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Expand Down Expand Up @@ -1412,7 +1412,7 @@ <h1>Source code for covsirphy.analysis.scenario</h1><div class="highlight"><pre>
<span class="n">delay_period</span> <span class="o">=</span> <span class="nb">int</span><span class="p">((</span><span class="n">low_lim</span> <span class="o">+</span> <span class="n">Q1</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span><span class="p">)</span>
<span class="k">return</span> <span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">delay_period</span><span class="p">),</span> <span class="n">df</span><span class="p">)</span></div>

<div class="viewcode-block" id="Scenario.fit"><a class="viewcode-back" href="../../../covsirphy.analysis.html#covsirphy.Scenario.fit">[docs]</a> <span class="k">def</span> <span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">oxcgrt_data</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">&quot;Main&quot;</span><span class="p">,</span> <span class="n">delay</span><span class="o">=</span><span class="p">(</span><span class="mi">7</span><span class="p">,</span> <span class="mi">31</span><span class="p">),</span> <span class="n">removed_cols</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">metric</span><span class="o">=</span><span class="s2">&quot;R2&quot;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<div class="viewcode-block" id="Scenario.fit"><a class="viewcode-back" href="../../../covsirphy.analysis.html#covsirphy.Scenario.fit">[docs]</a> <span class="k">def</span> <span class="nf">fit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">oxcgrt_data</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">&quot;Main&quot;</span><span class="p">,</span> <span class="n">delay</span><span class="o">=</span><span class="p">(</span><span class="mi">7</span><span class="p">,</span> <span class="mi">31</span><span class="p">),</span> <span class="n">removed_cols</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">metric</span><span class="o">=</span><span class="s2">&quot;MAPE&quot;</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Fit regressors to predict the parameter values in the future phases,</span>
<span class="sd"> assuming that indicators will impact on ODE parameter values/the number of cases with delay.</span>
Expand All @@ -1429,7 +1429,7 @@ <h1>Source code for covsirphy.analysis.scenario</h1><div class="highlight"><pre>
<span class="sd"> - None: Scenario.estimate_delay() calculate automatically</span>
<span class="sd"> removed_cols (list[str] or None): list of variables to remove from X dataset or None (indicators used to estimate delay period)</span>
<span class="sd"> metric (str): metric name</span>
<span class="sd"> kwargs: keyword arguments of sklearn.model_selection.train_test_split() and Scenario.fit_accuracy()</span>
<span class="sd"> kwargs: keyword arguments of sklearn.model_selection.train_test_split(), RegressorHandler.fit() and Scenario.fit_accuracy()</span>

<span class="sd"> Raises:</span>
<span class="sd"> covsirphy.UnExecutedError: Scenario.estimate() or Scenario.add() were not performed</span>
Expand Down Expand Up @@ -1486,7 +1486,7 @@ <h1>Source code for covsirphy.analysis.scenario</h1><div class="highlight"><pre>
<span class="n">delay</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_ensure_natural_int</span><span class="p">(</span><span class="n">delay</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">&quot;delay&quot;</span><span class="p">)</span>
<span class="c1"># Fit regression models</span>
<span class="n">handler</span> <span class="o">=</span> <span class="n">RegressionHandler</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="n">data</span><span class="p">,</span> <span class="n">model</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_model</span><span class="p">,</span> <span class="n">delay</span><span class="o">=</span><span class="n">delay</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
<span class="n">handler</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">metric</span><span class="o">=</span><span class="n">metric</span><span class="p">)</span>
<span class="n">handler</span><span class="o">.</span><span class="n">fit</span><span class="p">(</span><span class="n">metric</span><span class="o">=</span><span class="n">metric</span><span class="p">,</span> <span class="o">**</span><span class="n">find_args</span><span class="p">(</span><span class="n">RegressionHandler</span><span class="o">.</span><span class="n">fit</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_reghandler_dict</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="o">=</span> <span class="n">handler</span>
<span class="c1"># Accuracy</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fit_accuracy</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">name</span><span class="p">,</span> <span class="n">metric</span><span class="o">=</span><span class="n">metric</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
Expand All @@ -1507,19 +1507,22 @@ <h1>Source code for covsirphy.analysis.scenario</h1><div class="highlight"><pre>
<span class="k">raise</span> <span class="n">UnExecutedError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Scenario.fit(name=</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">)&quot;</span><span class="p">)</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_reghandler_dict</span><span class="p">[</span><span class="n">name</span><span class="p">]</span>

<div class="viewcode-block" id="Scenario.fit_accuracy"><a class="viewcode-back" href="../../../covsirphy.analysis.html#covsirphy.Scenario.fit_accuracy">[docs]</a> <span class="k">def</span> <span class="nf">fit_accuracy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">&quot;Main&quot;</span><span class="p">,</span> <span class="n">show_figure</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<div class="viewcode-block" id="Scenario.fit_accuracy"><a class="viewcode-back" href="../../../covsirphy.analysis.html#covsirphy.Scenario.fit_accuracy">[docs]</a> <span class="k">def</span> <span class="nf">fit_accuracy</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">&quot;Main&quot;</span><span class="p">,</span> <span class="n">metric</span><span class="o">=</span><span class="s2">&quot;MAPE&quot;</span><span class="p">,</span> <span class="n">show_figure</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> Create a plot to show the accuracy of forecasting (predicted vs. actual parameter values).</span>

<span class="sd"> Args:</span>
<span class="sd"> name (str): scenario name</span>
<span class="sd"> metric (str): metric name, refer to covsirphy.Evaluator.score()</span>
<span class="sd"> show_figure (bool): whether show figure or not</span>
<span class="sd"> kwargs: keyword arguments of RegressionHandler.pred_true_plot()</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">metric</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s2">&quot;metrics&quot;</span><span class="p">)</span> <span class="k">if</span> <span class="s2">&quot;metrics&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span> <span class="k">else</span> <span class="n">metric</span>
<span class="n">handler</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_get_fit_handler</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">name</span><span class="p">)</span>
<span class="c1"># Show predicted vs. actual plot</span>
<span class="k">if</span> <span class="n">show_figure</span><span class="p">:</span>
<span class="n">handler</span><span class="o">.</span><span class="n">pred_actual_plot</span><span class="p">(</span><span class="o">**</span><span class="n">find_args</span><span class="p">(</span><span class="n">RegressionHandler</span><span class="o">.</span><span class="n">pred_actual_plot</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">))</span></div>
<span class="n">handler</span><span class="o">.</span><span class="n">pred_actual_plot</span><span class="p">(</span>
<span class="n">metric</span><span class="o">=</span><span class="n">metric</span><span class="p">,</span> <span class="o">**</span><span class="n">find_args</span><span class="p">(</span><span class="n">RegressionHandler</span><span class="o">.</span><span class="n">pred_actual_plot</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">))</span></div>

<div class="viewcode-block" id="Scenario.predict"><a class="viewcode-back" href="../../../covsirphy.analysis.html#covsirphy.Scenario.predict">[docs]</a> <span class="k">def</span> <span class="nf">predict</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">days</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="s2">&quot;Main&quot;</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
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