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<title>FreesearchR • FreesearchR</title>
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<meta property="og:title" content="FreesearchR">
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<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
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<nav class="navbar navbar-expand-lg fixed-top bg-primary" data-bs-theme="dark" aria-label="Site navigation"><div class="container">
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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="">25.4.1</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<li class="active nav-item"><a class="nav-link" href="../articles/FreesearchR.html">Get started</a></li>
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<li class="nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
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<li class="nav-item"><a class="nav-link" href="../ROADMAP.html">Roadmap</a></li>
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<li class="nav-item"><a class="nav-link" href="../QA.html">Q&A</a></li>
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<li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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</ul>
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<ul class="navbar-nav">
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<li class="nav-item"><form class="form-inline" role="search">
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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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</form></li>
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<li class="nav-item"><a class="external-link nav-link" href="https://github.com/agdamsbo/FreesearchR/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
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</nav><div class="container template-article">
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<link href="FreesearchR_files/htmltools-fill-0.5.8.1/fill.css" rel="stylesheet">
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<script src="FreesearchR_files/htmlwidgets-1.6.4/htmlwidgets.js"></script><script src="FreesearchR_files/datagrid-binding-0.4.0/datagrid.js"></script><div class="row">
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<main id="main" class="col-md-9"><div class="page-header">
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<h1>FreesearchR</h1>
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<small class="dont-index">Source: <a href="https://github.com/agdamsbo/FreesearchR/blob/main/vignettes/FreesearchR.Rmd" class="external-link"><code>vignettes/FreesearchR.Rmd</code></a></small>
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<div class="d-none name"><code>FreesearchR.Rmd</code></div>
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</div>
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<div class="section level2">
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<h2 id="getting-started-with-freesearchr">Getting started with <strong><em>FreesearchR</em></strong><a class="anchor" aria-label="anchor" href="#getting-started-with-freesearchr"></a>
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</h2>
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<p>Below is a simple walk-trough and basic instructions for the
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functions on the FreesearchR app.</p>
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<div class="section level3">
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<h3 id="launching">Launching<a class="anchor" aria-label="anchor" href="#launching"></a>
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</h3>
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<p>The easiest way to get started is to launch <a href="https://agdamsbo.shinyapps.io/freesearcheR/" class="external-link">the hosted version of
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the app on shinyapps.io (click this link)</a>.</p>
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<p>Additionally you have the option to run the app locally with access
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to any data in your current working environment.</p>
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<p>To do this, open <em>R</em> (or RStudio or similar), and run the
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following code to install the latest version of
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<strong><em>FreesearchR</em></strong> 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"><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://pak.r-lib.org/" class="external-link">"pak"</a></span><span class="op">)</span></span>
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<span><span class="fu">pak</span><span class="fu">::</span><span class="fu"><a href="https://pak.r-lib.org/reference/pak.html" class="external-link">pak</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="fu">FreesearchR</span><span class="fu">::</span><span class="fu"><a href="../reference/launch_FreesearchR.html">launch_FreesearchR</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
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<p>As a small note, a standalone Windows app version is on the drawing
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board as well, but no time frame is available.</p>
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</div>
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<div class="section level3">
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<h3 id="importing-data">Importing data<a class="anchor" aria-label="anchor" href="#importing-data"></a>
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</h3>
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<p>Once in the app and in the “<strong>Import</strong>”, you have three
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options available for importing data: file upload, REDCap server export
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and local or sample data.</p>
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<p>After choosing a data source, you can set a threshold to filter data
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be completenes and further manually specify variables to include for
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analyses.</p>
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<div class="section level4">
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<h4 id="file-upload">File upload<a class="anchor" aria-label="anchor" href="#file-upload"></a>
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</h4>
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<p>Currently several data file formats are supported for easy import
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(csv, txt, xls(x), ods, rds, dta). If importing workbooks (xls(x) or
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ods), you are prompted to specify sheet(s) to import. If choosing
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multiple sheets, these are automatically merged by common variable(s),
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so please make sure that key variables are correctly named
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identically.</p>
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<p>A notification is posted with error or success. After succesfull
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import data can be previewed directly by clicking “click to see data” in
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the notification.</p>
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</div>
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<div class="section level4">
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<h4 id="redcap-server-export">REDCap server export<a class="anchor" aria-label="anchor" href="#redcap-server-export"></a>
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</h4>
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<p>Export data directly from a REDCap server. You need to first generate
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an API-token (<a href="https://confluence.research.cchmc.org/pages/viewpage.action?pageId=50987698" class="external-link">see
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these instruction</a>) in REDCap. Make sure you have the necessary
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rights to do so.</p>
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<p>Please don’t store the API-key on your device unless encrypted or in
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a keyring, as this may compromise data safety. Log in to your REDCap
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server and retrieve the token when needed.</p>
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<p>Type the correct webaddress of your REDCap server.</p>
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<p>The module will validate the information and you can click
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“Connect”.</p>
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<p>This will unfold options to preview your data dictionary (the main
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database metadata), choose fields/variables to download as well as
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filtering options.</p>
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</div>
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<div class="section level4">
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<h4 id="local-or-sample-data">Local or sample data<a class="anchor" aria-label="anchor" href="#local-or-sample-data"></a>
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</h4>
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</div>
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</div>
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<div class="section level3">
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<h3 id="evaluate">Evaluate<a class="anchor" aria-label="anchor" href="#evaluate"></a>
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</h3>
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<div class="section level4">
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<h4 id="baseline">Baseline<a class="anchor" aria-label="anchor" href="#baseline"></a>
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</h4>
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</div>
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<div class="section level4">
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<h4 id="correlation-matrix">Correlation matrix<a class="anchor" aria-label="anchor" href="#correlation-matrix"></a>
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</h4>
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</div>
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</div>
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<div class="section level3">
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<h3 id="visuals">Visuals<a class="anchor" aria-label="anchor" href="#visuals"></a>
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</h3>
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<p>There are a number of plotting options to visualise different aspects
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of the data.</p>
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<p>Below are the available plot types listed.</p>
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<div class="datagrid html-widget html-fill-item" height="600px" id="htmlwidget-ac96cb3ee4656e2e9ec3" style="width:100%;height:600px; margin-bottom: 15px;" width="100%">
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<div id="htmlwidget-ac96cb3ee4656e2e9ec3-container"></div>
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</div>
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<script type="application/json" data-for="htmlwidget-ac96cb3ee4656e2e9ec3">{"x":{"nrow":16,"ncol":3,"data":[["continuous","continuous","continuous","dichotomous","dichotomous","dichotomous","dichotomous","dichotomous","ordinal","ordinal","ordinal","ordinal","categorical","categorical","categorical","categorical"],["Violin plot","Scatter plot","Box plot","Stacked horizontal bars","Violin plot","Sankey plot","Box plot","Euler diagram","Stacked horizontal bars","Violin plot","Sankey plot","Box plot","Stacked horizontal bars","Violin plot","Sankey plot","Box plot"],["A modern alternative to the classic boxplot to visualise data distribution","A classic way of showing the association between to variables","A classic way to plot data distribution by groups","A classical way of visualising the distribution of an ordinal scale like the modified Ranking Scale and known as Grotta bars","A modern alternative to the classic boxplot to visualise data distribution","A way of visualising change between groups","A classic way to plot data distribution by groups","Generate area-proportional Euler diagrams to display set relationships","A classical way of visualising the distribution of an ordinal scale like the modified Ranking Scale and known as Grotta bars","A modern alternative to the classic boxplot to visualise data distribution","A way of visualising change between groups","A classic way to plot data distribution by groups","A classical way of visualising the distribution of an ordinal scale like the modified Ranking Scale and known as Grotta bars","A modern alternative to the classic boxplot to visualise data distribution","A way of visualising change between groups","A classic way to plot data distribution by groups"]],"colnames":["Data type","Plot type","Description"],"options":{"columns":[{"header":"Data type","name":"Data type","sortable":true,"filter":"select","align":"left","whiteSpace":"normal","renderer":{"styles":{"wordBreak":"normal"}}},{"header":"Plot type","name":"Plot type","sortable":true,"filter":"select","align":"left","whiteSpace":"normal","renderer":{"styles":{"wordBreak":"normal"}}},{"header":"Description","name":"Description","sortable":true,"filter":"select","align":"left","whiteSpace":"normal","renderer":{"styles":{"wordBreak":"normal"}}}],"bodyHeight":"fitToParent","draggable":false,"usageStatistics":false,"contextMenu":null,"rowHeight":"auto"},"theme":"striped","themeOptions":{"cell":{"normal":{"showHorizontalBorder":true}}},"language":"en","languageOptions":[],"filters":true,"rowAttributes":[],"validationInput":false,"dataAsInput":false,"dragInput":false},"evals":[],"jsHooks":[]}</script>
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</div>
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<div class="section level3">
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<h3 id="regression">Regression<a class="anchor" aria-label="anchor" href="#regression"></a>
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</h3>
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</div>
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<div class="section level3">
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<h3 id="download">Download<a class="anchor" aria-label="anchor" href="#download"></a>
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</h3>
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<div class="section level4">
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<h4 id="report">Report<a class="anchor" aria-label="anchor" href="#report"></a>
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</h4>
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</div>
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<div class="section level4">
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<h4 id="data">Data<a class="anchor" aria-label="anchor" href="#data"></a>
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</h4>
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</div>
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<div class="section level4">
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<h4 id="code">Code<a class="anchor" aria-label="anchor" href="#code"></a>
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</h4>
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</div>
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</div>
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</div>
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</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
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<div class="pkgdown-footer-right">
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<p>Developed by Andreas Gammelgaard Damsbo. Provided without <strong>any warranty</strong>.</p>
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