deploy: 15f0b34

_modules/cycquery/mimiciv.html

@@ -258,20 +258,13 @@ <h1>Source code for cycquery.mimiciv</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">QueryInterface</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="n">table</span><span class="p">)</span></div>
 
 
-<div class="viewcode-block" id="MIMICIVQuerier.diagnoses">
-<a class="viewcode-back" href="../../reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.diagnoses">[docs]</a>
-    <span class="k">def</span> <span class="nf">diagnoses</span><span class="p">(</span>
+<div class="viewcode-block" id="MIMICIVQuerier.diagnoses_icd">
+<a class="viewcode-back" href="../../reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.diagnoses_icd">[docs]</a>
+    <span class="k">def</span> <span class="nf">diagnoses_icd</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">QueryInterface</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Query MIMIC diagnosis data.</span>
 
-<span class="sd">        Parameters</span>
-<span class="sd">        ----------</span>
-<span class="sd">        join</span>
-<span class="sd">            Join arguments.</span>
-<span class="sd">        ops</span>
-<span class="sd">            Additional operations to apply to the query.</span>
-
 <span class="sd">        Returns</span>
 <span class="sd">        -------</span>
 <span class="sd">        cycquery.interface.QueryInterface</span>
@@ -290,6 +283,31 @@ <h1>Source code for cycquery.mimiciv</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">QueryInterface</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="n">table</span><span class="p">)</span></div>
 
 
+<div class="viewcode-block" id="MIMICIVQuerier.procedures_icd">
+<a class="viewcode-back" href="../../reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.procedures_icd">[docs]</a>
+    <span class="k">def</span> <span class="nf">procedures_icd</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">QueryInterface</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Query MIMIC procedures data.</span>
+
+<span class="sd">        Returns</span>
+<span class="sd">        -------</span>
+<span class="sd">        cycquery.interface.QueryInterface</span>
+<span class="sd">            Constructed query, wrapped in an interface object.</span>
+
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">table</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_table</span><span class="p">(</span><span class="s2">&quot;mimiciv_hosp&quot;</span><span class="p">,</span> <span class="s2">&quot;procedures_icd&quot;</span><span class="p">)</span>
+
+        <span class="c1"># Join with procedures dimension table.</span>
+        <span class="n">table</span> <span class="o">=</span> <span class="n">qo</span><span class="o">.</span><span class="n">Join</span><span class="p">(</span>
+            <span class="n">join_table</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">get_table</span><span class="p">(</span><span class="s2">&quot;mimiciv_hosp&quot;</span><span class="p">,</span> <span class="s2">&quot;d_icd_procedures&quot;</span><span class="p">),</span>
+            <span class="n">on</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;icd_code&quot;</span><span class="p">,</span> <span class="s2">&quot;icd_version&quot;</span><span class="p">],</span>
+            <span class="n">on_to_type</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;str&quot;</span><span class="p">,</span> <span class="s2">&quot;int&quot;</span><span class="p">],</span>
+        <span class="p">)(</span><span class="n">table</span><span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">QueryInterface</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="n">table</span><span class="p">)</span></div>
+
+
 <div class="viewcode-block" id="MIMICIVQuerier.labevents">
 <a class="viewcode-back" href="../../reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.labevents">[docs]</a>
     <span class="k">def</span> <span class="nf">labevents</span><span class="p">(</span>

_sources/reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.rst.txt

@@ -17,14 +17,15 @@ cycquery.mimiciv.MIMICIVQuerier
       :nosignatures:
 
       ~MIMICIVQuerier.chartevents
-      ~MIMICIVQuerier.diagnoses
+      ~MIMICIVQuerier.diagnoses_icd
       ~MIMICIVQuerier.get_table
       ~MIMICIVQuerier.labevents
       ~MIMICIVQuerier.list_columns
       ~MIMICIVQuerier.list_custom_tables
       ~MIMICIVQuerier.list_schemas
       ~MIMICIVQuerier.list_tables
       ~MIMICIVQuerier.patients
+      ~MIMICIVQuerier.procedures_icd
 
 
 

_sources/tutorials/mimiciv.ipynb.txt

@@ -107,7 +107,7 @@
     "    qo.ConditionInYears(\"admittime\", \"2015\"),\n",
     ")\n",
     "patient_admissions = patient_admissions.ops(ops)\n",
-    "diagnoses = querier.diagnoses()\n",
+    "diagnoses = querier.diagnoses_icd()\n",
     "diagnoses_ops = qo.Sequential(\n",
     "    qo.ConditionEquals(\"icd_version\", 10),\n",
     "    qo.ConditionSubstring(\"long_title\", \"schizophrenia\"),\n",
@@ -143,7 +143,7 @@
     "    qo.ConditionInYears(\"admittime\", \"2015\"),\n",
     ")\n",
     "patient_admissions = patient_admissions.ops(ops)\n",
-    "diagnoses = querier.diagnoses()\n",
+    "diagnoses = querier.diagnoses_icd()\n",
     "diagnoses_ops = qo.Sequential(\n",
     "    qo.ConditionEquals(\"icd_version\", 9),\n",
     "    qo.ConditionRegexMatch(\"long_title\", r\"(?=.*schizophrenia)(?=.*chronic)\"),\n",

api.html

@@ -538,14 +538,15 @@ <h1>API Reference<a class="headerlink" href="#api-reference" title="Link to this
 <li class="toctree-l4"><a class="reference internal" href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html">cycquery.mimiciv.MIMICIVQuerier</a><ul>
 <li class="toctree-l5"><a class="reference internal" href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier"><code class="docutils literal notranslate"><span class="pre">MIMICIVQuerier</span></code></a><ul>
 <li class="toctree-l6"><a class="reference internal" href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.chartevents"><code class="docutils literal notranslate"><span class="pre">MIMICIVQuerier.chartevents()</span></code></a></li>
-<li class="toctree-l6"><a class="reference internal" href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.diagnoses"><code class="docutils literal notranslate"><span class="pre">MIMICIVQuerier.diagnoses()</span></code></a></li>
+<li class="toctree-l6"><a class="reference internal" href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.diagnoses_icd"><code class="docutils literal notranslate"><span class="pre">MIMICIVQuerier.diagnoses_icd()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.get_table"><code class="docutils literal notranslate"><span class="pre">MIMICIVQuerier.get_table()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.labevents"><code class="docutils literal notranslate"><span class="pre">MIMICIVQuerier.labevents()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.list_columns"><code class="docutils literal notranslate"><span class="pre">MIMICIVQuerier.list_columns()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.list_custom_tables"><code class="docutils literal notranslate"><span class="pre">MIMICIVQuerier.list_custom_tables()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.list_schemas"><code class="docutils literal notranslate"><span class="pre">MIMICIVQuerier.list_schemas()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.list_tables"><code class="docutils literal notranslate"><span class="pre">MIMICIVQuerier.list_tables()</span></code></a></li>
 <li class="toctree-l6"><a class="reference internal" href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.patients"><code class="docutils literal notranslate"><span class="pre">MIMICIVQuerier.patients()</span></code></a></li>
+<li class="toctree-l6"><a class="reference internal" href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.procedures_icd"><code class="docutils literal notranslate"><span class="pre">MIMICIVQuerier.procedures_icd()</span></code></a></li>
 </ul>
 </li>
 </ul>

genindex.html

@@ -437,12 +437,12 @@ <h2 id="D">D</h2>
 
       <ul>
         <li><a href="reference/api/_autosummary/cycquery.mimiciii.MIMICIIIQuerier.html#cycquery.mimiciii.MIMICIIIQuerier.diagnoses">(MIMICIIIQuerier method)</a>
-</li>
-        <li><a href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.diagnoses">(MIMICIVQuerier method)</a>
 </li>
       </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.diagnoses_icd">diagnoses_icd() (MIMICIVQuerier method)</a>
+</li>
       <li><a href="reference/api/_autosummary/cycquery.ops.Distinct.html#cycquery.ops.Distinct">Distinct (class in cycquery.ops)</a>
 </li>
       <li><a href="reference/api/_autosummary/cycquery.ops.Drop.html#cycquery.ops.Drop">Drop (class in cycquery.ops)</a>
@@ -670,11 +670,13 @@ <h2 id="P">P</h2>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.patients">patients() (MIMICIVQuerier method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="reference/api/_autosummary/cycquery.omop.OMOPQuerier.html#cycquery.omop.OMOPQuerier.person">person() (OMOPQuerier method)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="reference/api/_autosummary/cycquery.ops.Sequential.html#cycquery.ops.Sequential.pop">pop() (Sequential method)</a>
+</li>
+      <li><a href="reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html#cycquery.mimiciv.MIMICIVQuerier.procedures_icd">procedures_icd() (MIMICIVQuerier method)</a>
 </li>
   </ul></td>
 </tr></table>

reference/api/_autosummary/cycquery.mimiciv.MIMICIVQuerier.html

@@ -200,7 +200,7 @@ <h1>cycquery.mimiciv.MIMICIVQuerier<a class="headerlink" href="#cycquery-mimiciv
 <tr class="row-odd"><td><p><a class="reference internal" href="#cycquery.mimiciv.MIMICIVQuerier.chartevents" title="cycquery.mimiciv.MIMICIVQuerier.chartevents"><code class="xref py py-obj docutils literal notranslate"><span class="pre">chartevents</span></code></a></p></td>
 <td><p>Query ICU chart events from the ICU module.</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="#cycquery.mimiciv.MIMICIVQuerier.diagnoses" title="cycquery.mimiciv.MIMICIVQuerier.diagnoses"><code class="xref py py-obj docutils literal notranslate"><span class="pre">diagnoses</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="#cycquery.mimiciv.MIMICIVQuerier.diagnoses_icd" title="cycquery.mimiciv.MIMICIVQuerier.diagnoses_icd"><code class="xref py py-obj docutils literal notranslate"><span class="pre">diagnoses_icd</span></code></a></p></td>
 <td><p>Query MIMIC diagnosis data.</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="#cycquery.mimiciv.MIMICIVQuerier.get_table" title="cycquery.mimiciv.MIMICIVQuerier.get_table"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_table</span></code></a></p></td>
@@ -224,6 +224,9 @@ <h1>cycquery.mimiciv.MIMICIVQuerier<a class="headerlink" href="#cycquery-mimiciv
 <tr class="row-odd"><td><p><a class="reference internal" href="#cycquery.mimiciv.MIMICIVQuerier.patients" title="cycquery.mimiciv.MIMICIVQuerier.patients"><code class="xref py py-obj docutils literal notranslate"><span class="pre">patients</span></code></a></p></td>
 <td><p>Query MIMIC patient data.</p></td>
 </tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#cycquery.mimiciv.MIMICIVQuerier.procedures_icd" title="cycquery.mimiciv.MIMICIVQuerier.procedures_icd"><code class="xref py py-obj docutils literal notranslate"><span class="pre">procedures_icd</span></code></a></p></td>
+<td><p>Query MIMIC procedures data.</p></td>
+</tr>
 </tbody>
 </table>
 <dl class="py method">
@@ -241,21 +244,15 @@ <h1>cycquery.mimiciv.MIMICIVQuerier<a class="headerlink" href="#cycquery-mimiciv
 </dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="cycquery.mimiciv.MIMICIVQuerier.diagnoses">
-<span class="sig-name descname"><span class="pre">diagnoses</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/cycquery/mimiciv.html#MIMICIVQuerier.diagnoses"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cycquery.mimiciv.MIMICIVQuerier.diagnoses" title="Link to this definition"></a></dt>
+<dt class="sig sig-object py" id="cycquery.mimiciv.MIMICIVQuerier.diagnoses_icd">
+<span class="sig-name descname"><span class="pre">diagnoses_icd</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/cycquery/mimiciv.html#MIMICIVQuerier.diagnoses_icd"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cycquery.mimiciv.MIMICIVQuerier.diagnoses_icd" title="Link to this definition"></a></dt>
 <dd><p>Query MIMIC diagnosis data.</p>
 <dl class="field-list simple">
-<dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>join</strong> – Join arguments.</p></li>
-<li><p><strong>ops</strong> – Additional operations to apply to the query.</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns<span class="colon">:</span></dt>
-<dd class="field-even"><p>Constructed query, wrapped in an interface object.</p>
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Constructed query, wrapped in an interface object.</p>
 </dd>
-<dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference internal" href="cycquery.interface.QueryInterface.html#cycquery.interface.QueryInterface" title="cycquery.interface.QueryInterface">cycquery.interface.QueryInterface</a></p>
+<dt class="field-even">Return type<span class="colon">:</span></dt>
+<dd class="field-even"><p><a class="reference internal" href="cycquery.interface.QueryInterface.html#cycquery.interface.QueryInterface" title="cycquery.interface.QueryInterface">cycquery.interface.QueryInterface</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -381,6 +378,20 @@ <h1>cycquery.mimiciv.MIMICIVQuerier<a class="headerlink" href="#cycquery-mimiciv
 adjusted based on the inferred approximate year of care.</p>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="cycquery.mimiciv.MIMICIVQuerier.procedures_icd">
+<span class="sig-name descname"><span class="pre">procedures_icd</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/cycquery/mimiciv.html#MIMICIVQuerier.procedures_icd"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#cycquery.mimiciv.MIMICIVQuerier.procedures_icd" title="Link to this definition"></a></dt>
+<dd><p>Query MIMIC procedures data.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Returns<span class="colon">:</span></dt>
+<dd class="field-odd"><p>Constructed query, wrapped in an interface object.</p>
+</dd>
+<dt class="field-even">Return type<span class="colon">:</span></dt>
+<dd class="field-even"><p><a class="reference internal" href="cycquery.interface.QueryInterface.html#cycquery.interface.QueryInterface" title="cycquery.interface.QueryInterface">cycquery.interface.QueryInterface</a></p>
+</dd>
+</dl>
+</dd></dl>
+
 </dd></dl>
 
 </section>