isoverse R Packages

This package provides easy access to the raw data and metadata stored in the file formats commonly encountered in scientific disciplines that make use of stable isotopes. It enables the reading and processing of stable isotope data directly from the data files and thus provides a foundational tool for platform-independent, efficient and reproducible data reduction. isoreader2 succeeds the isoreader package with a completely new architecture built around the isoextract command line tool, which makes it significantly faster and adds support for a wider range of file formats: Isodat continuous flow (.dxf, .cf), dual inlet (.did, .caf) and scan (.scn) files, Elementar IonOS (.iarc) and LyticOS (.larc) archives, SerCon Callisto (.bch) folders, and Thermo Qtegra (.imexp) notebooks. The extracted data comes with a consistent data structure and tools to aggregate, convert signal units, filter, and visualize the data.

This package provides data processing and reduction pipelines for the stable isotope data read by isoreader2, including peak detection, calibration, standardization, and visualization of isotope ratio mass spectrometry (IRMS) data. isoprocessor2 succeeds the isoprocessor package, rebuilt to work directly with the aggregated data structures of isoreader2. Note that this package is in early development and its interface may still change.

This package provides graphical user interface (GUI) components to explore stable isotope data files read with isoreader2. It ships ready-to-run explorer apps for continuous flow, dual inlet and scan data as well as file metadata, a Show code feature that writes out the isoreader2 code to reproduce whatever you are currently looking at, and a set of composable shiny modules that can be recombined into your own applications. isoexplorer succeeds the isoviewer package.

This package is intended for processing isotopocule measurements from an Orbitrap Isotope Solutions mass spectrometer. It reads the instrument’s .raw files directly (recommended) as well as the .isox output created by IsoX (legacy approach), and provides pipelines for identifying isotopocules, flagging satellite peaks, defining base peaks, calculating isotopocule ratios, evaluating shot noise and drift, and visualizing raw data, spectra and results.

This package is a unified one-stop command line interface to all common IRMS (isotope ratio mass spectrometry) file formats used in stable isotope geochemistry. It enables the reading and processing of stable isotope data directly from the data files and thus provides a foundational tool for platform-independent, efficient and reproducible data reduction. Due to the implementation following the example of tidyverse’s readr, isoreader takes care of error catching to avoid pipeline breaks because of problems encountered in source data files. It can read most Thermo dual inlet (.did, .caf), continuous flow (.dxf, .cf) and scan (.scn) data files as well as Elementar continuous flow data archives (.iarc) and Nu dual inlet files (.txt).

This package provides broad functionality for IRMS data processing and reduction pipelines for data read with the isoreader package, including signal conversion (voltage to current and back), time scaling (continuous flow chromatograms), isotope ratio calculations, delta value calculations, as well as easy-to-use highly flexible data calibration and visualization pipelines for continuous flow data.

The isoviewer graphical user interface (GUI) provided by this package is based on the functionality implemented by the isoreader and isoprocessor packages. The purpose of the GUI is two fold. First and foremost, it is a learning tool to illustrate how to build literate RMarkdown data processing files for IRMS data using the underlying packages as a unified interface for reading, converting and quickly visualizing various raw IRMS data file formats. The second purpose is to provide an example for a web-based IRMS data repository that is easy to run on any computer/server completely platform-independent and open-source. Towards this goal, the isoviewer package provides some rudimentary GUI modules that can be used in other more customized applications.

Stable isotope biogeochemistry uses a number of different representations of isotopic information and processes (ratios, abundances, delta values, alpha values, epsilon values, fractionation factors, reference frame shifts, mass balance calculations, mass-independent effects, etc., etc.) that are constantly being converted back and forth and used for different kinds of isotope arithmetic. Very frequently, the tangle of keeping track of this information and how all the calculations are done properly makes code very hard to read and prone to small mistakes that can make an enormous difference. The isotopia package helps with this type of isotope math by defining elemental isotopic data classes (ratio, abundance, delta, fractionation_factor and intensity) so that it can automatically keep track of what is a ratio, what is a delta value (and is it in permil notation or in ppm), etc., and implement a variety of safe guards to perform isotope arithmetic correctly.