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
).
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".
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.
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)
#> [1] FALSE
setSourceSpct(my.df)
is.source_spct(my.df)
#> [1] TRUE