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 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 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
)

Arguments

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)

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