publish: Since HRH capabilities are calibrated to 2018, make default …

…scaling_by_pop_growth scenario only expand capabilities to match pop growth from 2019 onwards (#1365) generated from commit de94ffa
UCL · May 27, 2024 · 3d28f21 · 3d28f21
1 parent 7b8612f
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diff --git a/.buildinfo b/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: b333840838cfc7d6a5a0ed7f2922a372
+config: 03d02af625979bbd5b1cfd6fd45f8162
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_data_sources.html b/_data_sources.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Core Functions &mdash; TLOmodel 0.1.dev2392+g4a55807 documentation</title>
+  <title>Core Functions &mdash; TLOmodel 0.1.dev2407+gde94ffa documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="_static/theme_overrides.css?v=6ea10ece" />
@@ -17,8 +17,8 @@
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=2acae80b"></script>
-        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/documentation_options.js?v=8142288c"></script>
+        <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
@@ -724,7 +724,7 @@ <h2>Road Traffic Injuries<a class="headerlink" href="#road-traffic-injuries" tit
 
   <div role="contentinfo">
     <p>
-      <span class="lastupdated">Last updated on Apr 23, 2024.
+      <span class="lastupdated">Last updated on May 27, 2024.
       </span></p>
   </div>
 

diff --git a/_downloads/0c4bdf8cd773bfb4f52e4c2bbe9e7bf3/PostnatalSupervisor.docx b/_downloads/0c4bdf8cd773bfb4f52e4c2bbe9e7bf3/PostnatalSupervisor.docx
diff --git a/_downloads/301500ba45190c666d8c19a28dffc897/Labour.docx b/_downloads/301500ba45190c666d8c19a28dffc897/Labour.docx
diff --git a/_downloads/4a5320a11982fb23ac089b13f8a649b1/NewbornOutcomes.docx b/_downloads/4a5320a11982fb23ac089b13f8a649b1/NewbornOutcomes.docx
diff --git a/_downloads/c434c86e394739c2c6cee146e3d4356d/PregnancySupervisor.docx b/_downloads/c434c86e394739c2c6cee146e3d4356d/PregnancySupervisor.docx
diff --git a/_downloads/d259ee2478d4ac9e09a19cb71e63d1a9/hsi_events.csv b/_downloads/d259ee2478d4ac9e09a19cb71e63d1a9/hsi_events.csv
diff --git a/_downloads/d82791bed460016d2333df303e847bc5/CareOfWomenDuringPregnancy.docx b/_downloads/d82791bed460016d2333df303e847bc5/CareOfWomenDuringPregnancy.docx
diff --git a/_hsi_events.html b/_hsi_events.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Alri &mdash; TLOmodel 0.1.dev2392+g4a55807 documentation</title>
+  <title>Alri &mdash; TLOmodel 0.1.dev2407+gde94ffa documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="_static/theme_overrides.css?v=6ea10ece" />
@@ -17,8 +17,8 @@
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="_static/documentation_options.js?v=2acae80b"></script>
-        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/documentation_options.js?v=8142288c"></script>
+        <script src="_static/doctools.js?v=9a2dae69"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
@@ -326,7 +326,7 @@ <h1>Tb<a class="headerlink" href="#tb" title="Link to this heading"></a></h1>
 
   <div role="contentinfo">
     <p>
-      <span class="lastupdated">Last updated on Apr 23, 2024.
+      <span class="lastupdated">Last updated on May 27, 2024.
       </span></p>
   </div>
 

diff --git a/_modules/index.html b/_modules/index.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; TLOmodel 0.1.dev2392+g4a55807 documentation</title>
+  <title>Overview: module code &mdash; TLOmodel 0.1.dev2407+gde94ffa documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/theme_overrides.css?v=6ea10ece" />
@@ -16,8 +16,8 @@
 
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=2acae80b"></script>
-        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/documentation_options.js?v=8142288c"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
@@ -156,7 +156,7 @@ <h1>All modules for which code is available</h1>
 
   <div role="contentinfo">
     <p>
-      <span class="lastupdated">Last updated on Apr 23, 2024.
+      <span class="lastupdated">Last updated on May 27, 2024.
       </span></p>
   </div>
 

diff --git a/_modules/tlo/analysis/hsi_events.html b/_modules/tlo/analysis/hsi_events.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>tlo.analysis.hsi_events &mdash; TLOmodel 0.1.dev2392+g4a55807 documentation</title>
+  <title>tlo.analysis.hsi_events &mdash; TLOmodel 0.1.dev2407+gde94ffa documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=d10597a4" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/theme_overrides.css?v=6ea10ece" />
@@ -16,8 +16,8 @@
 
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=2acae80b"></script>
-        <script src="../../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../../_static/documentation_options.js?v=8142288c"></script>
+        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />
@@ -582,6 +582,9 @@ <h1>Source code for tlo.analysis.hsi_events</h1><div class="highlight"><pre>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Entry point to do the inspection of HSI events when running as script.&quot;&quot;&quot;</span>
     <span class="n">args</span> <span class="o">=</span> <span class="n">_parse_command_line_args</span><span class="p">()</span>
     <span class="n">warnings</span><span class="o">.</span><span class="n">simplefilter</span><span class="p">(</span><span class="s1">&#39;ignore&#39;</span><span class="p">)</span>
+    <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">json_file</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">args</span><span class="o">.</span><span class="n">merge_json_details</span><span class="p">:</span>
+        <span class="n">msg</span> <span class="o">=</span> <span class="s2">&quot;Cannot merge details if JSON file not specified&quot;</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
     <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">json_file</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
         <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">json_file</span><span class="p">,</span> <span class="s1">&#39;r&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
             <span class="n">hsi_event_details</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
@@ -649,7 +652,7 @@ <h1>Source code for tlo.analysis.hsi_events</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>
-      <span class="lastupdated">Last updated on Apr 23, 2024.
+      <span class="lastupdated">Last updated on May 27, 2024.
       </span></p>
   </div>
 

diff --git a/_modules/tlo/analysis/life_expectancy.html b/_modules/tlo/analysis/life_expectancy.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>tlo.analysis.life_expectancy &mdash; TLOmodel 0.1.dev2392+g4a55807 documentation</title>
+  <title>tlo.analysis.life_expectancy &mdash; TLOmodel 0.1.dev2407+gde94ffa documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=d10597a4" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/theme_overrides.css?v=6ea10ece" />
@@ -16,8 +16,8 @@
 
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=2acae80b"></script>
-        <script src="../../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../../_static/documentation_options.js?v=8142288c"></script>
+        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />
@@ -349,7 +349,7 @@ <h1>Source code for tlo.analysis.life_expectancy</h1><div class="highlight"><pre
 
   <div role="contentinfo">
     <p>
-      <span class="lastupdated">Last updated on Apr 23, 2024.
+      <span class="lastupdated">Last updated on May 27, 2024.
       </span></p>
   </div>
 

diff --git a/_modules/tlo/analysis/utils.html b/_modules/tlo/analysis/utils.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>tlo.analysis.utils &mdash; TLOmodel 0.1.dev2392+g4a55807 documentation</title>
+  <title>tlo.analysis.utils &mdash; TLOmodel 0.1.dev2407+gde94ffa documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=d10597a4" />
       <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../../../_static/theme_overrides.css?v=6ea10ece" />
@@ -16,8 +16,8 @@
 
         <script src="../../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=2acae80b"></script>
-        <script src="../../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../../_static/documentation_options.js?v=8142288c"></script>
+        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />
@@ -377,13 +377,11 @@ <h1>Source code for tlo.analysis.utils</h1><div class="highlight"><pre>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="k">def</span> <span class="nf">get_multiplier</span><span class="p">(</span><span class="n">_draw</span><span class="p">,</span> <span class="n">_run</span><span class="p">):</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Helper function to get the multiplier from the simulation, if do_scaling=True.</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Helper function to get the multiplier from the simulation.</span>
 <span class="sd">        Note that if the scaling factor cannot be found a `KeyError` is thrown.&quot;&quot;&quot;</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="n">do_scaling</span><span class="p">:</span>
-            <span class="k">return</span> <span class="mf">1.0</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">load_pickled_dataframes</span><span class="p">(</span><span class="n">results_folder</span><span class="p">,</span> <span class="n">_draw</span><span class="p">,</span> <span class="n">_run</span><span class="p">,</span> <span class="s1">&#39;tlo.methods.population&#39;</span>
-                                           <span class="p">)[</span><span class="s1">&#39;tlo.methods.population&#39;</span><span class="p">][</span><span class="s1">&#39;scaling_factor&#39;</span><span class="p">][</span><span class="s1">&#39;scaling_factor&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="k">return</span> <span class="n">load_pickled_dataframes</span><span class="p">(</span>
+            <span class="n">results_folder</span><span class="p">,</span> <span class="n">_draw</span><span class="p">,</span> <span class="n">_run</span><span class="p">,</span> <span class="s1">&#39;tlo.methods.population&#39;</span>
+        <span class="p">)[</span><span class="s1">&#39;tlo.methods.population&#39;</span><span class="p">][</span><span class="s1">&#39;scaling_factor&#39;</span><span class="p">][</span><span class="s1">&#39;scaling_factor&#39;</span><span class="p">]</span><span class="o">.</span><span class="n">values</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
 
     <span class="k">if</span> <span class="n">custom_generate_series</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
         <span class="c1"># If there is no `custom_generate_series` provided, it implies that function required selects the specified</span>
@@ -416,7 +414,10 @@ <h1>Source code for tlo.analysis.utils</h1><div class="highlight"><pre>
                 <span class="n">df</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span> <span class="o">=</span> <span class="n">load_pickled_dataframes</span><span class="p">(</span><span class="n">results_folder</span><span class="p">,</span> <span class="n">draw</span><span class="p">,</span> <span class="n">run</span><span class="p">,</span> <span class="n">module</span><span class="p">)[</span><span class="n">module</span><span class="p">][</span><span class="n">key</span><span class="p">]</span>
                 <span class="n">output_from_eval</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span> <span class="o">=</span> <span class="n">generate_series</span><span class="p">(</span><span class="n">df</span><span class="p">)</span>
                 <span class="k">assert</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span> <span class="o">==</span> <span class="nb">type</span><span class="p">(</span><span class="n">output_from_eval</span><span class="p">),</span> <span class="s1">&#39;Custom command does not generate a pd.Series&#39;</span>
-                <span class="n">res</span><span class="p">[</span><span class="n">draw_run</span><span class="p">]</span> <span class="o">=</span> <span class="n">output_from_eval</span> <span class="o">*</span> <span class="n">get_multiplier</span><span class="p">(</span><span class="n">draw</span><span class="p">,</span> <span class="n">run</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">do_scaling</span><span class="p">:</span>
+                    <span class="n">res</span><span class="p">[</span><span class="n">draw_run</span><span class="p">]</span> <span class="o">=</span> <span class="n">output_from_eval</span> <span class="o">*</span> <span class="n">get_multiplier</span><span class="p">(</span><span class="n">draw</span><span class="p">,</span> <span class="n">run</span><span class="p">)</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">res</span><span class="p">[</span><span class="n">draw_run</span><span class="p">]</span> <span class="o">=</span> <span class="n">output_from_eval</span>
 
             <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
                 <span class="c1"># Some logs could not be found - probably because this run failed.</span>
@@ -1332,6 +1333,7 @@ <h1>Source code for tlo.analysis.utils</h1><div class="highlight"><pre>
             <span class="s2">&quot;mode_appt_constraints&quot;</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
             <span class="s2">&quot;cons_availability&quot;</span><span class="p">:</span> <span class="s2">&quot;default&quot;</span><span class="p">,</span>
             <span class="s2">&quot;beds_availability&quot;</span><span class="p">:</span> <span class="s2">&quot;default&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;equip_availability&quot;</span><span class="p">:</span> <span class="s2">&quot;all&quot;</span><span class="p">,</span>  <span class="c1"># &lt;--- NB. Existing calibration is assuming all equipment is available</span>
         <span class="p">},</span>
     <span class="p">}</span></div>
 
@@ -1458,7 +1460,7 @@ <h1>Source code for tlo.analysis.utils</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>
-      <span class="lastupdated">Last updated on Apr 23, 2024.
+      <span class="lastupdated">Last updated on May 27, 2024.
       </span></p>
   </div>