Finds and imports spectra files from a folder. Currently works for reflectance files generated in Ocean Optics SpectraSuite (USB2000, USB4000 and Jaz spectrometers), CRAIC software (after exporting) and Avantes (before or after exporting).
Folder in which files are located (defaults to current working directory).
File extension to be searched for, without the "." (defaults to
txt). You can also use a character vector to specify multiple file
A vector with two numbers determining the wavelength limits to be
considered (defaults to
Character to be used to identify decimal plates
Column delimiting characters to be considered in addition to the default (which are: tab, space, and ";")
Should subdirectories within the
where folder be included in
the search? (defaults to
Should subdirectory path be included in the name of the
spectra? (defaults to
Should the extension search be case insensitive? (defaults
A data frame, of class
rspec, containing individual imported
spectral files as columns.
Reflectance values are interpolated to the nearest wavelength integer.
You can customise the type of parallel processing used by this function with
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
(progress bar, acoustic feedback, nothing, etc.)
Gruson H, White TE, Maia R (2019) lightr: import spectral data and metadata in R. Journal of Open Source Software, 4(43), 1857, doi:10.21105/joss.01857 .
lightr::lr_get_spec() for a more flexible version of this function
(e.g. uninterpolated wavelengths), and
lightr::lr_get_metadata() for the retrieval
and import of spectral metadata.
See https://docs.ropensci.org/lightr/ for the complete, and up-to-date, list
of supported file formats.
# Import and inspect example spectral data with a range of set to 400-700nm. rspecdata <- getspec(system.file("testdata", package = "lightr"), ext = "ttt", lim = c(400, 700)) #> 2 files found; importing spectra: head(rspecdata) #> wl avantes_export avantes_export_long #> 1 400 4.0899 5.639232 #> 2 401 3.9514 6.342615 #> 3 402 4.1269 6.147300 #> 4 403 4.2617 6.010692 #> 5 404 4.1683 6.333537 #> 6 405 4.0871 6.490569