photobiology: source_spct – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

source_spct

Spectral-object constructor

Description

These functions can be used to create spectral objects derived from generic_spct. They take as arguments numeric vectors for the data character scalars for attributes, and a logical flag.

Usage

source_spct(
  w.length = NULL,
  s.e.irrad = NULL,
  s.q.irrad = NULL,
  time.unit = c("second", "day", "exposure"),
  bswf.used = c("none", "unknown"),
  comment = NULL,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  multiple.wl = 1L,
  idfactor = NULL,
  ...
)

calibration_spct(
  w.length = NULL,
  irrad.mult = NA_real_,
  comment = NULL,
  instr.desc = NA,
  multiple.wl = 1L,
  idfactor = NULL,
  ...
)

raw_spct(
  w.length = NULL,
  counts = NA_real_,
  comment = NULL,
  instr.desc = NA,
  instr.settings = NA,
  multiple.wl = 1L,
  idfactor = NULL,
  ...
)

cps_spct(
  w.length = NULL,
  cps = NA_real_,
  comment = NULL,
  instr.desc = NA,
  instr.settings = NA,
  multiple.wl = 1L,
  idfactor = NULL,
  ...
)

generic_spct(
  w.length = NULL,
  comment = NULL,
  multiple.wl = 1L,
  idfactor = NULL,
  ...
)

response_spct(
  w.length = NULL,
  s.e.response = NULL,
  s.q.response = NULL,
  time.unit = c("second", "day", "exposure"),
  response.type = c("response", "action"),
  comment = NULL,
  multiple.wl = 1L,
  idfactor = NULL,
  ...
)

filter_spct(
  w.length = NULL,
  Tfr = NULL,
  Tpc = NULL,
  Afr = NULL,
  A = NULL,
  Tfr.type = c("total", "internal"),
  comment = NULL,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  multiple.wl = 1L,
  idfactor = NULL,
  ...
)

reflector_spct(
  w.length = NULL,
  Rfr = NULL,
  Rpc = NULL,
  Rfr.type = c("total", "specular"),
  comment = NULL,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  multiple.wl = 1L,
  idfactor = NULL,
  ...
)

object_spct(
  w.length = NULL,
  Rfr = NULL,
  Tfr = NULL,
  Afr = NULL,
  Tfr.type = c("total", "internal"),
  Rfr.type = c("total", "specular"),
  comment = NULL,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  multiple.wl = 1L,
  idfactor = NULL,
  ...
)

chroma_spct(
  w.length = NULL,
  x,
  y,
  z,
  comment = NULL,
  strict.range = getOption("photobiology.strict.range", default = FALSE),
  multiple.wl = 1L,
  idfactor = NULL,
  ...
)

Arguments

`w.length`	numeric vector with wavelengths in nanometres
`s.e.irrad`	numeric vector with spectral energy irradiance in [W m-2 nm-1] or [J d-1 m-2 nm-1]
`s.q.irrad`	numeric A vector with spectral photon irradiance in [mol s-1 m-2 nm-1] or [mol d-1 m-2 nm-1].
`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.
`bswf.used`	character A string indicating the BSWF used, if any, for spectral effective irradiance or exposure ("none" or the name of the BSWF).
`comment`	character A string to be added as a comment attribute to the object created.
`strict.range`	logical Flag indicating whether off-range values result in an error instead of a warning.
`multiple.wl`	numeric Maximum number of repeated w.length entries with same value.
`idfactor`	character Name of factor distinguishing multiple spectra when stored logitudinally (required if mulitple.wl > 1).
`...`	other arguments passed to `tibble()`
`irrad.mult`	numeric vector with multipliers for each detector pixel.
`instr.desc`	a list
`counts`	numeric vector with raw counts expressed per scan
`instr.settings`	a list
`cps`	numeric vector with linearized raw counts expressed per second
`s.e.response`	numeric vector with spectral energy irradiance in W m-2 nm-1 or J d-1 m-2 nm-1
`s.q.response`	numeric vector with spectral photon irradiance in mol s-1 m-2 nm-1 or mol d-1 m-2 nm-1
`response.type`	a character string, either "response" or "action".
`Tfr`	numeric vector with spectral transmittance as fraction of one
`Tpc`	numeric vector with spectral transmittance as percent values
`Afr`	numeric vector of absorptance as fraction of one
`A`	numeric vector of absorbance values (log10 based a.u.)
`Tfr.type`	character string indicating whether transmittance and absorptance values are "total" or "internal" values
`Rfr`	numeric vector with spectral reflectance as fraction of one
`Rpc`	numeric vector with spectral reflectance as percent values
`Rfr.type`	character A string, either "total" or "specular".
`x, y, z`	numeric colour coordinates

Value

A object of class generic_spct or a class derived from it, depending on the function used. In other words an object of a class with the same name as the constructor function.

Note

The functions can be used to add only one spectral quantity to a spectral object. Some of the functions have different arguments, for the same quantity expressed in different units. An actual parameter can be supplied to only one of these formal parameters in a given call to any of these functions.

"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.

source_spct

Description

Usage

Arguments

Value

Note

See Also

photobiology

We don't support your browser anymore