photobiology (version 0.11.4)

fshift: 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, ...)
# S3 method for default
fshift(x, ...)
# S3 method for 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 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 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 reflector_spct
fshift(x, range = c(wl_min(x), wl_min(x) + 10), f = "min", qty.out = NULL, ...)
# S3 method for 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 raw_spct
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "mean",
  qty.out = NULL,
  ...
)
# S3 method for cps_spct
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "mean",
  qty.out = NULL,
  ...
)
# S3 method for generic_spct
fshift(x, range = c(wl_min(x), wl_min(x) + 10), f = "mean", col.names, ...)
# S3 method for 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 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 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 raw_mspct
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "min",
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for cps_mspct
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "min",
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for generic_mspct
fshift(
  x,
  range = c(wl_min(x), wl_min(x) + 10),
  f = "min",
  col.names,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

Value

A copy of x with the spectral data values replaced with values zero-shifted.

a new object of the same class as x.

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.

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):

See Also

Other rescaling functions: fscale(), getNormalized(), getScaled(), is_normalized(), is_scaled(), normalize(), setNormalized(), setScaled()