rspec2mspct: Convert "pavo::rspec" objects

In photobiologyInOut: Read Spectral and Logged Data from Foreign Files

Convert "pavo::rspec" objects

Description

Convert between 'pavo::rspec' objects containing spectral reflectance data into spectral objects (xxxx_spct, xxxx_mspct) as defined in package 'photobiology'.

Usage

rspec2mspct(
  x,
  member.class = "reflector_spct",
  spct.data.var = "Rpc",
  multiplier = 1,
  ...
)

rspec2spct(x, multiplier = 1, ...)

Arguments

x	rspec object
member.class	character One of the spectrum classes defined in package 'photobiology'.
spct.data.var	character The name to be used for the 'spc' data when constructing the spectral objects.
multiplier	numeric A multiplier to be applied to the 'rspc' data to do unit or scale conversion.
...	currently ignored.

Warning!

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.

Note

Objects of class pavo::rspec do not contain metadata or class data from which the quantity measured and the units of expression could be obtained. When using this function the user needs to use parameter multiplier to convert the data to what is expected by the object constructors defined in package 'photobiology' and use parameter spct.data.var to select the quantity.

pavo::rspec 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.

Examples

# example run only if 'pavo' is available
if (requireNamespace("pavo", quietly = TRUE)) {
  library(pavo)
  data(sicalis, package = "pavo")
  sicalis.mspct <- rspec2mspct(sicalis)
  class(sicalis.mspct)

  data(teal, package = "pavo")
  teal.spct <- rspec2spct(teal)
  class(teal.spct)
  levels(teal.spct[["spct.idx"]])
  angles <- seq(from = 15, to = 75, by = 5) # from teal's documentation
  teal.spct[["angle"]] <- angles[as.numeric(teal.spct[["spct.idx"]])]
  teal.spct
}

photobiologyInOut documentation built on Sept. 14, 2024, 5:06 p.m.