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

These functions return a spectral object of the same class as the one supplied as argument but with the spectral data on a shifted scale. A range of wavelengths is taken a reference (zero or another numeric constant) and a summary is calculated for this waveband. The difference between the computed and reference value are used to shift the scale so that these two values match in the returned object.

Usage

fshift(x, ...)

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

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

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

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

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

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

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

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

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

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

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

## S3 method for class 'generic_mspct'
fshift(x, range = c(min(x), 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.

Methods (by class)