photobiology (version 0.11.3)

setGenericSpct: 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)

Value

x

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.)

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!

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).

See Also

Other set and unset spectral class functions: rmDerivedSpct()

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)