isoverse R Packages
isoreader
# run in RStudio or R console to install:
if (!requireNamespace("devtools", quietly = T)) install.packages("devtools")
devtools::install_github("isoverse/isoreader")
This package is intended as 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. Although implemented in R, it provides easy export to Python using the shared R/Python feather file format. 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. At present, it can read most Thermo dual inlet (.did, .caf) and continuous flow (.dxf, .cf) data files as well as Elementar continuous flow data archives (.iarc) and Nu dual inlet files (.txt) with additional extensions for other file formats in the works.
: Please provide comments/suggestions and file bug reports or feature requests on GitHub
isoprocessor
# run in RStudio or R console to install:
if (!requireNamespace("devtools", quietly = T)) install.packages("devtools")
devtools::install_github("isoverse/isoprocessor")
This package provides broad functionality for IRMS data processing and reduction pipelines 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. Additional tools on O17 corrections, H3 factor calculation, peak detection, baseline correction, etc are in the works.
: Explore all functionality and vignettes of the isoprocessor package interactively on binder:
: Please provide comments/suggestions and file bug reports or feature requests on GitHub
isoviewer
# run in RStudio or R console to install:
if (!requireNamespace("devtools", quietly = T)) install.packages("devtools")
devtools::install_github("isoverse/isoviewer")
The isoviewer graphical user interface (GUI) provided by this package is based on the functionlity 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.
: Please provide comments/suggestions and file bug reports or feature requests on GitHub
isoorbi
# run in RStudio or R console to install:
if (!requireNamespace("devtools", quietly = T)) install.packages("devtools")
devtools::install_github("isoverse/isoorbi")
This package is intended for processing isotopocule measurements from an Orbitrap Iso mass spectrometer.
: Please provide comments/suggestions and file bug reports or feature requests on GitHub
isotopia
# run in RStudio or R console to install:
if (!requireNamespace("devtools", quietly = T)) install.packages("devtools")
devtools::install_github("isoverse/isotopia")
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.
: Please provide comments/suggestions and file bug reports or feature requests on GitHub
clumpedr
# run in RStudio or R console to install:
if (!requireNamespace("devtools", quietly = T)) install.packages("devtools")
devtools::install_github("isoverse/clumpedr")
Tools for clumped carbonate isotope data analysis.
: Please provide comments/suggestions and file bug reports or feature requests on GitHub