photobiology (version 0.10.6)

fscale: Rescale 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 rescaled based on summary function f applied over a specific range or wavelengths and a target value for the summary value.

Usage

fscale(x, ...)
# S3 method for default
fscale(x, ...)
# S3 method for source_spct
fscale(
  x,
  range = NULL,
  f = "mean",
  target = 1,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  set.scaled = target == 1,
  ...
)
# S3 method for response_spct
fscale(
  x,
  range = NULL,
  f = "mean",
  target = 1,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  set.scaled = target == 1,
  ...
)
# S3 method for filter_spct
fscale(
  x,
  range = NULL,
  f = "mean",
  target = 1,
  qty.out = getOption("photobiology.filter.qty", default = "transmittance"),
  set.scaled = target == 1,
  ...
)
# S3 method for reflector_spct
fscale(
  x,
  range = NULL,
  f = "mean",
  target = 1,
  qty.out = NULL,
  set.scaled = target == 1,
  ...
)
# S3 method for raw_spct
fscale(x, range = NULL, f = "mean", target = 1, set.scaled = target == 1, ...)
# S3 method for cps_spct
fscale(x, range = NULL, f = "mean", target = 1, set.scaled = target == 1, ...)
# S3 method for generic_spct
fscale(
  x,
  range = NULL,
  f = "mean",
  target = 1,
  set.scaled = target == 1,
  col.names,
  ...
)
# S3 method for source_mspct
fscale(
  x,
  range = NULL,
  f = "mean",
  target = 1,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  set.scaled = target == 1,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for response_mspct
fscale(
  x,
  range = NULL,
  f = "mean",
  target = 1,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  set.scaled = target == 1,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for filter_mspct
fscale(
  x,
  range = NULL,
  f = "mean",
  target = 1,
  qty.out = getOption("photobiology.filter.qty", default = "transmittance"),
  set.scaled = target == 1,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for reflector_mspct
fscale(
  x,
  range = NULL,
  f = "mean",
  target = 1,
  qty.out = NULL,
  set.scaled = target == 1,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for raw_mspct
fscale(
  x,
  range = NULL,
  f = "mean",
  target = 1,
  set.scaled = target == 1,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for cps_mspct
fscale(
  x,
  range = NULL,
  f = "mean",
  target = 1,
  set.scaled = target == 1,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)
# S3 method for generic_mspct
fscale(
  x,
  range = NULL,
  f = "mean",
  target = 1,
  set.scaled = target == 1,
  col.names,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

Arguments

x

An R object

...

additional named arguments passed down to f.

range

numeric. 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" or "total" for scaling so that this summary value becomes 1 for the returned object, or the name of a function taking x as first argument and returning a numeric value.

target

numeric A constant used as target value for scaling.

unit.out

character. Allowed values "energy", and "photon", or its alias "quantum".

set.scaled

logical or NULL Flag indicating if the data is to be marked as "scaled" or not.

qty.out

character. Allowed values "transmittance", and "absorbance".

col.names

character vector containing the names of columns or variables to which to apply the scaling.

.parallel

logical 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 original spectral data values replaced with rescaled values, and the "scaled" attribute set to a list describing the scaling applied.

a new object of the same class as x.

Methods (by class)

• default: Default for generic function

• source_spct:

• response_spct:

• filter_spct:

• reflector_spct:

• raw_spct:

• cps_spct:

• generic_spct:

• source_mspct:

• response_mspct:

• filter_mspct:

• reflector_mspct:

• raw_mspct:

• cps_mspct:

• generic_mspct:

See Also

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

Examples

# NOT RUN {
fscale(sun.spct)
fscale(sun.spct, f = "mean") # same as default
fscale(sun.spct, f = "mean", na.rm = TRUE)
fscale(sun.spct, range = c(400, 700)) # default is whole spectrum
fscale(sun.spct, f = e_irrad, range = c(400, 700))
s400.spct <- fscale(sun.spct,
                    f = e_irrad,
                    range = c(400, 700),
                    target = 400) # a target in W m-2
s400.spct
e_irrad(s400.spct, c(400, 700))

# }