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 todigits
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 functionclean(source_spct)
: Replace off-range values in a source spectrumclean(filter_spct)
: Replace off-range values in a filter spectrumclean(reflector_spct)
: Replace off-range values in a reflector spectrumclean(solute_spct)
: Replace off-range values in a solute spectrumclean(object_spct)
: Replace off-range values in an object spectrumclean(response_spct)
: Replace off-range values in a response spectrumclean(cps_spct)
: Replace off-range values in a counts per second spectrumclean(raw_spct)
: Replace off-range values in a raw counts spectrumclean(generic_spct)
: Replace off-range values in a generic spectrumclean(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)
: