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lisphilar · May 18, 2021 · 6a0b9df · 6a0b9df
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diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
@@ -70,7 +70,7 @@
 
 
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+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/analysis/data_handler.html b/docs/_modules/covsirphy/analysis/data_handler.html
@@ -68,7 +68,7 @@
 
 
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-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/analysis/example_data.html b/docs/_modules/covsirphy/analysis/example_data.html
@@ -68,7 +68,7 @@
 
 
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-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/analysis/model_validator.html b/docs/_modules/covsirphy/analysis/model_validator.html
@@ -68,7 +68,7 @@
 
 
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-                2.20.0
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diff --git a/docs/_modules/covsirphy/analysis/param_tracker.html b/docs/_modules/covsirphy/analysis/param_tracker.html
@@ -68,7 +68,7 @@
 
 
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diff --git a/docs/_modules/covsirphy/analysis/phase_tracker.html b/docs/_modules/covsirphy/analysis/phase_tracker.html
@@ -68,7 +68,7 @@
 
 
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+                2.20.0-alpha
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@@ -68,7 +68,7 @@
 
 
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-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/cleaning/cbase.html b/docs/_modules/covsirphy/cleaning/cbase.html
@@ -68,7 +68,7 @@
 
 
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+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/cleaning/country_data.html b/docs/_modules/covsirphy/cleaning/country_data.html
@@ -68,7 +68,7 @@
 
 
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-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/cleaning/covid19datahub.html b/docs/_modules/covsirphy/cleaning/covid19datahub.html
@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/cleaning/dataloader.html b/docs/_modules/covsirphy/cleaning/dataloader.html
@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/cleaning/japan_data.html b/docs/_modules/covsirphy/cleaning/japan_data.html
@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/cleaning/jhu_complement.html b/docs/_modules/covsirphy/cleaning/jhu_complement.html
@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                2.20.0
+                2.20.0-alpha
               </div>
 
 

diff --git a/docs/_modules/covsirphy/cleaning/jhu_data.html b/docs/_modules/covsirphy/cleaning/jhu_data.html
@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                2.20.0
+                2.20.0-alpha
               </div>
 
 
@@ -215,10 +215,10 @@ <h1>Source code for covsirphy.cleaning.jhu_data</h1><div class="highlight"><pre>
         <span class="n">CleaningBase</span><span class="o">.</span><span class="n">C</span><span class="p">,</span> <span class="n">CleaningBase</span><span class="o">.</span><span class="n">F</span><span class="p">,</span> <span class="n">CleaningBase</span><span class="o">.</span><span class="n">R</span><span class="p">,</span>
     <span class="p">]</span>
     <span class="n">OPTINAL_COLS</span> <span class="o">=</span> <span class="p">[</span><span class="n">CleaningBase</span><span class="o">.</span><span class="n">ISO3</span><span class="p">,</span> <span class="n">CleaningBase</span><span class="o">.</span><span class="n">N</span><span class="p">]</span>
-    <span class="c1"># Columns of self._clean_df</span>
+    <span class="c1"># Columns of self._cleaned_df</span>
     <span class="n">RAW_COLS</span> <span class="o">=</span> <span class="p">[</span>
         <span class="n">CleaningBase</span><span class="o">.</span><span class="n">DATE</span><span class="p">,</span> <span class="n">CleaningBase</span><span class="o">.</span><span class="n">ISO3</span><span class="p">,</span> <span class="n">CleaningBase</span><span class="o">.</span><span class="n">COUNTRY</span><span class="p">,</span> <span class="n">CleaningBase</span><span class="o">.</span><span class="n">PROVINCE</span><span class="p">,</span>
-        <span class="n">CleaningBase</span><span class="o">.</span><span class="n">C</span><span class="p">,</span> <span class="n">CleaningBase</span><span class="o">.</span><span class="n">F</span><span class="p">,</span> <span class="n">CleaningBase</span><span class="o">.</span><span class="n">R</span><span class="p">,</span> <span class="n">CleaningBase</span><span class="o">.</span><span class="n">N</span>
+        <span class="n">CleaningBase</span><span class="o">.</span><span class="n">C</span><span class="p">,</span> <span class="n">CleaningBase</span><span class="o">.</span><span class="n">CI</span><span class="p">,</span> <span class="n">CleaningBase</span><span class="o">.</span><span class="n">F</span><span class="p">,</span> <span class="n">CleaningBase</span><span class="o">.</span><span class="n">R</span><span class="p">,</span> <span class="n">CleaningBase</span><span class="o">.</span><span class="n">N</span>
     <span class="p">]</span>
     <span class="c1"># Columns of self.cleaned()</span>
     <span class="n">CLEANED_COLS</span> <span class="o">=</span> <span class="p">[</span>
@@ -234,6 +234,7 @@ <h1>Source code for covsirphy.cleaning.jhu_data</h1><div class="highlight"><pre>
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">citation</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
         <span class="c1"># Raw data</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_raw</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_parse_raw</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">REQUIRED_COLS</span><span class="p">,</span> <span class="n">optional_cols</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">OPTINAL_COLS</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_raw</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">CI</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
         <span class="c1"># Data cleaning</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_cleaned_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">RAW_COLS</span><span class="p">)</span> <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_raw</span><span class="o">.</span><span class="n">empty</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">_cleaning</span><span class="p">()</span>
         <span class="c1"># Citation</span>

diff --git a/docs/_modules/covsirphy/cleaning/linelist.html b/docs/_modules/covsirphy/cleaning/linelist.html
@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/cleaning/oxcgrt.html b/docs/_modules/covsirphy/cleaning/oxcgrt.html
@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/cleaning/pcr_data.html b/docs/_modules/covsirphy/cleaning/pcr_data.html
@@ -68,7 +68,7 @@
 
 
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-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/cleaning/population.html b/docs/_modules/covsirphy/cleaning/population.html
@@ -68,7 +68,7 @@
 
 
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-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/cleaning/pyramid.html b/docs/_modules/covsirphy/cleaning/pyramid.html
@@ -68,7 +68,7 @@
 
 
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-                2.20.0
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diff --git a/docs/_modules/covsirphy/cleaning/vaccine_data.html b/docs/_modules/covsirphy/cleaning/vaccine_data.html
@@ -68,7 +68,7 @@
 
 
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-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/ode/mbase.html b/docs/_modules/covsirphy/ode/mbase.html
@@ -68,7 +68,7 @@
 
 
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-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/ode/ode_handler.html b/docs/_modules/covsirphy/ode/ode_handler.html
@@ -68,7 +68,7 @@
 
 
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-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/ode/sewirf.html b/docs/_modules/covsirphy/ode/sewirf.html
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-                2.20.0
+                2.20.0-alpha
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-                2.20.0
+                2.20.0-alpha
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@@ -68,7 +68,7 @@
 
 
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-                2.20.0
+                2.20.0-alpha
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@@ -68,7 +68,7 @@
 
 
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-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/ode/sirfv.html b/docs/_modules/covsirphy/ode/sirfv.html
@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                2.20.0
+                2.20.0-alpha
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+                2.20.0-alpha
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-                2.20.0
+                2.20.0-alpha
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@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/simulation/estimator.html b/docs/_modules/covsirphy/simulation/estimator.html
@@ -68,7 +68,7 @@
 
 
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-                2.20.0
+                2.20.0-alpha
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-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/trend/trend_plot.html b/docs/_modules/covsirphy/trend/trend_plot.html
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-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/util/argument.html b/docs/_modules/covsirphy/util/argument.html
@@ -68,7 +68,7 @@
 
 
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-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/util/error.html b/docs/_modules/covsirphy/util/error.html
@@ -68,7 +68,7 @@
 
 
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-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/util/evaluator.html b/docs/_modules/covsirphy/util/evaluator.html
@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                2.20.0
+                2.20.0-alpha
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diff --git a/docs/_modules/covsirphy/util/filer.html b/docs/_modules/covsirphy/util/filer.html
@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                2.20.0
+                2.20.0-alpha
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