hyperSpec2mspct: Convert 'hyperSpec::hyperSpec' objects

View source: R/foreign-conversion.r

hyperSpec2mspctR Documentation

Convert 'hyperSpec::hyperSpec' objects


Convert hyperSpec::hyperSpec objects containing VIS and UV radiation data into spectral objects (xxxx_spct, xxxx_mspct) as defined in package 'photobiology' and vice versa, preserving as much information as possible. As hyperSpec can contain other kinds of spectral data, it does make sense to use these functions only with objects containing data that can be handled by both packages.


hyperSpec2mspct(x, member.class, spct.data.var, multiplier = 1, ...)

hyperSpec2spct(x, multiplier = 1, ...)

mspct2hyperSpec(x, spct.data.var, multiplier = 1, ...)

spct2hyperSpec(x, spct.data.var = NULL, multiplier = 1, ...)



hyperSpec object


character One of the spectrum classes defined in package 'photobiology'.


character The name to be used for the 'spc' data when constructing the spectral objects.


numeric A multiplier to be applied to the 'spc' data to do unit or scale conversion. For example "a.u." units in some examples in package 'hyperSpec' seem to have scale factors applied.


currently ignored.


Always check the sanity of the imported or exported data values, as guessing is needed when matching the different classes, and the functions defined here are NOT guaranteed to return valid data wihtout help from the user through optional function arguments.


Objects of class hyperSpec::hyperSpec contain metadata or class data from which the quantity measured and the units of expression can be obtained. However, units as included in the objects are not well documented making automatic conversion difficult. When using this function the user may need to use parameter multiplier to scale the data to what is expected by the object constructors defined in package 'photobiology' and use parameter spct.data.var to select the quantity.

hyperSpec::hyperSpec objects may use memory more efficiently than spectral objects of the classes for collections of spectra defined in package 'photobiology' as wavelengths are assumed to be the same for all member spectra, and stored only once while this assumption is not made for collections of spectra, allowing different wavelengths and lengths for the component spectra. Wavelengths are stored for each spectrum, but as spectral classes are derived from 'tbl_df' in many cases no redundant copies of wavelength data will be made in memory in spite of the more flexible semantics of the objects.


# example run only if 'hyperSpec' is available
if (requireNamespace("hyperSpec", quietly = TRUE)) {
  wl(laser) <- 
    list(wl = 1e7 / (1/405e-7 - wl (laser)),
         label = expression (lambda / nm))
  laser.mspct <- hyperSpec2mspct(laser, "source_spct", "s.e.irrad")

photobiologyInOut documentation built on July 26, 2023, 5:15 p.m.