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Adding vignette help to CommonDataModel #458

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aedin Nov 10, 2021
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<h1 class="title toc-ignore">GettingStarted_CommonDataModel</h1>
<h4 class="author">Aedin Culhane</h4>
<h4 class="date">11/9/2021</h4>



<p>This vignette used the R code presented by Claire, at the OHDSI tutorial session on 9th November 2021 and hopefully presented a useful starter on this package</p>
<p>Before we start we’ll make a local folder for output</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>currentfolder<span class="ot">=</span> here<span class="sc">::</span><span class="fu">here</span>()</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>outputfolder <span class="ot">=</span> <span class="fu">paste0</span>(currentfolder,<span class="st">&quot;out&quot;</span>)</span></code></pre></div>
<p>To install this package from Github, we’ll check if you already have devtools (you likely do if not this code will install it)</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="cf">if</span> (<span class="sc">!</span><span class="st">&quot;devtools&quot;</span> <span class="sc">%in%</span> <span class="fu">installed.packages</span>()) </span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">install.packages</span>(<span class="st">&quot;devtools&quot;</span>) <span class="cf">else</span></span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">print</span>(<span class="st">&quot;Found devtools&quot;</span>)</span></code></pre></div>
<pre><code>## [1] &quot;Found devtools&quot;</code></pre>
<p>Now install the R package CommonDataModel from the OHDSI repository on github</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>devtools<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">&quot;OHDSI/CommonDataModel&quot;</span>)</span></code></pre></div>
<pre><code>##
##
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##

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##

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─ building ‘CommonDataModel_0.1.0.tar.gz’
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## </code></pre>
<div id="introduction-to-the-commondatamodel-package" class="section level2">
<h2>Introduction to the CommonDataModel package</h2>
<p>List the currently supported SQL dialets</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>CommonDataModel<span class="sc">::</span><span class="fu">listSupportedDialects</span>()</span></code></pre></div>
<pre><code>## [1] &quot;oracle&quot; &quot;postgresql&quot; &quot;pdw&quot; &quot;redshift&quot; &quot;impala&quot;
## [6] &quot;netezza&quot; &quot;bigquery&quot; &quot;sql server&quot;</code></pre>
<p>List the currently supported Common Data Model (CDM)</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>CommonDataModel<span class="sc">::</span><span class="fu">listSupportedVersions</span>()</span></code></pre></div>
<pre><code>## [1] &quot;5.3&quot; &quot;5.4&quot;</code></pre>
</div>
<div id="to-generate-ddls" class="section level2">
<h2>To generate DDLs</h2>
<p>There are multiple way to generate DDLs</p>
<ol style="list-style-type: decimal">
<li>Use the buildRelease function to generate text files in the dialect of your choice This function will put the output files in the folder you specify</li>
</ol>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>CommonDataModel<span class="sc">::</span><span class="fu">buildRelease</span>(<span class="at">cdmVersions =</span> <span class="st">&quot;5.4&quot;</span>,</span>
<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a> <span class="at">targetDialects =</span> <span class="st">&quot;postgresql&quot;</span>,</span>
<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a> <span class="at">outputfolder =</span> outputfolder)</span></code></pre></div>
<ol start="2" style="list-style-type: decimal">
<li>If you have an empty schema ready to go, the package will connect and instantiate the tables for you</li>
</ol>
<p>2a. To start you need to download DatabaseConnector in order to connect to your database</p>
<p>to install DatabaseConnector</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>devtools<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">&quot;OHDSI/DatabaseConnector&quot;</span>)</span></code></pre></div>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(DatabaseConnector)</span></code></pre></div>
<p>Please replace with your own username/password and path to the file DatabaseConnector_Jars</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a>cd<span class="ot">&lt;-</span> DatabaseConnector<span class="sc">::</span><span class="fu">createConnectionDetails</span>(<span class="at">dbms =</span> <span class="st">&quot;postgresql&quot;</span>,</span>
<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a> <span class="at">server=</span><span class="st">&quot;localhost/ohdsi&quot;</span>,</span>
<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a> <span class="at">user=</span><span class="st">&quot;postgres&quot;</span>,</span>
<span id="cb13-4"><a href="#cb13-4" aria-hidden="true" tabindex="-1"></a> <span class="at">password =</span> <span class="st">&quot;postgres&quot;</span>,</span>
<span id="cb13-5"><a href="#cb13-5" aria-hidden="true" tabindex="-1"></a> <span class="at">pathToDriver =</span> <span class="st">&quot;~/Documents/DatabaseConnector_Jars&quot;</span>)</span>
<span id="cb13-6"><a href="#cb13-6" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb13-7"><a href="#cb13-7" aria-hidden="true" tabindex="-1"></a>CommonDataModel<span class="sc">::</span><span class="fu">executeDdl</span>(<span class="at">connectionDetails =</span> cdm,</span>
<span id="cb13-8"><a href="#cb13-8" aria-hidden="true" tabindex="-1"></a> <span class="at">cdmVersion =</span> <span class="st">&quot;5.4&quot;</span>,</span>
<span id="cb13-9"><a href="#cb13-9" aria-hidden="true" tabindex="-1"></a> <span class="at">cdmDatabaseSchema =</span> <span class="st">&quot;ohdsi_demo&quot;</span>)</span></code></pre></div>
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