct):
clean(object_mspct):
clean(solute_mspct):
clean(response_mspct):
clean(cps_mspct):
clean(raw_mspct):
clean(generic_mspct):