read.jdx: JCAMP-DX Import for Shimadzu Library Spectra

In hyperSpec: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

JCAMP-DX Import for Shimadzu Library Spectra

Description

this is a first rough import function for JCAMP-DX spectra.

Usage

read.jdx(
  filename = stop("filename is needed"),
  encoding = "",
  header = list(),
  keys.hdr2data = FALSE,
  ...,
  NA.symbols = c("NA", "N/A", "N.A."),
  collapse.multi = TRUE,
  wl.tolerance = hy.getOption("wl.tolerance"),
  collapse.equal = TRUE
)

Arguments

filename	file name and path of the .jdx file
encoding	encoding of the JCAMP-DX file (used by base::readLines())
header	list with manually set header values
keys.hdr2data	index vector indicating which header entries should be tranfered into the extra data. Usually a character vector of labels (lowercase, without and dashes, blanks, underscores). If TRUE, all header entries are read.
...	further parameters handed to the data import function, e.g. parameter meaning default xtol tolerance for checking calculated x values against checkpoints at beginning of line XFACTOR ytol tolerance for checking Y values against MINY and MAXY YFACTOR
NA.symbols	character vector of text values that should be converted to NA
collapse.multi	should hyperSpec objects from multispectra files be collapsed into one hyperSpec object (if FALSE, a list of hyperSpec objects is returned).
wl.tolerance, collapse.equal	see collapse

Details

So far, AFFN and PAC formats are supported for simple XYDATA, DATA TABLEs and PEAK TABLEs.

NTUPLES / PAGES are not (yet) supported.

DIF, DUF, DIFDUP and SQZ data formats are not (yet) supported.

Value

hyperSpec object

Note

JCAMP-DX support is incomplete and the functions may change without notice. See vignette ("fileio") and the details section.

Author(s)

C. Beleites with contributions by Bryan Hanson

hyperSpec documentation built on May 29, 2024, 7:28 a.m.