lr_get_spec: Extract spectral data from spectra files

In lightr: Read Spectrometric Data and Metadata

Extract spectral data from spectra files

Description

Finds and imports reflectance/transmittance/absorbance data from spectra files in a given location.

Usage

lr_get_spec(
  where = getwd(),
  ext = "txt",
  lim = c(300, 700),
  decimal = ".",
  sep = NULL,
  subdir = FALSE,
  subdir.names = FALSE,
  ignore.case = TRUE,
  interpolate = TRUE
)

Arguments

where	Folder in which files are located (defaults to current working directory).
ext	File extension to be searched for, without the "." (defaults to txt). You can also use a character vector to specify multiple file extensions.
lim	A vector with two numbers determining the wavelength limits to be considered (defaults to c(300, 700)).
decimal	Character to be used to identify decimal plates (defaults to .).
sep	Column delimiting characters to be considered in addition to the default (which are: tab, space, and ";")
subdir	Should subdirectories within the where folder be included in the search? (defaults to FALSE).
subdir.names	Should subdirectory path be included in the name of the spectra? (defaults to FALSE).
ignore.case	Should the extension search be case insensitive? (defaults to TRUE)
interpolate	Boolean indicated whether spectral data should be interpolated and pruned at every nanometre. Note that this option can only work if all input data samples the same wavelengths. Defaults to TRUE.

Details

You can customise the type of parallel processing used by this function with the future::plan() function. This works on all operating systems, as well as high performance computing (HPC) environment. Similarly, you can customise the way progress is shown with the progressr::handlers() functions (progress bar, acoustic feedback, nothing, etc.)

Value

A data.frame, containing the wavelengths in the first column and individual imported spectral files in the subsequent columns.

See Also

pavo::getspec()

Examples

spcs <- lr_get_spec(system.file("testdata", package = "lightr"), ext = "jdx")
head(spcs)

lightr documentation built on May 29, 2024, 1:27 a.m.