photobiology (version 0.9.6)

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 class 'default':
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 '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"), ...)

## 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"), ...)

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

## 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"), ...)

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

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

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

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"

col.names

character The name of the variable to clean

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
• 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:
• response_mspct:
• cps_mspct:
• raw_mspct:
• generic_mspct: