(DEPRECATED) JCAMP-DX import for Shimadzu library spectra

This function is deprecated and will be removed in the next release of hyperSpec package. Please use function hySpc.read.jdx::read_jdx() instead. More on functions in package hySpc.read.jdx here (link).

Old description:

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

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.

read.jdx(
  filename = NULL,
  encoding = "",
  header = list(),
  keys.hdr2data = FALSE,
  ...,
  NA.symbols = c("NA", "N/A", "N.A."),
  collapse.multi = TRUE,
  wl.tolerance = hy_get_option("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 transferred 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

Value

hyperSpec object

Note

JCAMP-DX support is incomplete and the functions may change without notice.

Author

C. Beleites with contributions by Bryan Hanson