photobiology: wls_at_target – R documentation

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wls_at_target

Find wavelengths values corresponding to a target spectral value

Description

Find wavelength values corresponding to a target spectral value in a spectrum. The name of the column of the spectral data to be used is inferred from the class of x and the argument passed to unit.out or filter.qty or their defaults that depend on R options set.

Usage

wls_at_target(
  x,
  target = NULL,
  interpolate = FALSE,
  idfactor = FALSE,
  na.rm = FALSE,
  ...
)

## Default S3 method:
wls_at_target(
  x,
  target = NULL,
  interpolate = FALSE,
  idfactor = FALSE,
  na.rm = FALSE,
  ...
)

## S3 method for class 'data.frame'
wls_at_target(
  x,
  target = "half.maximum",
  interpolate = FALSE,
  idfactor = FALSE,
  na.rm = FALSE,
  x.var.name = NULL,
  y.var.name = NULL,
  ...
)

## S3 method for class 'generic_spct'
wls_at_target(
  x,
  target = "half.maximum",
  interpolate = FALSE,
  idfactor = FALSE,
  na.rm = FALSE,
  col.name = NULL,
  y.var.name = col.name,
  ...
)

## S3 method for class 'source_spct'
wls_at_target(
  x,
  target = "half.maximum",
  interpolate = FALSE,
  idfactor = FALSE,
  na.rm = FALSE,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...
)

## S3 method for class 'response_spct'
wls_at_target(
  x,
  target = "half.maximum",
  interpolate = FALSE,
  idfactor = FALSE,
  na.rm = FALSE,
  unit.out = getOption("photobiology.radiation.unit", default = "energy"),
  ...
)

## S3 method for class 'filter_spct'
wls_at_target(
  x,
  target = "half.maximum",
  interpolate = FALSE,
  idfactor = FALSE,
  na.rm = FALSE,
  filter.qty = getOption("photobiology.filter.qty", default = "transmittance"),
  ...
)

## S3 method for class 'reflector_spct'
wls_at_target(
  x,
  target = "half.maximum",
  interpolate = FALSE,
  idfactor = FALSE,
  na.rm = FALSE,
  ...
)

## S3 method for class 'cps_spct'
wls_at_target(
  x,
  target = "half.maximum",
  interpolate = FALSE,
  idfactor = FALSE,
  na.rm = FALSE,
  ...
)

## S3 method for class 'generic_mspct'
wls_at_target(
  x,
  target = "half.maximum",
  interpolate = FALSE,
  idfactor = FALSE,
  na.rm = FALSE,
  ...,
  .parallel = FALSE,
  .paropts = NULL
)

Arguments

`x`	data.frame or spectrum object.
`target`	numeric value indicating the spectral quantity value for which wavelengths are to be searched and interpolated if need. The character string "half.maximum" is also accepted as argument.
`interpolate`	logical Indicating whether the nearest wavelength value in `x` should be returned or a value calculated by linear interpolation between wavelength values straddling the target.
`idfactor`	logical or character Generates an index column of factor type. If `idfactor = TRUE` then the column is auto named spct.idx. Alternatively the column name can be directly passed as argument to `idfactor` as a character string.
`na.rm`	logical indicating whether `NA` values should be stripped before searching for the target.
`...`	currently ignored.
`x.var.name, y.var.name, col.name`	character The name of the columns in which to search for the target value. Use of `col.name` is deprecated, and is a synonym for `y.var.name`.
`unit.out`	character One of "energy" or "photon"
`filter.qty`	character One of "transmittance" or "absorbance"
`.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 data.frame or a spectrum object of the same class as x with fewer rows, possibly even no rows. If FALSE is passed to interpolate a subset of x is returned, otherwise a new object of the same class containing interpolated wavelengths for the target value is returned.

Methods (by class)

default: Default returning always an empty object of the same class as x.
data.frame: Method for "data.frame" objects.
generic_spct: Method for "generic_spct" objects.
source_spct: Method for "source_spct" objects.
response_spct: Method for "response_spct" objects.
filter_spct: Method for "filter_spct" objects.
reflector_spct: Method for "reflector_spct" objects.
cps_spct: Method for "cps_spct" objects.
generic_mspct: Method for "generic_mspct" objects.

Note

When interpolation is used, only column w.length and the column against which the target value was compared are included in the returned object, otherwise, all columns in x are returned. We implement support for data.frame to simplify the coding of 'ggplot2' stats using this function.

Examples

wls_at_target(sun.spct, target = 0.1)
wls_at_target(sun.spct, target = 2e-6, unit.out = "photon")
wls_at_target(polyester.spct, target = "HM")
wls_at_target(polyester.spct, target = "HM", interpolate = TRUE)
wls_at_target(polyester.spct, target = "HM", idfactor = "target")
wls_at_target(polyester.spct, target = "HM", filter.qty = "absorbance")

photobiology

Photobiological Calculations

v0.10.10

GPL (>= 2)

Authors

Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>), Glenn Davis [ctb], Agnese Fazio [ctb]

Initial release

2022-03-24