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isoreader2

Overview

This package provides easy access to common IRMS (isotope ratio mass spectrometry) file formats, enabling the reading and processing of stable isotope data directly from the data files for platform-independent (Windows, Mac, Linux), efficient, and reproducible data reduction.

isoreader2 succeeds the isoreader package with a completely new architecture built around the isoextract command-line tool. This makes isoreader2 signifcantely faster, and more versatile with support for the following file formats:

Extension Measurement type Produced by
.dxf Continuous flow Thermo Fisher Isodat
.cf Continuous flow (legacy) Thermo Fisher Isodat
.bch Continuous flow SerCon Callisto
.iarc Continuous flow Elementar IonOS
.larc Continuous flow Elementar LyticOS
.imexp* Continuous flow Thermo Fisher Qtegra
.did Dual inlet Thermo Fisher Isodat
.caf Dual inlet (legacy) Thermo Fisher Isodat
.scn Scan Thermo Fisher Isodat

* the first step of reading Qtegra notebooks (extraction of the virtual file system) requires a Windows computer at present but we’re working on a solution that works on all major operating systems

Installation

isoreader2 is not yet on the Comprehensive R Archive Network (CRAN) but you can install the latest version from GitHub as shown below. If you are on Windows, make sure to install the equivalent version of Rtools for your version of R (e.g. for the latest R 4.5 and 4.6, use RTools4.5 - you can find out which version you have with getRversion() from an R console).

# checks that you are set up to build R packages from source
if (!requireNamespace("pkgbuild", quietly = TRUE)) {
  install.packages("pkgbuild")
}
pkgbuild::check_build_tools()

# installs the latest isoreader2 package from GitHub
if (!requireNamespace("pak", quietly = TRUE)) {
  install.packages("pak")
}
pak::pak("isoverse/isoreader2")

# check/install isoextract
isoreader2::ir_check_isoextract()

Package structure

Click on the individual functions to jump straight to their documenation.

ir_filterir_join_metadatair_export_data_to_excelir_save_aggregated_datair_load_aggregated_datair_filter_metadatair_mutate_metadataV or Aor cpsinformation functionsprocessing functionsisoreader core functionsauxiliary functions(optional)visualization functionscore functions, essentialinput from userdata files ir_read_isofiles ir_find_isofiles ir_aggregate_isofiles ir_plot_scans ir_plot_dual_inlet ir_plot_continuous_flow ir_find_continuous_flow ir_find_dual_inlet ir_find_scans ir_get_data isotope data files/archivesdxfcfbchiarclarcimexpdidcafscnstorage file (parquet)output spreadsheet (xlsx)xlsxto downstream processing

Getting help

If you encounter a bug, please file an issue with a minimal reproducible example on GitHub. Example files are very helpful for fixing bugs so please consider including an example data file (you will have to attach it as a zip archive).

isoverse isoverse logo

This package is part of the isoverse suite of data tools for stable isotopes. If you like the functionality that isoverse packages provide, please help us spread the word and include an isoverse or individual package logo on one of your posters or slides. All logos are posted in high resolution in this repository. If you have suggestions for new features or other constructive feedback, please let us know on this short feeback form.

Funding NSF logo

This project is supported by a grant from the US National Science Foundation (EAR-2411458) to Sebastian Kopf.