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<!DOCTYPE html>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.4.1</span>
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<div class="section level2">
<h2 id="about">About<a class="anchor" aria-label="anchor" href="#about"></a>
</h2>
<p>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 <a href="https://github.com/sebkopf/isoread" class="external-link">isoread</a> package and is designed to fit into a larger framework of IRMS data tools that includes the web-based graphical user interface package <a href="https://github.com/isoverse/isoviewer" class="external-link">isoviewer</a> and the data processing and visualization pipeline <a href="https://github.com/isoverse/isoprocessor" class="external-link">isoprocessor</a>.</p>
<p><a href="https://isoreader.isoverse.org/" class="external-link">isoreader</a> 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 <a href="https://www.tidyverse.org/" class="external-link">tidyverse</a> 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 <a href="https://readr.tidyverse.org/" class="external-link">readr</a>) and works great with <a href="https://www.tidyverse.org/" class="external-link">tidyverse</a> packages such as <a href="https://tidyr.tidyverse.org/" class="external-link">tidyr</a>, <a href="https://dplyr.tidyverse.org/" class="external-link">dplyr</a> and <a href="https://ggplot2.tidyverse.org/" class="external-link">ggplot</a>.</p>
</div>
<div class="section level2">
<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
</h2>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Note: isoreader is temporarily not available on CRAN because of a missing dependency, please install directly from GitHub using the commands below</span></span>
<span><span class="co"># install.packages("isoreader")</span></span>
<span><span class="kw">if</span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"devtools"</span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"devtools"</span><span class="op">)</span></span>
<span><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"isoverse/isoreader"</span><span class="op">)</span></span></code></pre></div>
<p>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):</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># optional extensions</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"feather"</span>, <span class="st">"openxlsx"</span>, <span class="st">"xml2"</span>, <span class="st">"BiocManager"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu">install</span><span class="op">(</span><span class="st">"rhdf5"</span><span class="op">)</span></span></code></pre></div>
<p>To install the current development version of isoreader directly from GitHub, please use the devtools package:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># installs the development tools package if not yet installed</span></span>
<span><span class="kw">if</span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"devtools"</span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"devtools"</span><span class="op">)</span></span>
<span><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"isoverse/isoreader"</span><span class="op">)</span></span></code></pre></div>
<p>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 <code>digest</code> package sometimes causes trouble - re-install with <code>remove.packages("digest"); install.packages("digest")</code>.</p>
</div>
<div class="section level2">
<h2 id="show-me-some-code">Show me some code<a class="anchor" aria-label="anchor" href="#show-me-some-code"></a>
</h2>
<p>You can, for example, automatically read the data from <strong>all</strong> 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 <code>isoreader</code> package. For a more detailed example including continuous flow and dual inlet file reads, check out our <a href="https://isoreader.isoverse.org/articles/quick_start.html" class="external-link"><strong>Quick Start Vignette</strong></a>.</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="http://isoreader.isoverse.org">isoreader</a></span><span class="op">)</span></span>
<span><span class="va">data_folder</span> <span class="op"><-</span> <span class="fu"><a href="reference/iso_get_reader_example.html">iso_get_reader_examples_folder</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="va">iso_files</span> <span class="op"><-</span> <span class="fu"><a href="reference/iso_read_scan.html">iso_read_scan</a></span><span class="op">(</span><span class="va">data_folder</span><span class="op">)</span></span>
<span><span class="co">#> Info: preparing to read 4 data files...</span></span>
<span><span class="co">#> Info: reading file 'background_scan_example.scn' with '.scn' reader...</span></span>
<span><span class="co">#> Info: reading file 'full_scan_example.scn' with '.scn' reader...</span></span>
<span><span class="co">#> Info: reading file 'peak_shape_scan_example.scn' with '.scn' reader...</span></span>
<span><span class="co">#> Info: reading file 'time_scan_example.scn' with '.scn' reader...</span></span>
<span><span class="co">#> Info: finished reading 4 files in 1.34 secs</span></span>
<span></span>
<span><span class="va">iso_files</span></span>
<span><span class="co">#> Data from 4 scan iso files: </span></span>
<span><span class="co">#> # A tibble: 4 × 6</span></span>
<span><span class="co">#> file_id file_path_ file_subpath raw_data file_info method_info</span></span>
<span><span class="co">#> <chr> <chr> <chr> <glue> <chr> <chr> </span></span>
<span><span class="co">#> 1 background_scan_exampl… backgroun… <NA> 525 mea… 8 entries resistors </span></span>
<span><span class="co">#> 2 full_scan_example.scn full_scan… <NA> 799 mea… 8 entries resistors </span></span>
<span><span class="co">#> 3 peak_shape_scan_exampl… peak_shap… <NA> 220 mea… 7 entries resistors </span></span>
<span><span class="co">#> 4 time_scan_example.scn time_scan… <NA> 5532 me… 8 entries resistors</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="supported-file-types">Supported File Types<a class="anchor" aria-label="anchor" href="#supported-file-types"></a>
</h2>
<p>Currently supported file types:</p>
<table class="table">
<colgroup>
<col width="22%">
<col width="14%">
<col width="14%">
<col width="48%">
</colgroup>
<thead><tr class="header">
<th align="left">type</th>
<th align="left">extension</th>
<th align="left">software</th>
<th align="left">description</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">continuous flow</td>
<td align="left">.cf</td>
<td align="left">Isodat</td>
<td align="left">Continuous Flow file format (older)</td>
</tr>
<tr class="even">
<td align="left">continuous flow</td>
<td align="left">.cf.rds</td>
<td align="left">isoreader</td>
<td align="left">R Data Storage</td>
</tr>
<tr class="odd">
<td align="left">continuous flow</td>
<td align="left">.dxf</td>
<td align="left">Isodat</td>
<td align="left">Continuous Flow file format (newer)</td>
</tr>
<tr class="even">
<td align="left">continuous flow</td>
<td align="left">.iarc</td>
<td align="left">ionOS</td>
<td align="left">Continuous Flow data archive</td>
</tr>
<tr class="odd">
<td align="left">dual inlet</td>
<td align="left">.caf</td>
<td align="left">Isodat</td>
<td align="left">Dual Inlet file format (older)</td>
</tr>
<tr class="even">
<td align="left">dual inlet</td>
<td align="left">.di.rds</td>
<td align="left">isoreader</td>
<td align="left">R Data Storage</td>
</tr>
<tr class="odd">
<td align="left">dual inlet</td>
<td align="left">.did</td>
<td align="left">Isodat</td>
<td align="left">Dual Inlet file format (newer)</td>
</tr>
<tr class="even">
<td align="left">dual inlet</td>
<td align="left">.txt</td>
<td align="left">Nu</td>
<td align="left">Dual Inlet file format</td>
</tr>
<tr class="odd">
<td align="left">scan</td>
<td align="left">.scan.rds</td>
<td align="left">isoreader</td>
<td align="left">R Data Storage</td>
</tr>
<tr class="even">
<td align="left">scan</td>
<td align="left">.scn</td>
<td align="left">Isodat</td>
<td align="left">Scan file format</td>
</tr>
</tbody>
</table>
</div>
<div class="section level2">
<h2 id="documentation">Documentation<a class="anchor" aria-label="anchor" href="#documentation"></a>
</h2>
<ul>
<li>for a quick introduction, check out the aforementioned <a href="https://isoreader.isoverse.org/articles/quick_start.html" class="external-link"><strong>Quick Start Vignette</strong></a>
</li>
<li>for a full reference of all available functions, see the <strong><a href="https://isoreader.isoverse.org/reference/" class="external-link">Function Reference</a></strong>
</li>
<li>for function help within RStudio, simply start typing <code>?iso_</code> in the console and a list of available function will appear (all functions share the <code>iso_</code> prefix)</li>
<li>for a detailed example of how to work with continuous flow data files, see the vignette on <strong><a href="https://isoreader.isoverse.org/articles/continuous_flow.html" class="external-link">Continuous Flow</a></strong>
</li>
<li>for a detailed example of how to work with dual inlet data files, see the vignette on <strong><a href="https://isoreader.isoverse.org/articles/dual_inlet.html" class="external-link">Dual Inlet</a></strong>
</li>
<li>for a detailed example of how to work with scan data files, see the vignette on <strong><a href="https://isoreader.isoverse.org/articles/scan.html" class="external-link">Scans</a></strong>
</li>
</ul>
</div>
<div class="section level2">
<h2 id="troubleshooting">Troubleshooting<a class="anchor" aria-label="anchor" href="#troubleshooting"></a>
</h2>
<p>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 <a href="https://github.com/isoverse/isoreader/issues" class="external-link">issue tracker</a>. Likewise if you run into any unexpected behavior or uncaught errors. Most isoreader functionality is continuously tested on Unix and Windows systems using <a href="https://github.com/isoverse/isoreader/actions?workflow=R-CMD-check" class="external-link">GitHub Actions</a>. 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.</p>
</div>
<div class="section level2">
<h2 id="development">Development<a class="anchor" aria-label="anchor" href="#development"></a>
</h2>
<p>If you are interested in helping with development, that’s fantastic! Please fork the repository and branch off from the <a href="https://github.com/isoverse/isoreader/tree/dev" class="external-link">dev branch</a> since it contains the most up-to-date development version of <a href="https://isoreader.isoverse.org/" class="external-link">isoreader</a>. Make sure to write <a href="https://r-pkgs.org/tests.html" class="external-link"><code>testthat</code> tests</a> 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 <code>make auto_test</code> in the <a href="https://isoreader.isoverse.org/" class="external-link">isoreader</a> directory from command line (it will test everything automatically in a completely separate R session).</p>
</div>
<div class="section level2">
<h2 id="open-source">Open Source<a class="anchor" aria-label="anchor" href="#open-source"></a>
</h2>
<p><a href="https://isoreader.isoverse.org/" class="external-link">isoreader</a> is and will always be fully open-source (i.e. free as in <strong>freedom</strong> and free as in <strong>free beer</strong>) and is provided as is. The source code is released under GPL-2.</p>
</div>
<div class="section level2">
<h2 id="isoverse-">isoverse <a href="https://www.isoverse.org" class="external-link"><img src="reference/figures/isoverse_logo_thumb.png" align="right" height="138.5"></a>
<a class="anchor" aria-label="anchor" href="#isoverse-"></a>
</h2>
<p>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 <a href="https://github.com/isoverse/logos" class="external-link">this repository</a>.</p>
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<h2 data-toc-skip>Links</h2>
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<li><a href="https://cloud.r-project.org/package=isoreader" class="external-link">View on CRAN</a></li>
<li><a href="https://github.com/isoverse/isoreader/" class="external-link">Browse source code</a></li>
<li><a href="https://github.com/isoverse/isoreader/issues" class="external-link">Report a bug</a></li>
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<h2 data-toc-skip>License</h2>
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<li>GPL (>= 2)</li>
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<h2 data-toc-skip>Citation</h2>
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<li><a href="authors.html#citation">Citing isoreader</a></li>
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<h2 data-toc-skip>Developers</h2>
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<li>Sebastian Kopf <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0002-2044-0201" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li>Brett Davidheiser-Kroll <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0002-6153-7851" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li>Ilja Kocken <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0003-2196-8718" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
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<p>Developed by Sebastian Kopf, Brett Davidheiser-Kroll, Ilja Kocken.</p>
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