R: Shift the scale of a spectrum using a summary function

fshift {photobiology}

R Documentation

Shift the scale of a spectrum using a summary function

Description

The fshift() methods return a spectral object of the same class as the one supplied as argument but with the spectral data on a zero-shifted scale. A range of wavelengths is taken as a zero reference and the summary calculated with f for this waveband is substracted. This results in a zero shift (= additive correction) to the values in the returned object. Metadata attributes are retained unchanged.

Usage

fshift(x, ...)

## Default S3 method:
fshift(x, ...)

## S3 method for class 'source_spct'
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "mean",
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...
)

## S3 method for class 'response_spct'
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "mean",
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...
)

## S3 method for class 'filter_spct'
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "min",
  qty.out = getOption("photobiology.filter.qty", default = "transmittance"),
  ...
)

## S3 method for class 'reflector_spct'
fshift(x, range = c(wl_min(x), wl_min(x) + 10), f = "min", qty.out = NULL, ...)

## S3 method for class 'source_mspct'
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "mean",
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...
)

## S3 method for class 'raw_spct'
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "mean",
  qty.out = NULL,
  ...
)

## S3 method for class 'cps_spct'
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "mean",
  qty.out = NULL,
  ...
)

## S3 method for class 'generic_spct'
fshift(x, range = c(wl_min(x), wl_min(x) + 10), f = "mean", col.names, ...)

## S3 method for class 'response_mspct'
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "mean",
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

## S3 method for class 'filter_mspct'
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "min",
  qty.out = getOption("photobiology.filter.qty", default = "transmittance"),
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

## S3 method for class 'reflector_mspct'
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "min",
  qty.out = NULL,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

## S3 method for class 'raw_mspct'
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "min",
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

## S3 method for class 'cps_mspct'
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "min",
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

## S3 method for class 'generic_mspct'
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "min",
  col.names,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

Arguments

`x`	An R object
`...`	additional named arguments passed down to `f`.
`range`	An R object on which `range()` returns a numeric vector of length 2 with the limits of a range of wavelengths in nm, with min and max wavelengths (nm)
`f`	character string "mean", "min" or "max" for scaling so that this summary value becomes the origin of the spectral data scale in the returned object, or the name of a function taking `x` as first argument and returning a numeric value.
`unit.out`	character Allowed values "energy", and "photon", or its alias "quantum"
`qty.out`	character Allowed values "transmittance", and "absorbance"
`col.names`	character vector containing the names of columns or variables to which to apply the scale shift.
`.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 with the spectral data values replaced with values zero-shifted.

a new object of the same class as x.

Methods (by class)

fshift(default): Default for generic function
fshift(source_spct):
fshift(response_spct):
fshift(filter_spct):
fshift(reflector_spct):
fshift(source_mspct):
fshift(raw_spct):
fshift(cps_spct):
fshift(generic_spct):
fshift(response_mspct):
fshift(filter_mspct):
fshift(reflector_mspct):
fshift(raw_mspct):
fshift(cps_mspct):
fshift(generic_mspct):

Note

Method fshift is not implemented for solute_spct objects as the spectral data stored in them are a description of an intensive property of a substance. To represent solutions of specific concentrations of solutes, filter_spct objects can be used.