publish: Update contributors (#1450)

generated from commit d9d3f62

.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: 03d02af625979bbd5b1cfd6fd45f8162
+config: c5e7d63c8b98330e189802d8c25b429f
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_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.dev2407+gde94ffa documentation</title>
+  <title>Core Functions &mdash; TLOmodel 0.1.dev2435+gd9d3f62 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" />
@@ -17,7 +17,7 @@
 
         <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=8142288c"></script>
+        <script src="_static/documentation_options.js?v=f3d69a25"></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>
@@ -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 May 27, 2024.
+      <span class="lastupdated">Last updated on Aug 02, 2024.
       </span></p>
   </div>
 

_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.dev2407+gde94ffa documentation</title>
+  <title>Alri &mdash; TLOmodel 0.1.dev2435+gd9d3f62 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" />
@@ -17,7 +17,7 @@
 
         <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=8142288c"></script>
+        <script src="_static/documentation_options.js?v=f3d69a25"></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>
@@ -200,7 +200,8 @@ <h1>HealthSeekingBehaviour<a class="headerlink" href="#healthseekingbehaviour" t
 <section id="hiv">
 <h1>Hiv<a class="headerlink" href="#hiv" title="Link to this heading"></a></h1>
 <ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">Prevention_Circumcision</span></code> at facility level 1a with appointment footprint: <code class="docutils literal notranslate"><span class="pre">MaleCirc</span></code>.</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">PalliativeCare</span></code> at facility level 2 with appointment footprint:  and bed days footprint: <code class="docutils literal notranslate"><span class="pre">general_bed</span></code> (17 days).</p></li>
+<li><p><code class="docutils literal notranslate"><span class="pre">Prevention_Circumcision</span></code> at facility level 1b with appointment footprint: <code class="docutils literal notranslate"><span class="pre">MaleCirc</span></code>.</p></li>
 <li><p><code class="docutils literal notranslate"><span class="pre">Prevention_Infant</span></code> at facility level 1a with appointment footprint: <code class="docutils literal notranslate"><span class="pre">Peds</span></code>, <code class="docutils literal notranslate"><span class="pre">VCTNegative</span></code>.</p></li>
 <li><p><code class="docutils literal notranslate"><span class="pre">Prevention_Prep</span></code> at facility level 1a with appointment footprint: <code class="docutils literal notranslate"><span class="pre">PharmDispensing</span></code>, <code class="docutils literal notranslate"><span class="pre">VCTNegative</span></code>.</p></li>
 <li><p><code class="docutils literal notranslate"><span class="pre">Test</span></code> at facility level 1a with appointment footprint: <code class="docutils literal notranslate"><span class="pre">VCTNegative</span></code>.</p></li>
@@ -307,6 +308,7 @@ <h1>Stunting<a class="headerlink" href="#stunting" title="Link to this heading">
 <section id="tb">
 <h1>Tb<a class="headerlink" href="#tb" title="Link to this heading"></a></h1>
 <ul class="simple">
+<li><p><code class="docutils literal notranslate"><span class="pre">PalliativeCare</span></code> at facility level 2 with appointment footprint:  and bed days footprint: <code class="docutils literal notranslate"><span class="pre">general_bed</span></code> (8 days).</p></li>
 <li><p><code class="docutils literal notranslate"><span class="pre">Prevention_Ipt</span></code> at facility level 1a with appointment footprint: <code class="docutils literal notranslate"><span class="pre">Over5OPD</span></code>.</p></li>
 <li><p><code class="docutils literal notranslate"><span class="pre">Test_Clinical</span></code> at facility level 1a with appointment footprint: <code class="docutils literal notranslate"><span class="pre">Under5OPD</span></code>.</p></li>
 <li><p><code class="docutils literal notranslate"><span class="pre">Test_FollowUp</span></code> at facility level 1a with appointment footprint: <code class="docutils literal notranslate"><span class="pre">TBFollowUp</span></code>.</p></li>
@@ -326,7 +328,7 @@ <h1>Tb<a class="headerlink" href="#tb" title="Link to this heading"></a></h1>
 
   <div role="contentinfo">
     <p>
-      <span class="lastupdated">Last updated on May 27, 2024.
+      <span class="lastupdated">Last updated on Aug 02, 2024.
       </span></p>
   </div>
 

_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.dev2407+gde94ffa documentation</title>
+  <title>Overview: module code &mdash; TLOmodel 0.1.dev2435+gd9d3f62 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" />
@@ -16,7 +16,7 @@
 
         <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=8142288c"></script>
+        <script src="../_static/documentation_options.js?v=f3d69a25"></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>
@@ -156,7 +156,7 @@ <h1>All modules for which code is available</h1>
 
   <div role="contentinfo">
     <p>
-      <span class="lastupdated">Last updated on May 27, 2024.
+      <span class="lastupdated">Last updated on Aug 02, 2024.
       </span></p>
   </div>
 

_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.dev2407+gde94ffa documentation</title>
+  <title>tlo.analysis.hsi_events &mdash; TLOmodel 0.1.dev2435+gd9d3f62 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" />
@@ -16,7 +16,7 @@
 
         <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=8142288c"></script>
+        <script src="../../../_static/documentation_options.js?v=f3d69a25"></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>
@@ -140,7 +140,7 @@ <h1>Source code for tlo.analysis.hsi_events</h1><div class="highlight"><pre>
         <span class="n">module</span> <span class="o">=</span> <span class="n">importlib</span><span class="o">.</span><span class="n">import_module</span><span class="p">(</span><span class="sa">f</span><span class="s1">&#39;tlo.methods.</span><span class="si">{</span><span class="n">module_name</span><span class="si">}</span><span class="s1">&#39;</span><span class="p">)</span>
         <span class="n">tlo_module_classes</span> <span class="o">=</span> <span class="p">[</span>
             <span class="n">obj</span> <span class="k">for</span> <span class="n">_</span><span class="p">,</span> <span class="n">obj</span> <span class="ow">in</span> <span class="n">inspect</span><span class="o">.</span><span class="n">getmembers</span><span class="p">(</span><span class="n">module</span><span class="p">)</span>
-            <span class="k">if</span> <span class="n">is_valid_tlo_module_subclass</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">excluded_modules</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">is_valid_tlo_module_subclass</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="p">{})</span>
         <span class="p">]</span>
         <span class="n">hsi_event_classes</span> <span class="o">=</span> <span class="p">[</span>
             <span class="n">obj</span> <span class="k">for</span> <span class="n">_</span><span class="p">,</span> <span class="n">obj</span> <span class="ow">in</span> <span class="n">inspect</span><span class="o">.</span><span class="n">getmembers</span><span class="p">(</span><span class="n">module</span><span class="p">)</span>
@@ -652,7 +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 May 27, 2024.
+      <span class="lastupdated">Last updated on Aug 02, 2024.
       </span></p>
   </div>
 

_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.dev2407+gde94ffa documentation</title>
+  <title>tlo.analysis.life_expectancy &mdash; TLOmodel 0.1.dev2435+gd9d3f62 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" />
@@ -16,7 +16,7 @@
 
         <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=8142288c"></script>
+        <script src="../../../_static/documentation_options.js?v=f3d69a25"></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>
@@ -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 May 27, 2024.
+      <span class="lastupdated">Last updated on Aug 02, 2024.
       </span></p>
   </div>
 

_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.dev2407+gde94ffa documentation</title>
+  <title>tlo.analysis.utils &mdash; TLOmodel 0.1.dev2435+gd9d3f62 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" />
@@ -16,7 +16,7 @@
 
         <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=8142288c"></script>
+        <script src="../../../_static/documentation_options.js?v=f3d69a25"></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>
@@ -1337,6 +1337,44 @@ <h1>Source code for tlo.analysis.utils</h1><div class="highlight"><pre>
         <span class="p">},</span>
     <span class="p">}</span></div>
 
+
+<div class="viewcode-block" id="get_parameters_for_standard_mode2_runs">
+<a class="viewcode-back" href="../../../reference/tlo.analysis.utils.html#tlo.analysis.utils.get_parameters_for_standard_mode2_runs">[docs]</a>
+<span class="k">def</span> <span class="nf">get_parameters_for_standard_mode2_runs</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">Dict</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Returns a dictionary of parameters and their updated values to indicate</span>
+<span class="sd">    the &quot;standard mode 2&quot; scenario.</span>
+
+<span class="sd">    The return dict is in the form:</span>
+<span class="sd">    e.g. {</span>
+<span class="sd">            &#39;Depression&#39;: {</span>
+<span class="sd">                &#39;pr_assessed_for_depression_for_perinatal_female&#39;: 1.0,</span>
+<span class="sd">                &#39;pr_assessed_for_depression_in_generic_appt_level1&#39;: 1.0,</span>
+<span class="sd">                },</span>
+<span class="sd">            &#39;Hiv&#39;: {</span>
+<span class="sd">                &#39;prob_start_art_or_vs&#39;: 1.0,</span>
+<span class="sd">                }</span>
+<span class="sd">         }</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">return</span> <span class="p">{</span>
+        <span class="s2">&quot;SymptomManager&quot;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s2">&quot;spurious_symptoms&quot;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="p">},</span>
+        <span class="s2">&quot;HealthSystem&quot;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s1">&#39;Service_Availability&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;*&#39;</span><span class="p">],</span>
+            <span class="s2">&quot;use_funded_or_actual_staffing&quot;</span><span class="p">:</span> <span class="s2">&quot;actual&quot;</span><span class="p">,</span>
+            <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;mode_appt_constraints_postSwitch&quot;</span><span class="p">:</span> <span class="mi">2</span><span class="p">,</span> <span class="c1"># &lt;-- Include a transition to mode 2, to pick up any issues with this</span>
+            <span class="s2">&quot;year_mode_switch&quot;</span><span class="p">:</span> <span class="mi">2012</span><span class="p">,</span> <span class="c1"># &lt;-- Could make this quite soon, but I&#39;d say &gt;1 year</span>
+            <span class="s2">&quot;tclose_overwrite&quot;</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="c1"># &lt;-- In most of our runs in mode 2, we chose to overwrite tclose</span>
+            <span class="s2">&quot;tclose_days_offset_overwrite&quot;</span><span class="p">:</span> <span class="mi">7</span><span class="p">,</span> <span class="c1"># &lt;-- and usually set it to 7.</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>
+
 
 
 <div class="viewcode-block" id="get_parameters_for_improved_healthsystem_and_healthcare_seeking">
@@ -1460,7 +1498,7 @@ <h1>Source code for tlo.analysis.utils</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>
-      <span class="lastupdated">Last updated on May 27, 2024.
+      <span class="lastupdated">Last updated on Aug 02, 2024.
       </span></p>
   </div>