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Extract spectral data from spectra files

Source: R/get_spec.R
lr_get_spec.Rd

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.

Value

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

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.)

See also

pavo::getspec()

Examples

spcs <- lr_get_spec(system.file("testdata", package = "lightr"), ext = "jdx")
#> 1 files found; importing spectra:
head(spcs)
#>    wl OceanOptics_period
#> 1 300           154.3030
#> 2 301           129.2981
#> 3 302           115.9120
#> 4 303           122.5818
#> 5 304           125.9307
#> 6 305           152.3136