R: Convert an R object into a spectrum object.

setGenericSpct {photobiology}

R Documentation

Convert an R object into a spectrum object.

Description

Sets the class attribute of a data.frame or an object of a derived class to "generic_spct".

Usage

setGenericSpct(x, multiple.wl = 1L, idfactor = NULL)

setCalibrationSpct(
  x,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  multiple.wl = 1L,
  idfactor = NULL
)

setRawSpct(
  x,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  multiple.wl = 1L,
  idfactor = NULL
)

setCpsSpct(
  x,
  time.unit = "second",
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  multiple.wl = 1L,
  idfactor = NULL
)

setFilterSpct(
  x,
  Tfr.type = c("total", "internal"),
  Rfr.constant = NA_real_,
  thickness = NA_real_,
  attenuation.mode = NA_character_,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  multiple.wl = 1L,
  idfactor = NULL
)

setSoluteSpct(
  x,
  K.type = c("attenuation", "absorption", "scattering"),
  name = NA_character_,
  mass = NA_character_,
  formula = NA_character_,
  structure = grDevices::as.raster(matrix()),
  ID = NA_character_,
  solvent.name = NA_character_,
  solvent.ID = NA_character_,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  multiple.wl = 1L,
  idfactor = NULL
)

setReflectorSpct(
  x,
  Rfr.type = c("total", "specular"),
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  multiple.wl = 1L,
  idfactor = NULL
)

setObjectSpct(
  x,
  Tfr.type = c("total", "internal"),
  Rfr.type = c("total", "specular"),
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  multiple.wl = 1L,
  idfactor = NULL
)

setResponseSpct(
  x,
  time.unit = "second",
  response.type = "response",
  multiple.wl = 1L,
  idfactor = NULL
)

setSourceSpct(
  x,
  time.unit = "second",
  bswf.used = c("none", "unknown"),
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  multiple.wl = 1L,
  idfactor = NULL
)

setChromaSpct(x, multiple.wl = 1L, idfactor = NULL)

Arguments

`x`	data.frame, list or generic_spct and derived classes
`multiple.wl`	numeric Maximum number of repeated `w.length` entries with same value.
`idfactor`	character Name of factor distinguishing multiple spectra when stored longitudinally (required if `mulitple.wl` > 1).
`strict.range`	logical Flag indicating whether off-range values result in an error instead of a warning.
`time.unit`	character string indicating the time unit used for spectral irradiance or exposure (`"second"`, `"day"` or `"exposure"`) or an object of class duration as defined in package lubridate.
`Tfr.type`	character Either "total" or "internal".
`Rfr.constant`	numeric The value of the reflection factor [`/1`].
`thickness`	numeric The thickness of the material.
`attenuation.mode`	character One of `"reflection"`, `"absorption"` or `"mixed"`.
`K.type`	character A string, either "attenuation", "absorption" or "scattering".
`name`, `solvent.name`	character The names of the substance and of the solvent. A named character vector, with member names such as "IUPAC" for the authority.
`mass`	numeric The mass in Dalton (Da = g/mol).
`formula`	character The molecular formula.
`structure`	raster A bitmap of the structure.
`ID`, `solvent.ID`	character The IDs of the substance and of the solvent. A named character vector, with member names such as "ChemSpider" or "PubChen" for the authority.
`Rfr.type`	character A string, either "total" or "specular".
`response.type`	a character string, either `"response"` or `"action"`.
`bswf.used`	character A string, either `"none"` or the name of a BSWF. (Users seldom need to change the default, as this metadata value is in normal use set by operators or functions that apply a BSWF.)

Details

This method alters x itself by reference and in addition returns the modified x invisibly. The wavelength values and data are checked for validity and out-of-range values trigger warnings. These checks are done during construction by means of the matching check_spct methods, unless checks have been disabled by setting the corresponding option (see enable_check_spct).

Value

Functions

setCalibrationSpct(): Set class of a an object to "calibration_spct".
setRawSpct(): Set class of a an object to "raw_spct".
setCpsSpct(): Set class of a an object to "cps_spct".
setFilterSpct(): Set class of an object to "filter_spct".
setSoluteSpct(): Set class of an object to "solute_spct".
setReflectorSpct(): Set class of a an object to "reflector_spct".
setObjectSpct(): Set class of an object to "object_spct".
setResponseSpct(): Set class of an object to "response_spct".
setSourceSpct(): Set class of an object to "source_spct".
setChromaSpct(): Set class of an object to "chroma_spct".

Warning!

Not entering metadata when creating an object will limit the available operations!

Note

"internal" transmittance is defined as the transmittance of the material body itself, while "total" transmittance includes the effects of surface reflectance on the amount of light transmitted. For non-diffusing materials like glass an approximate Rfr.constant value can be used to inter-convert total and internal transmittance values. Use NA if the the mode is not known, or not applicable, e.g., for materials subject to internal scattering. The validity of computations related to thickness of the material or length of the light path depends on the availability and accuracy of the metadata.

Particles in suspension unlike dissolved solutes scatter light. Thus two different processes can attenuate light in liquid media: absorption and scattering. Coefficients of attenuation are always based on measurements of internal absorbance or internal transmittance. In practice this is achieved by using as reference pure solvent in a vessel, such as a spectrometer cuvette, called blank. The measurement of the blank is done sequentially, before or after the sample of interest in single beam spectrophotometers and concurrently in double beam spectrophotometers. K.type describes the process of attenuation: "attenuation", "absorption" or "scattering", with "attenuation" used for cases of mixed modes of attenuation. Set K.type = NA if not available or unknown, or not applicable.

"specular" reflectance is defined as that measured by collecting the light reflected by the surface at the “mirror” of the angle of incidence; i.e., using a probe with a narrow angle of aperture. Usually measured close to normal angle of incidence. "total" reflectance is defined as that measured by collecting all the light reflected by the surface; i.e., using an integrating sphere. In a mirror, reflectance is mostly specular, while on the white surface of a sheet of paper scattering predominates. In the first case the value for total reflectance is not much more than for specular reflectance, while in the second case the difference is much larger as the "specular" component is much smaller.

Examples

my.df <- data.frame(w.length = 300:309, s.e.irrad = rep(100, 10))
is.source_spct(my.df)
setSourceSpct(my.df)
is.source_spct(my.df)

[Package photobiology version 0.11.2 Index]