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photobiology (version 0.11.3)

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):