isoreader

About

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 is an extension and highly stream-lined re-implementation of the proof-of-concept isoread package and is designed to fit into a larger framework of IRMS data tools that includes the web-based graphical user interface package isoviewer and the data processing and visualization pipeline isoprocessor.

isoreader enables the reading and processing of stable isotope data directly from the data files and thus provides a tool for platform-independent (Windows, Mac, Linux), efficient and reproducible data reduction. Although implemented in R, it can be used in both RMarkdown as well as Jupyter data processing notebooks and also provides functionality for easy export to Python using the shared R/Python feather file format. 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) with additional extensions for other file formats in the works. Due to the dynamic implementation and design based on the popular tidyverse style of R programming, isoreader is easily extendable, takes care of error catching to avoid pipeline breaks due to problems encountered in source data files (modeled after readr) and works great with tidyverse packages such as tidyr, dplyr and ggplot.

Installation

# Note: isoreader is temporarily not available on CRAN because of a missing dependency, please install directly from GitHub using the commands below
# install.packages("isoreader")
if(!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
devtools::install_github("isoverse/isoreader")

Some isoreader features including Excel and feather export depend on optional packages that are not required for the core functionality of isoreader. To use this functionality, please install the following packages manually if not already installed (isoreader will throw an informative warning if they are needed but missing):

# optional extensions
install.packages(c("feather", "openxlsx", "xml2", "BiocManager"))
BiocManager::install("rhdf5")

To install the current development version of isoreader directly from GitHub, please use the devtools package:

# installs the development tools package if not yet installed
if(!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
devtools::install_github("isoverse/isoreader")

Troubleshooting note: depending on your workspace and operating system, you may have to re-start your R session or manually install some dependencies. For example, the digest package sometimes causes trouble - re-install with remove.packages("digest"); install.packages("digest").

Show me some code

You can, for example, automatically read the data from all supported scan files in a directory (and all its subdirectories) simply by providing the path to the folder. The following code demonstrates this with the example data files bundled with the isoreader package. For a more detailed example including continuous flow and dual inlet file reads, check out our Quick Start Vignette.

library(isoreader)
data_folder <- iso_get_reader_examples_folder()
iso_files <- iso_read_scan(data_folder)
#> Info: preparing to read 4 data files...
#> Info: reading file 'background_scan_example.scn' with '.scn' reader...
#> Info: reading file 'full_scan_example.scn' with '.scn' reader...
#> Info: reading file 'peak_shape_scan_example.scn' with '.scn' reader...
#> Info: reading file 'time_scan_example.scn' with '.scn' reader...
#> Info: finished reading 4 files in 1.34 secs

iso_files
#> Data from 4 scan iso files: 
#> # A tibble: 4 × 6
#>   file_id                 file_path_ file_subpath raw_data file_info method_info
#>   <chr>                   <chr>      <chr>        <glue>   <chr>     <chr>      
#> 1 background_scan_exampl… backgroun… <NA>         525 mea… 8 entries resistors  
#> 2 full_scan_example.scn   full_scan… <NA>         799 mea… 8 entries resistors  
#> 3 peak_shape_scan_exampl… peak_shap… <NA>         220 mea… 7 entries resistors  
#> 4 time_scan_example.scn   time_scan… <NA>         5532 me… 8 entries resistors

Supported File Types

Currently supported file types:

type	extension	software	description
continuous flow	.cf	Isodat	Continuous Flow file format (older)
continuous flow	.cf.rds	isoreader	R Data Storage
continuous flow	.dxf	Isodat	Continuous Flow file format (newer)
continuous flow	.iarc	ionOS	Continuous Flow data archive
dual inlet	.caf	Isodat	Dual Inlet file format (older)
dual inlet	.di.rds	isoreader	R Data Storage
dual inlet	.did	Isodat	Dual Inlet file format (newer)
dual inlet	.txt	Nu	Dual Inlet file format
scan	.scan.rds	isoreader	R Data Storage
scan	.scn	Isodat	Scan file format

Documentation

for a quick introduction, check out the aforementioned Quick Start Vignette
for a full reference of all available functions, see the Function Reference
for function help within RStudio, simply start typing ?iso_ in the console and a list of available function will appear (all functions share the iso_ prefix)
for a detailed example of how to work with continuous flow data files, see the vignette on Continuous Flow
for a detailed example of how to work with dual inlet data files, see the vignette on Dual Inlet
for a detailed example of how to work with scan data files, see the vignette on Scans

Troubleshooting

If you run into a file format that is not currently supported or any issues with supported formats, please file a request/bug report in the issue tracker. Likewise if you run into any unexpected behavior or uncaught errors. Most isoreader functionality is continuously tested on Unix and Windows systems using GitHub Actions. This makes it possible to ensure proper functionality and catch issues quickly, however, sometimes something slips through or is not yet automatically tested. We try to make sure to fix such errors as soon as possible but ask for patience due to the small development team. If you have the skills and are willing to fix problems yourself, that’s great, please take a look at the development section below.

Development

If you are interested in helping with development, that’s fantastic! Please fork the repository and branch off from the dev branch since it contains the most up-to-date development version of isoreader. Make sure to write testthat tests for your work (stored in the tests/testthat directory). All tests can be run automatically and continuously during development to make it easier to spot any code problems on the go. The easiest way to run them is by running make auto_test in the isoreader directory from command line (it will test everything automatically in a completely separate R session).

Open Source

isoreader is and will always be fully open-source (i.e. free as in freedom and free as in free beer) and is provided as is. The source code is released under GPL-2.

isoverse

This package is part of the isoverse suite of data tools for stable isotopes. If you like the functionality that isoverse packages provide to the geochemical community, 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.

isoverse / isoreader

readme