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

Source: R/spct.clean.r
clean.Rd

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

Usage

clean(x, range, range.s.data, fill, ...)

# Default S3 method
clean(x, range, range.s.data, fill, ...)

# S3 method for class '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 class '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 class 'reflector_spct'
clean(x, range = x, range.s.data = c(0, 1), fill = range.s.data, ...)

# S3 method for class 'solute_spct'
clean(x, range = x, range.s.data = c(0, NA), fill = range.s.data, ...)

# S3 method for class 'object_spct'
clean(
  x,
  range = x,
  range.s.data = c(0, 1),
  fill = range.s.data,
  min.Afr = NULL,
  ...
)

# S3 method for class '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 class 'cps_spct'
clean(x, range = x, range.s.data = c(0, NA), fill = range.s.data, ...)

# S3 method for class 'raw_spct'
clean(
  x,
  range = x,
  range.s.data = c(NA_real_, NA_real_),
  fill = range.s.data,
  ...
)

# S3 method for class 'generic_spct'
clean(
  x,
  range = x,
  range.s.data = c(NA_real_, NA_real_),
  fill = range.s.data,
  col.names,
  ...
)

# S3 method for class '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 class '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 class 'reflector_mspct'
clean(
  x,
  range = NULL,
  range.s.data = c(0, 1),
  fill = range.s.data,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class '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 class 'solute_mspct'
clean(
  x,
  range = NULL,
  range.s.data = c(0, NA),
  fill = range.s.data,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class '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 class 'cps_mspct'
clean(
  x,
  range = NULL,
  range.s.data = c(0, NA),
  fill = range.s.data,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'raw_mspct'
clean(
  x,
  range = NULL,
  range.s.data = c(0, NA),
  fill = range.s.data,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

# S3 method for class 'generic_mspct'
clean(
  x,
  range = x,
  range.s.data = c(NA_real_, NA_real_),
  fill = range.s.data,
  col.names,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

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.

Value

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

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):

Note

In the case of object_spct objects, cleaning is done first on the Rfr and Tfr columns and subsequently Afr estimated and if needed half of deviation of Afr from the expected minimum value subtracted from each of Rfr and Tfr.