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Convert raw counts data into spectral transmittance or spectral reflectance.

Usage

s_fraction_corrected(x, ...)

# Default S3 method
s_fraction_corrected(x, ...)

# S3 method for class 'list'
s_fraction_corrected(
  x,
  reference.value = 1,
  type = "internal",
  time = NULL,
  correction.method,
  qty.out = "Tfr",
  descriptor = NULL,
  dyn.range = NULL,
  locale = NULL,
  verbose = getOption("photobiology.verbose", default = FALSE),
  ...
)

# S3 method for class 'raw_mspct'
s_fraction_corrected(
  x,
  spct.names = c(sample = "sample", reference = "reference", dark = "dark"),
  reference.value = 1,
  type = switch(qty.out, Tfr = "internal", Rfr = "total"),
  correction.method,
  dyn.range = NULL,
  qty.out = "Tfr",
  verbose = getOption("photobiology.verbose", default = FALSE),
  ...
)

Arguments

x

A named list of one to three vectors of file names, with names "sample", "reference", and "dark". Or a raw_mspt object, or a raw_spct object.

...

Named argument passed to photobiology::cps2irrad which is the final calculation step.

reference.value

numeric or filter_spct or reflector_spct object, with the fractional transmittance or reflectance of the reference.

type

character One of "internal" or "total".

time

a POSIXct object, but if NULL the date stored in file is used, and if NA no date variable is added

correction.method

A named list of constants and functions defining the method to be sued for stray light and dark signal corrections.

qty.out

character, one of "Tfr", "Rfr".

descriptor

A named list with a descriptor of the characteristics of the spectrometer (if serial number does not agree an error is triggered).

dyn.range

numeric Effective dynamic range of the spectrometer.

locale

The locale controls defaults that vary from place to place. The default locale is US-centric (like R), but you can use locale to create your own locale that controls things like the default time zone, encoding, decimal mark, big mark, and day/month names.

verbose

Logical indicating the level of warnings wanted.

spct.names

named character vector of length three, to map names in x to those expected.

Methods (by class)

  • s_fraction_corrected(default): Default for generic function.

  • s_fraction_corrected(list): Default for generic function.

  • s_fraction_corrected(raw_mspct): Default for generic function.

Note

Currently s_fraction_corrected.list allows processing of files written by OceanOptics' SpectraSuite software, from protocols with integration-time bracketing or not, with a dark reference measurement or not. Four measurements components are recognized: a "sample" measurement, a "referenece" measurement using a clear or white, a "filter" measurement with a UV-blocking filter in the light pass, and a "dark" measurement. Only "sample" and "reference" are mandatory. Data should be raw counts, either corrected for detector non-linearity or not. All three spectra should be acquired using the same instrument settings to achieve good accuracy.

See also

Other functions for conversion of raw-counts data: raw2corr_cps(), raw2cps(), s_irrad_corrected()