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@edward-burn
edward-burn committed Jan 6, 2025
1 parent 10a0550 commit ae5f9aa
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32 changes: 16 additions & 16 deletions _book/adding_features.html
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Expand Up @@ -332,7 +332,7 @@ <h2 data-number="10.1" class="anchored" data-anchor-id="adding-specific-demograp
<div class="cell-output cell-output-stdout">
<pre><code>Rows: ??
Columns: 18
Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\Rtmpq811zM\file23145c04563c.duckdb]
Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpWwfN77\file9f701d7f6a51.duckdb]
$ condition_occurrence_id &lt;int&gt; 1, 3, 8, 9, 12, 18, 19, 20, 21, 23, 24, …
$ person_id &lt;int&gt; 2, 7, 16, 16, 25, 42, 42, 42, 44, 47, 47…
$ condition_concept_id &lt;int&gt; 381316, 381316, 381316, 313217, 381316, …
Expand Down Expand Up @@ -364,7 +364,7 @@ <h2 data-number="10.1" class="anchored" data-anchor-id="adding-specific-demograp
<pre><code>&lt;SQL&gt;
SELECT
condition_occurrence_id,
og_002_1736169508.person_id AS person_id,
og_002_1736175189.person_id AS person_id,
condition_concept_id,
condition_start_date,
condition_start_datetime,
Expand All @@ -381,7 +381,7 @@ <h2 data-number="10.1" class="anchored" data-anchor-id="adding-specific-demograp
condition_status_source_value,
age,
RHS.sex AS sex
FROM og_002_1736169508
FROM og_002_1736175189
LEFT JOIN (
SELECT
person_id,
Expand All @@ -399,13 +399,13 @@ <h2 data-number="10.1" class="anchored" data-anchor-id="adding-specific-demograp
day_of_birth
FROM (
SELECT DISTINCT person_id
FROM og_002_1736169508
FROM og_002_1736175189
) LHS
INNER JOIN main.person
ON (LHS.person_id = person.person_id)
) q01
) RHS
ON (og_002_1736169508.person_id = RHS.person_id)</code></pre>
ON (og_002_1736175189.person_id = RHS.person_id)</code></pre>
</div>
</div>
<p>We now have two variables added containing values for age and sex.</p>
Expand All @@ -415,7 +415,7 @@ <h2 data-number="10.1" class="anchored" data-anchor-id="adding-specific-demograp
<div class="cell-output cell-output-stdout">
<pre><code>Rows: ??
Columns: 18
Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\Rtmpq811zM\file23145c04563c.duckdb]
Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpWwfN77\file9f701d7f6a51.duckdb]
$ condition_occurrence_id &lt;int&gt; 1, 3, 8, 9, 12, 18, 19, 20, 21, 23, 24, …
$ person_id &lt;int&gt; 2, 7, 16, 16, 25, 42, 42, 42, 44, 47, 47…
$ condition_concept_id &lt;int&gt; 381316, 381316, 381316, 313217, 381316, …
Expand Down Expand Up @@ -479,7 +479,7 @@ <h2 data-number="10.2" class="anchored" data-anchor-id="adding-multiple-demograp
<div class="cell-output cell-output-stdout">
<pre><code>Rows: ??
Columns: 27
Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\Rtmpq811zM\file23145c04563c.duckdb]
Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpWwfN77\file9f701d7f6a51.duckdb]
$ drug_exposure_id &lt;int&gt; 245761, 245762, 245763, 245765, 245766, 2…
$ person_id &lt;int&gt; 7764, 7764, 7764, 7764, 7764, 7764, 7764,…
$ drug_concept_id &lt;int&gt; 40213227, 40213201, 40213198, 40213154, 4…
Expand Down Expand Up @@ -545,8 +545,8 @@ <h2 data-number="10.2" class="anchored" data-anchor-id="adding-multiple-demograp
<span id="cb18-4"><a href="#cb18-4" aria-hidden="true" tabindex="-1"></a> dplyr<span class="sc">::</span><span class="fu">show_query</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code>&lt;SQL&gt;
SELECT og_004_1736169512.*
FROM og_004_1736169512
SELECT og_004_1736175192.*
FROM og_004_1736175192
WHERE (sex = 'Male')</code></pre>
</div>
</div>
Expand Down Expand Up @@ -646,7 +646,7 @@ <h2 data-number="10.3" class="anchored" data-anchor-id="creating-categories"><sp
<div class="cell-output cell-output-stdout">
<pre><code>Rows: ??
Columns: 20
Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\Rtmpq811zM\file23145c04563c.duckdb]
Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpWwfN77\file9f701d7f6a51.duckdb]
$ condition_occurrence_id &lt;int&gt; 1, 3, 8, 9, 12, 18, 19, 20, 21, 23, 24, …
$ person_id &lt;int&gt; 2, 7, 16, 16, 25, 42, 42, 42, 44, 47, 47…
$ condition_concept_id &lt;int&gt; 381316, 381316, 381316, 313217, 381316, …
Expand Down Expand Up @@ -683,7 +683,7 @@ <h2 data-number="10.4" class="anchored" data-anchor-id="adding-custom-variables"
<div class="cell-output cell-output-stdout">
<pre><code>Rows: ??
Columns: 6
Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\Rtmpq811zM\file23145c04563c.duckdb]
Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpWwfN77\file9f701d7f6a51.duckdb]
$ observation_period_id &lt;int&gt; 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 1…
$ person_id &lt;int&gt; 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 1…
$ observation_period_start_date &lt;date&gt; 2014-05-09, 1977-04-11, 2014-04-19, 201…
Expand Down Expand Up @@ -711,7 +711,7 @@ <h2 data-number="10.4" class="anchored" data-anchor-id="adding-custom-variables"
<div class="cell-output cell-output-stdout">
<pre><code>Rows: ??
Columns: 2
Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\Rtmpq811zM\file23145c04563c.duckdb]
Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpWwfN77\file9f701d7f6a51.duckdb]
$ person_id &lt;int&gt; 2, 7, 16, 18, 25, 36, 42, 44, 47, 51, 52,…
$ condition_occurrence_records &lt;dbl&gt; 1, 1, 2, 2, 1, 4, 3, 2, 5, 1, 3, 2, 1, 4,…</code></pre>
</div>
Expand Down Expand Up @@ -739,7 +739,7 @@ <h2 data-number="10.4" class="anchored" data-anchor-id="adding-custom-variables"
FROM main.person
LEFT JOIN (
SELECT person_id, COUNT(*) AS condition_occurrence_records
FROM og_002_1736169508
FROM og_002_1736175189
GROUP BY person_id
) RHS
ON (person.person_id = RHS.person_id)
Expand All @@ -766,7 +766,7 @@ <h2 data-number="10.4" class="anchored" data-anchor-id="adding-custom-variables"
<span id="cb33-2"><a href="#cb33-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">tally</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># Source: SQL [?? x 1]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\Rtmpq811zM\file23145c04563c.duckdb]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpWwfN77\file9f701d7f6a51.duckdb]
n
&lt;dbl&gt;
1 9967</code></pre>
Expand All @@ -775,7 +775,7 @@ <h2 data-number="10.4" class="anchored" data-anchor-id="adding-custom-variables"
<span id="cb35-2"><a href="#cb35-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">tally</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># Source: SQL [?? x 1]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\Rtmpq811zM\file23145c04563c.duckdb]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpWwfN77\file9f701d7f6a51.duckdb]
n
&lt;dbl&gt;
1 337509</code></pre>
Expand All @@ -788,7 +788,7 @@ <h2 data-number="10.4" class="anchored" data-anchor-id="adding-custom-variables"
<span id="cb37-6"><a href="#cb37-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">tally</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># Source: SQL [?? x 1]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\Rtmpq811zM\file23145c04563c.duckdb]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpWwfN77\file9f701d7f6a51.duckdb]
n
&lt;dbl&gt;
1 410683</code></pre>
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20 changes: 10 additions & 10 deletions _book/cdm_reference.html
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Expand Up @@ -330,7 +330,7 @@ <h2 data-number="4.2" class="anchored" data-anchor-id="referencing-tables-from-t
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">tbl</span>(<span class="st">"person"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># Source: table&lt;person&gt; [?? x 18]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpUr8Ddi\file77844cb87adf.duckdb]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpGmTcrD\file9b9c2e786dbe.duckdb]
person_id gender_concept_id year_of_birth month_of_birth day_of_birth
&lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt;
1 1 8532 1970 4 24
Expand All @@ -355,7 +355,7 @@ <h2 data-number="4.2" class="anchored" data-anchor-id="referencing-tables-from-t
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">tbl</span>(<span class="st">"observation_period"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># Source: table&lt;observation_period&gt; [?? x 5]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpUr8Ddi\file77844cb87adf.duckdb]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpGmTcrD\file9b9c2e786dbe.duckdb]
observation_period_id person_id observation_period_s…¹ observation_period_e…²
&lt;int&gt; &lt;int&gt; &lt;date&gt; &lt;date&gt;
1 1 1 2014-05-09 2023-05-12
Expand All @@ -382,7 +382,7 @@ <h2 data-number="4.2" class="anchored" data-anchor-id="referencing-tables-from-t
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">count</span>() </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># Source: SQL [?? x 2]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpUr8Ddi\file77844cb87adf.duckdb]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpGmTcrD\file9b9c2e786dbe.duckdb]
# Groups: year_of_birth
year_of_birth n
&lt;int&gt; &lt;dbl&gt;
Expand Down Expand Up @@ -492,7 +492,7 @@ <h2 data-number="4.3" class="anchored" data-anchor-id="creating-a-reference-to-t
<div class="sourceCode cell-code" id="cb25"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a>cdm<span class="sc">$</span>person</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># Source: table&lt;main.person&gt; [?? x 18]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpUr8Ddi\file77844cb87adf.duckdb]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpGmTcrD\file9b9c2e786dbe.duckdb]
person_id gender_concept_id year_of_birth month_of_birth day_of_birth
&lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt;
1 1 8532 1970 4 24
Expand All @@ -516,7 +516,7 @@ <h2 data-number="4.3" class="anchored" data-anchor-id="creating-a-reference-to-t
<div class="sourceCode cell-code" id="cb27"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb27-1"><a href="#cb27-1" aria-hidden="true" tabindex="-1"></a>cdm[[<span class="st">"observation_period"</span>]]</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># Source: table&lt;main.observation_period&gt; [?? x 5]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpUr8Ddi\file77844cb87adf.duckdb]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpGmTcrD\file9b9c2e786dbe.duckdb]
observation_period_id person_id observation_period_s…¹ observation_period_e…²
&lt;int&gt; &lt;int&gt; &lt;date&gt; &lt;date&gt;
1 1 1 2014-05-09 2023-05-12
Expand Down Expand Up @@ -547,7 +547,7 @@ <h2 data-number="4.4" class="anchored" data-anchor-id="mutability-of-the-cdm-ref
<span id="cb29-4"><a href="#cb29-4" aria-hidden="true" tabindex="-1"></a>cdm<span class="sc">$</span>person</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># Source: SQL [?? x 18]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpUr8Ddi\file77844cb87adf.duckdb]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpGmTcrD\file9b9c2e786dbe.duckdb]
person_id gender_concept_id year_of_birth month_of_birth day_of_birth
&lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt;
1 1 8532 1970 4 24
Expand Down Expand Up @@ -575,7 +575,7 @@ <h2 data-number="4.4" class="anchored" data-anchor-id="mutability-of-the-cdm-ref
<span id="cb31-2"><a href="#cb31-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">tally</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># Source: SQL [?? x 1]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpUr8Ddi\file77844cb87adf.duckdb]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpGmTcrD\file9b9c2e786dbe.duckdb]
n
&lt;dbl&gt;
1 78</code></pre>
Expand All @@ -591,7 +591,7 @@ <h2 data-number="4.4" class="anchored" data-anchor-id="mutability-of-the-cdm-ref
<span id="cb33-6"><a href="#cb33-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">tally</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># Source: SQL [?? x 1]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpUr8Ddi\file77844cb87adf.duckdb]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpGmTcrD\file9b9c2e786dbe.duckdb]
n
&lt;dbl&gt;
1 10754</code></pre>
Expand Down Expand Up @@ -651,7 +651,7 @@ <h3 data-number="4.5.1" class="anchored" data-anchor-id="cdm-name"><span class="
<span id="cb44-4"><a href="#cb44-4" aria-hidden="true" tabindex="-1"></a>cdm<span class="sc">$</span>cdm_source</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stdout">
<pre><code># Source: table&lt;main.cdm_source&gt; [?? x 10]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpUr8Ddi\file77844cb87adf.duckdb]
# Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpGmTcrD\file9b9c2e786dbe.duckdb]
cdm_source_name cdm_source_abbreviation cdm_holder source_description
&lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt;
1 Synthea Synthea "" Synthea Synthetic Data
Expand Down Expand Up @@ -689,7 +689,7 @@ <h3 data-number="4.5.3" class="anchored" data-anchor-id="cdm-source"><span class
<div class="cell">
<div class="sourceCode cell-code" id="cb52"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb52-1"><a href="#cb52-1" aria-hidden="true" tabindex="-1"></a><span class="fu">attr</span>(<span class="fu">cdmSource</span>(cdm), <span class="st">"dbcon"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output cell-output-stderr">
<pre><code>&lt;duckdb_connection e2500 driver=&lt;duckdb_driver dbdir='C:\Users\eburn\AppData\Local\Temp\RtmpUr8Ddi\file77844cb87adf.duckdb' read_only=FALSE bigint=numeric&gt;&gt;</code></pre>
<pre><code>&lt;duckdb_connection 5f920 driver=&lt;duckdb_driver dbdir='C:\Users\eburn\AppData\Local\Temp\RtmpGmTcrD\file9b9c2e786dbe.duckdb' read_only=FALSE bigint=numeric&gt;&gt;</code></pre>
</div>
</div>
</section>
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