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276 lines
20 KiB
HTML
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<title>Easy data analysis for clinicians • FreesearchR</title>
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<meta property="og:title" content="Easy data analysis for clinicians">
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<meta name="description" content="Easily evaluate and analyse clinical health data in your browser, either based on a hosted version or run on your own device. Import data from multiple sources, summarise, modify and visualise data and create regression models. Export key metrics and regression analysis results in a publication ready document format.">
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<meta property="og:description" content="Easily evaluate and analyse clinical health data in your browser, either based on a hosted version or run on your own device. Import data from multiple sources, summarise, modify and visualise data and create regression models. Export key metrics and regression analysis results in a publication ready document format.">
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<a class="navbar-brand me-2" href="index.html">FreesearchR</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">26.3.4</small>
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<li><a class="dropdown-item" href="articles/session.html">Session info</a></li>
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<input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json">
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<main id="main" class="col-md-9"><div class="section level1">
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<div class="page-header">
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<img src="logo.png" class="logo" alt=""><h1 id="freesearchr-">FreesearchR
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<a class="anchor" aria-label="anchor" href="#freesearchr-"></a>
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</h1>
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</div>
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<!-- badges: start -->
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<p>The <a href="https://app.freesearchr.org" class="external-link"><strong><em>FreesearchR</em></strong></a> is a simple, clinical health data exploration and analysis tool to democratise clinical research by assisting any researcher to easily evaluate and analyse data and export publication ready results.</p>
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<p><a href="https://app.freesearchr.org" class="external-link"><strong><em>FreesearchR</em></strong></a> is free and open-source, and is <a href="https://app.freesearchr.org" class="external-link">accessible in your web browser through this link</a>. The app can also run locally, please <a href="#run-locally-on-your-own-machine-sec-run-locally">see below</a>.</p>
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<p>All feedback is welcome and can be shared as a GitHub issue. Any suggestions on collaboration is much welcomed. Please reach out!</p>
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<div class="float">
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<img src="./reference/figures/demo.gif" alt="FreesearchR demo"><div class="figcaption">FreesearchR demo</div>
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</div>
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<div class="section level2">
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<h2 id="motivation">Motivation<a class="anchor" aria-label="anchor" href="#motivation"></a>
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</h2>
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<p>This app has the following simple goals:</p>
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<ol style="list-style-type: decimal">
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<li><p>help the health clinician getting an overview of data in quality improvement projects and clinical research</p></li>
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<li><p>help learners get a good start analysing data and coding in <em>R</em></p></li>
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<li><p>ease quick data overview and basic visualisations for any clinical researcher</p></li>
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</ol>
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<p>Here’s a polished and restructured version of your README section for clarity, conciseness, and user-friendliness:</p>
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</div>
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<div class="section level2">
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<h2 id="run-locally-on-your-own-machine">Run Locally on Your Own Machine<a class="anchor" aria-label="anchor" href="#run-locally-on-your-own-machine"></a>
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</h2>
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<p>The <strong>FreesearchR</strong> app can be run locally on your machine, ensuring no data is transmitted externally. Below are the available options for setup and configuration.</p>
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<div class="section level3">
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<h3 id="configuration--data-loading">Configuration & Data Loading<a class="anchor" aria-label="anchor" href="#configuration--data-loading"></a>
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</h3>
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<p>The app can be configured either by passing a named list to <code>run_app()</code> or by setting environment variables in a <strong>Docker Compose</strong> file. The following variables control data access and display behavior. If no values are provided, the app will use the defaults listed below.</p>
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<p><strong>Configuration Variables</strong></p>
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<table class="table">
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<colgroup>
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<col width="22%">
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<col width="68%">
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<col width="9%">
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</colgroup>
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<thead><tr class="header">
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<th>Variable</th>
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<th>Description</th>
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<th>Default</th>
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</tr></thead>
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<tbody>
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<tr class="odd">
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<td><code>INCLUDE_GLOBALENV</code></td>
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<td>Load datasets already present in the global R environment into the app</td>
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<td><code>FALSE</code></td>
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</tr>
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<tr class="even">
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<td><code>DATA_LIMIT_DEFAULT</code></td>
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<td>Default number of observations for previewing or working with a dataset</td>
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<td><code>10,000</code></td>
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</tr>
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<tr class="odd">
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<td><code>DATA_LIMIT_UPPER</code></td>
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<td>Maximum number of observations a user can set for the upper limit. If set to 0, no uppper limit is applied.</td>
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<td><code>100,000</code></td>
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</tr>
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<tr class="even">
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<td><code>DATA_LIMIT_LOWER</code></td>
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<td>Minimum number of observations a user can set for the lower limit</td>
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<td><code>1</code></td>
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</tr>
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</tbody>
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</table>
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</div>
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<div class="section level3">
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<h3 id="run-from-r-or-rstudio">Run from R (or RStudio)<a class="anchor" aria-label="anchor" href="#run-from-r-or-rstudio"></a>
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</h3>
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<p>If you’re working with data in R, <strong>FreesearchR</strong> is a quick and easy tool for exploratory analysis.</p>
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<ol style="list-style-type: decimal">
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<li><p><strong>Requirement:</strong> Ensure you have <a href="https://www.r-project.org/" class="external-link">R</a> installed, and optionally an editor like <a href="https://posit.co/download/rstudio-desktop/" class="external-link">RStudio</a>.</p></li>
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<li>
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<p>Open the <strong>R console</strong> and run the following code to install the <a href="https://github.com/agdamsbo/FreesearchR" class="external-link">FreesearchR</a> package and launch the app:</p>
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://devtools.r-lib.org/" class="external-link">"devtools"</a></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>
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<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">"agdamsbo/FreesearchR"</span><span class="op">)</span></span>
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<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="https://github.com/agdamsbo/FreesearchR" class="external-link">FreesearchR</a></span><span class="op">)</span></span>
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<span><span class="co"># Load sample data (e.g., mtcars) to make it available in the app</span></span>
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<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">mtcars</span><span class="op">)</span></span>
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<span><span class="fu"><a href="reference/launch_FreesearchR.html">launch_FreesearchR</a></span><span class="op">(</span>INCLUDE_GLOBALENV<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
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</li>
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</ol>
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<p>All the variables specified above can also be passed to the app on launch from R. Set DATA_LIMIT_UPPER=0 to remove upper data limit. This limit is set to protect the online app version from choking and crashing on large data sets.</p>
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</div>
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<div class="section level3">
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<h3 id="running-with-docker-compose">Running with Docker Compose<a class="anchor" aria-label="anchor" href="#running-with-docker-compose"></a>
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</h3>
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<p>For advanced users, you can deploy <strong>FreesearchR</strong> using Docker. A data folder can be mounted to <code>/app/data</code> to automatically load supported file types (<code>.csv</code>, <code>.tsv</code>, <code>.txt</code>, <code>.xls</code>, <code>.xlsx</code>, <code>.ods</code>, <code>.dta</code>, <code>.rds</code>) at startup.</p>
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<p>To mount a local data folder, add a <code>volumes</code> entry to your <code>docker-compose.yml</code> file:</p>
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<div class="sourceCode" id="cb2"><pre class="sourceCode yaml"><code class="sourceCode yaml"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="fu">services</span><span class="kw">:</span></span>
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<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="at"> </span><span class="fu">shiny</span><span class="kw">:</span></span>
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<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a><span class="at"> </span><span class="fu">image</span><span class="kw">:</span><span class="at"> ghcr.io/agdamsbo/freesearchr:latest</span></span>
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<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a><span class="at"> </span><span class="fu">volumes</span><span class="kw">:</span></span>
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<span id="cb2-5"><a href="#cb2-5" tabindex="-1"></a><span class="at"> </span><span class="kw">-</span><span class="at"> ./data:/app/data:ro</span></span>
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<span id="cb2-6"><a href="#cb2-6" tabindex="-1"></a><span class="at"> </span><span class="fu">environment</span><span class="kw">:</span></span>
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<span id="cb2-7"><a href="#cb2-7" tabindex="-1"></a><span class="at"> </span><span class="kw">-</span><span class="at"> INCLUDE_GLOBALENV=FALSE</span></span>
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<span id="cb2-8"><a href="#cb2-8" tabindex="-1"></a><span class="at"> </span><span class="kw">-</span><span class="at"> DATA_LIMIT_DEFAULT=10000</span></span>
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<span id="cb2-9"><a href="#cb2-9" tabindex="-1"></a><span class="at"> </span><span class="kw">-</span><span class="at"> DATA_LIMIT_UPPER=100000</span></span>
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<span id="cb2-10"><a href="#cb2-10" tabindex="-1"></a><span class="at"> </span><span class="kw">-</span><span class="at"> DATA_LIMIT_LOWER=1</span></span>
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<span id="cb2-11"><a href="#cb2-11" tabindex="-1"></a><span class="at"> </span><span class="fu">ports</span><span class="kw">:</span></span>
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<span id="cb2-12"><a href="#cb2-12" tabindex="-1"></a><span class="at"> </span><span class="kw">-</span><span class="at"> </span><span class="st">'3838:3838'</span></span>
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<span id="cb2-13"><a href="#cb2-13" tabindex="-1"></a><span class="at"> </span><span class="fu">restart</span><span class="kw">:</span><span class="at"> on-failure</span></span></code></pre></div>
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<ul>
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<li><p>The <code>:ro</code> flag mounts the folder as <strong>read-only</strong>, preventing the app from modifying your original data files.</p></li>
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<li><p>If no volume is mounted, the app will start without any preloaded datasets.</p></li>
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</ul>
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</div>
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</div>
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<div class="section level2">
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<h2 id="code-of-conduct">Code of Conduct<a class="anchor" aria-label="anchor" href="#code-of-conduct"></a>
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</h2>
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<p>Please note that the <strong><em>FreesearchR</em></strong> project is published with a <a href="https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html" class="external-link">Contributor Code of Conduct</a>. By contributing to this project, you agree to abide by its terms.</p>
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</div>
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<div class="section level2">
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<h2 id="translators">Translators<a class="anchor" aria-label="anchor" href="#translators"></a>
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</h2>
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<p>Thank you very much to all translators having helped to translate and validate translation drafts.</p>
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</div>
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<div class="section level2">
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<h2 id="acknowledgements">Acknowledgements<a class="anchor" aria-label="anchor" href="#acknowledgements"></a>
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</h2>
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<p>Like any other project, this project was never possible without the great work of others. These are some of the sources and packages I have used:</p>
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<ul>
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<li><p>The <strong><em>FreesearchR</em></strong> app is built with <a href="https://shiny.posit.co/" class="external-link">Shiny</a> and based on <a href="https://www.r-project.org/" class="external-link"><em>R</em></a>.</p></li>
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<li><p><a href="https://www.danieldsjoberg.com/gtsummary/" class="external-link">gtsummary</a>: superb and flexible way to create publication-ready analytical and summary tables.</p></li>
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<li><p><a href="https://github.com/dreamRs" class="external-link">dreamRs</a>: maintainers of a broad selection of great extensions and tools for <a href="https://shiny.posit.co/" class="external-link">Shiny</a>.</p></li>
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<li><p><a href="https://easystats.github.io/easystats/" class="external-link">easystats</a>: the <a href="https://easystats.github.io/performance/articles/check_model.html" class="external-link"><code>performance::check_model()</code></a> function was central in sparking the idea to create a data analysis tool.</p></li>
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<li><p><a href="https://biogen-inc.github.io/IDEAFilter/" class="external-link">IDEAfilter</a>: a visually appealing data filter function based on the <a href="https://github.com/dgkf/shinyDataFilter" class="external-link">{shinyDataFilter}</a>.</p></li>
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</ul>
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<p>This project was all written by a human and not by any AI-based tools.</p>
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<p>The online <strong><em>FreesearchR</em></strong> app contains a tracking script, transmitting minimal data on usage. No uploaded data is transmitted anywhere. Have a look at the <a href="https://analytics.gdamsbo.dk/share/2i4BNpMcDMB9lJvF/agdamsbo.shinyapps.io" class="external-link">tracking data here</a>. No tracking data is sent running the app locally (see above).</p>
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</div>
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</div>
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</main><aside class="col-md-3"><div class="links">
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<h2 data-toc-skip>Links</h2>
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<ul class="list-unstyled">
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<li><a href="https://github.com/agdamsbo/FreesearchR/" class="external-link">Browse source code</a></li>
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<li><a href="https://github.com/agdamsbo/FreesearchR/issues" class="external-link">Report a bug</a></li>
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</ul>
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</div>
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<div class="license">
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<h2 data-toc-skip>License</h2>
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||
<ul class="list-unstyled">
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<li><a href="LICENSE.html">Full license</a></li>
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<li><small>AGPL (>= 3)</small></li>
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</ul>
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</div>
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<div class="community">
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<h2 data-toc-skip>Community</h2>
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<ul class="list-unstyled">
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<li><a href="CODE_OF_CONDUCT.html">Code of conduct</a></li>
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</ul>
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</div>
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<div class="citation">
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<h2 data-toc-skip>Citation</h2>
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<ul class="list-unstyled">
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<li><a href="authors.html#citation">Citing FreesearchR</a></li>
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</ul>
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</div>
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<div class="developers">
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<h2 data-toc-skip>Developers</h2>
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<ul class="list-unstyled">
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<li>Andreas Gammelgaard Damsbo <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0002-7559-1154" 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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<li><a href="authors.html">More about authors...</a></li>
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</ul>
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</div>
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<div class="dev-status">
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<h2 data-toc-skip>Dev status</h2>
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<ul class="list-unstyled">
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<li><a href="https://lifecycle.r-lib.org/articles/stages.html#experimental" class="external-link"><img src="https://img.shields.io/badge/lifecycle-experimental-orange.svg" alt="Lifecycle: experimental"></a></li>
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