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| --- | ||
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| <li>CohortGenerator module</li> | ||
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| <div class="section" id="module-Generators.CohortGenerator"> | ||
| <span id="cohortgenerator-module"></span><h1>CohortGenerator module<a class="headerlink" href="#module-Generators.CohortGenerator" title="Permalink to this headline">¶</a></h1> | ||
| <p>Cohort Generator Module</p> | ||
| <p>This module manages code for defining and materializing cohorts of patients | ||
| for medical prediction tasks.</p> | ||
| <dl class="class"> | ||
| <dt id="Generators.CohortGenerator.Cohort"> | ||
| <em class="property">class </em><code class="sig-prename descclassname">Generators.CohortGenerator.</code><code class="sig-name descname">Cohort</code><span class="sig-paren">(</span><em class="sig-param">schema_name=''</em>, <em class="sig-param">cohort_table_name=None</em>, <em class="sig-param">cohort_generation_script=None</em>, <em class="sig-param">cohort_generation_kwargs=None</em>, <em class="sig-param">first=None</em>, <em class="sig-param">verbose=True</em>, <em class="sig-param">outcome_col_name='y'</em><span class="sig-paren">)</span><a class="headerlink" href="#Generators.CohortGenerator.Cohort" title="Permalink to this definition">¶</a></dt> | ||
| <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p> | ||
| <p>An object to hold cohort definitions and materialize cohort tables.</p> | ||
| <p>This class serves two purposes. First, by setting <cite>cohort_generation_script</cite> and <cite>cohort_generation_kwargs</cite>, | ||
| the rules by which a cohort is defined are laid out. Second, by calling the <cite>build</cite> method and passing in a | ||
| OMOP standard database, these rules are applied to retrieve an actual table of cohort members and outcomes which can | ||
| be used for downstream tasks</p> | ||
| <dl class="field-list simple"> | ||
| <dt class="field-odd">Parameters</dt> | ||
| <dd class="field-odd"><ul class="simple"> | ||
| <li><p><strong>cohort_generation_script</strong> (<em>str</em>) – A path to a SQL file containing a script to generate the cohort. This script may contain templated terms in the form <cite>{param}</cite>.</p></li> | ||
| <li><p><strong>cohort_generation_kwargs</strong> (<em>dict</em>) – Keyword arguments to format any templated terms in the SQL script found at <cite>cohort_generation_script</cite>.</p></li> | ||
| <li><p><strong>first</strong> (<em>int</em>) – Limit the cohort to the first <cite>first</cite> patients satisfying the cohort definition. This allows for faster prototyping.</p></li> | ||
| </ul> | ||
| </dd> | ||
| </dl> | ||
| <dl class="method"> | ||
| <dt id="Generators.CohortGenerator.Cohort.build"> | ||
| <code class="sig-name descname">build</code><span class="sig-paren">(</span><em class="sig-param">db</em>, <em class="sig-param">replace=False</em><span class="sig-paren">)</span><a class="headerlink" href="#Generators.CohortGenerator.Cohort.build" title="Permalink to this definition">¶</a></dt> | ||
| <dd><p>Materialize the cohort table in database <cite>db</cite> using the script provided at initialization.</p> | ||
| <dl class="field-list simple"> | ||
| <dt class="field-odd">Parameters</dt> | ||
| <dd class="field-odd"><p><strong>db</strong> (<a class="reference internal" href="dbutils.html#Utils.dbutils.Database" title="Utils.dbutils.Database"><em>Utils.dbutils.Database</em></a>) – The database on which queries are to be run</p> | ||
| </dd> | ||
| <dt class="field-even">Returns</dt> | ||
| <dd class="field-even"><p>None</p> | ||
| </dd> | ||
| </dl> | ||
| </dd></dl> | ||
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| <dl class="method"> | ||
| <dt id="Generators.CohortGenerator.Cohort.get_num_examples"> | ||
| <code class="sig-name descname">get_num_examples</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#Generators.CohortGenerator.Cohort.get_num_examples" title="Permalink to this definition">¶</a></dt> | ||
| <dd><p>Get the size of the cohort.</p> | ||
| <dl class="field-list simple"> | ||
| <dt class="field-odd">Returns</dt> | ||
| <dd class="field-odd"><p>The number of patients in the cohort, returns a value of 0 if the cohort has not yet been materialized.</p> | ||
| </dd> | ||
| <dt class="field-even">Return type</dt> | ||
| <dd class="field-even"><p>int</p> | ||
| </dd> | ||
| </dl> | ||
| </dd></dl> | ||
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| <dl class="method"> | ||
| <dt id="Generators.CohortGenerator.Cohort.is_built"> | ||
| <code class="sig-name descname">is_built</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#Generators.CohortGenerator.Cohort.is_built" title="Permalink to this definition">¶</a></dt> | ||
| <dd><p>Checks whether or not the cohort has been materialized yet.</p> | ||
| <dl class="field-list simple"> | ||
| <dt class="field-odd">Returns</dt> | ||
| <dd class="field-odd"><p>A boolean representing whether or not the cohort has been materialized yet</p> | ||
| </dd> | ||
| <dt class="field-even">Return type</dt> | ||
| <dd class="field-even"><p>bool</p> | ||
| </dd> | ||
| </dl> | ||
| </dd></dl> | ||
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| </dd></dl> | ||
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| <div class="section" id="module-Generators.FeatureGenerator"> | ||
| <span id="featuregenerator-module"></span><h1>FeatureGenerator module<a class="headerlink" href="#module-Generators.FeatureGenerator" title="Permalink to this headline">¶</a></h1> | ||
| <dl class="class"> | ||
| <dt id="Generators.FeatureGenerator.Feature"> | ||
| <em class="property">class </em><code class="sig-prename descclassname">Generators.FeatureGenerator.</code><code class="sig-name descname">Feature</code><span class="sig-paren">(</span><em class="sig-param">feature_sql_file</em>, <em class="sig-param">feature_sql_params</em>, <em class="sig-param">temporal=True</em><span class="sig-paren">)</span><a class="headerlink" href="#Generators.FeatureGenerator.Feature" title="Permalink to this definition">¶</a></dt> | ||
| <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p> | ||
| <p>A single time-series based feature to be used for modelling.</p> | ||
| <p>This class serves as a wrapper for a SQL script used to collect a single set of features (such as a time series of diagnoses) | ||
| for each of the members of a cohort. Note that the cohort is not specified here, and only needs to be specified just before actually collecting data.</p> | ||
| <dl class="field-list simple"> | ||
| <dt class="field-odd">Parameters</dt> | ||
| <dd class="field-odd"><ul class="simple"> | ||
| <li><p><strong>feature_sql_file</strong> (<em>str</em>) – A path to a SQL file containing a script to generate the feature. This script may contain templated terms in the form <cite>{param}</cite>.</p></li> | ||
| <li><p><strong>feature_sql_params</strong> (<em>dict</em>) – Keyword arguments to format any templated terms in the SQL script found at <cite>feature_sql_file</cite>.</p></li> | ||
| </ul> | ||
| </dd> | ||
| </dl> | ||
| </dd></dl> | ||
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| <dl class="class"> | ||
| <dt id="Generators.FeatureGenerator.FeatureSet"> | ||
| <em class="property">class </em><code class="sig-prename descclassname">Generators.FeatureGenerator.</code><code class="sig-name descname">FeatureSet</code><span class="sig-paren">(</span><em class="sig-param">db</em>, <em class="sig-param">dtcols=('feature_start_date'</em>, <em class="sig-param">'person_start_date'</em>, <em class="sig-param">'person_end_date')</em>, <em class="sig-param">id_col='person_id'</em>, <em class="sig-param">time_col='feature_start_date'</em>, <em class="sig-param">feature_col='concept_name'</em><span class="sig-paren">)</span><a class="headerlink" href="#Generators.FeatureGenerator.FeatureSet" title="Permalink to this definition">¶</a></dt> | ||
| <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p> | ||
| <p>A collection of features to be used for modelling</p> | ||
| <p>This class contains a group of <cite>Feature</cite> objects, and coordinates gathering each of these features for a cohort of patients and formatting | ||
| the collected data into an efficient format.</p> | ||
| <dl class="field-list simple"> | ||
| <dt class="field-odd">Parameters</dt> | ||
| <dd class="field-odd"><p><strong>db</strong> (<em>Utils.dbutils.Database</em>) – The database from which the features are to be extracted.</p> | ||
| </dd> | ||
| </dl> | ||
| <dl class="method"> | ||
| <dt id="Generators.FeatureGenerator.FeatureSet.add"> | ||
| <code class="sig-name descname">add</code><span class="sig-paren">(</span><em class="sig-param">feature</em><span class="sig-paren">)</span><a class="headerlink" href="#Generators.FeatureGenerator.FeatureSet.add" title="Permalink to this definition">¶</a></dt> | ||
| <dd><p>Add a new Feature object to the FeatureSet (only temporal features supported for now)</p> | ||
| <dl class="field-list simple"> | ||
| <dt class="field-odd">Parameters</dt> | ||
| <dd class="field-odd"><p><strong>feature</strong> (<a class="reference internal" href="#Generators.FeatureGenerator.Feature" title="Generators.FeatureGenerator.Feature"><em>Feature</em></a>) – The feature to add</p> | ||
| </dd> | ||
| <dt class="field-even">Returns</dt> | ||
| <dd class="field-even"><p>None</p> | ||
| </dd> | ||
| </dl> | ||
| </dd></dl> | ||
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| <dl class="method"> | ||
| <dt id="Generators.FeatureGenerator.FeatureSet.add_default_features"> | ||
| <code class="sig-name descname">add_default_features</code><span class="sig-paren">(</span><em class="sig-param">default_features</em>, <em class="sig-param">schema_name=None</em>, <em class="sig-param">cohort_name=None</em><span class="sig-paren">)</span><a class="headerlink" href="#Generators.FeatureGenerator.FeatureSet.add_default_features" title="Permalink to this definition">¶</a></dt> | ||
| <dd></dd></dl> | ||
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| <dl class="method"> | ||
| <dt id="Generators.FeatureGenerator.FeatureSet.build"> | ||
| <code class="sig-name descname">build</code><span class="sig-paren">(</span><em class="sig-param">cohort</em>, <em class="sig-param">cache_file='/tmp/store.csv'</em>, <em class="sig-param">from_cached=False</em><span class="sig-paren">)</span><a class="headerlink" href="#Generators.FeatureGenerator.FeatureSet.build" title="Permalink to this definition">¶</a></dt> | ||
| <dd><p>Populate a feature set using the features in self._temporal_features. This function call will actually collect the dataset, and thus incur significant runtime.</p> | ||
| <dl class="field-list simple"> | ||
| <dt class="field-odd">Parameters</dt> | ||
| <dd class="field-odd"><ul class="simple"> | ||
| <li><p><strong>cohort</strong> (<a class="reference internal" href="CohortGenerator.html#Generators.CohortGenerator.Cohort" title="Generators.CohortGenerator.Cohort"><em>Generators.CohortGenerator.Cohort</em></a>) – The cohort whose members data will be collected for.</p></li> | ||
| <li><p><strong>cache_file</strong> (<em>str</em>) – A location to store a raw dump of data generated by feature SQL queries</p></li> | ||
| <li><p><strong>from_cached</strong> (<em>bool</em>) – Try to load data directly from cache_file rather than first populating it by running SQL scripts</p></li> | ||
| </ul> | ||
| </dd> | ||
| <dt class="field-even">Returns</dt> | ||
| <dd class="field-even"><p>None</p> | ||
| </dd> | ||
| </dl> | ||
| </dd></dl> | ||
|
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| <dl class="method"> | ||
| <dt id="Generators.FeatureGenerator.FeatureSet.get_feature_names"> | ||
| <code class="sig-name descname">get_feature_names</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#Generators.FeatureGenerator.FeatureSet.get_feature_names" title="Permalink to this definition">¶</a></dt> | ||
| <dd></dd></dl> | ||
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| <dl class="method"> | ||
| <dt id="Generators.FeatureGenerator.FeatureSet.get_num_features"> | ||
| <code class="sig-name descname">get_num_features</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#Generators.FeatureGenerator.FeatureSet.get_num_features" title="Permalink to this definition">¶</a></dt> | ||
| <dd></dd></dl> | ||
|
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| <dl class="method"> | ||
| <dt id="Generators.FeatureGenerator.FeatureSet.get_sparr_rep"> | ||
| <code class="sig-name descname">get_sparr_rep</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#Generators.FeatureGenerator.FeatureSet.get_sparr_rep" title="Permalink to this definition">¶</a></dt> | ||
| <dd><p>Get the sparse array representation (if it is populated by self.build()) | ||
| :returns: A sparse array of data if populated, else None</p> | ||
| </dd></dl> | ||
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