An Introduction to readJDX

library("readJDX")
rm(list = ls())

desc <- packageDescription("readJDX")
set.seed(999)
knitr::opts_chunk$set(tidy = TRUE,
  fig.height = 7, fig.width = 7,
  fig.fullwidth = TRUE, echo = FALSE)

This vignette is based on readJDX version r desc$Version.

Background

The JCAMP-DX format was developed as an manufacturer-independent means of sharing spectroscopic data (\href{http://www.jcamp-dx.org}{www.jcamp-dx.org}). The standard is described in a series of publications (\cite{McDonald1988, Grasselli1991, Davies1993, Lampen1994, Lampen1999, Bumbach2001, Cammack2006, Woollett2012}). JCAMP-DX was developed during a time when data storage was expensive, and hence makes extensive use of compression schemes. The original application was to IR spectroscopy, but the standard has evolved over time to accommodate other spectroscopies.

File Structure

JCAMP-DX files consist of two parts:

Challenges When Reading Files

The JCAMP-DX standard allows a lot of flexibility and instrument manufacturers have written widely varying export functions. Some of the challenges in reading a JCAMP-DX file include:

Supported Formats

Formats That are Not Supported

Practical Matters

readJDX tries its best to deal with all these options. If you have a file that you believe should be supported but gives an error, please file an issue at GitHub. Be sure to attach the file that is giving you problems.

Before release, readJDX is tested against a large collection of files with varying formats. A few of these files were obtained locally. Others were collected from publically available sources (e.g. \href{http://www.jcamp-dx.org/testdata.html}{http://www.jcamp-dx.org/testdata.html}). These files are not included with the package to save space, and in addition, while they are publically available, for many of them the licensing status is unclear (i.e. the OWNER entry).

The JCAMP standard requires a number of checks on the integrity of the data decompression process. readJDX implements most of these either directly or indirectly. Verification is important, and we have found JCAMP files that were not written correctly in the process of checking integrity. For details about how data decompression is checked, please see the original source files.



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readJDX documentation built on April 17, 2021, 1:08 a.m.