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ukhsa-collaboration · Dec 2, 2024 · 6cb462a · 6cb462a
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diff --git a/...1a5d259d0a7ddc7f289ec60e589f4a806c9cd.svg → ...f77d696f06d90cfe794348a3a8a9ed4fda355.svg b/...1a5d259d0a7ddc7f289ec60e589f4a806c9cd.svg → ...f77d696f06d90cfe794348a3a8a9ed4fda355.svg
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diff --git a/dev/_sources/notebooks/solution.ipynb b/dev/_sources/notebooks/solution.ipynb
@@ -23,7 +23,6 @@
    "outputs": [],
    "source": [
     "from graphviz import Digraph\n",
-    "import dot2tex\n",
     "\n",
     "\n",
     "dot = Digraph()\n",

diff --git a/dev/notebooks/model_solver.html b/dev/notebooks/model_solver.html
@@ -698,7 +698,7 @@ <h3>Random parameters<a class="headerlink" href="#random-parameters" title="Perm
 </div>
 </details>
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-<img alt="../_images/be4ae4c11a1304fa4414157061431fe28527b30f866193c5126cd8bafeda7a13.png" src="../_images/be4ae4c11a1304fa4414157061431fe28527b30f866193c5126cd8bafeda7a13.png" />
+<img alt="../_images/8eb19b52964851c7dfc623c89c02660e0da21a947e9f01816546d4ea715b0cd3.png" src="../_images/8eb19b52964851c7dfc623c89c02660e0da21a947e9f01816546d4ea715b0cd3.png" />
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 </div>
 <!-- ```{tip}
@@ -859,7 +859,7 @@ <h3>Fixed parameters<a class="headerlink" href="#id3" title="Permalink to this h
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-<img alt="../_images/ab50278c905639162fd81570b6c91c90040e36b13c8fb10d8b6a041f42d048e8.png" src="../_images/ab50278c905639162fd81570b6c91c90040e36b13c8fb10d8b6a041f42d048e8.png" />
+<img alt="../_images/ec0835cd5bc559e7339ba76140a4816b87774d5f05656d465b7d9a6e3b070658.png" src="../_images/ec0835cd5bc559e7339ba76140a4816b87774d5f05656d465b7d9a6e3b070658.png" />
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@@ -968,7 +968,7 @@ <h3>Random parameters<a class="headerlink" href="#id4" title="Permalink to this
 </div>
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-<img alt="../_images/c449b82a567a8b7d01aecdb4606f516724153da4a21571f1e17de27b37d6bcd0.png" src="../_images/c449b82a567a8b7d01aecdb4606f516724153da4a21571f1e17de27b37d6bcd0.png" />
+<img alt="../_images/557468ef9d162c5c6bde944eea0fc6dca82c6e2761121e0b0e1f812d1b10ff20.png" src="../_images/557468ef9d162c5c6bde944eea0fc6dca82c6e2761121e0b0e1f812d1b10ff20.png" />
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@@ -1017,7 +1017,7 @@ <h2>Summary<a class="headerlink" href="#summary" title="Permalink to this headin
 </div>
 </details>
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-<img alt="../_images/da813d94ef62234569a926902a0648cf35b164af8afc1300bddc41eab143afda.png" src="../_images/da813d94ef62234569a926902a0648cf35b164af8afc1300bddc41eab143afda.png" />
+<img alt="../_images/96148ec47ab7da464e97107badafb5acd4a2e719d6d31a7498329328c46aee4c.png" src="../_images/96148ec47ab7da464e97107badafb5acd4a2e719d6d31a7498329328c46aee4c.png" />
 </div>
 </div>
 <!-- ## Repeatable Simulation

diff --git a/dev/notebooks/paramfit/params_via_optimization.html b/dev/notebooks/paramfit/params_via_optimization.html
@@ -553,7 +553,7 @@ <h2>Gradient calculations<a class="headerlink" href="#gradient-calculations" tit
 </div>
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-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>32.5 ms ± 154 μs per loop (mean ± std. dev. of 7 runs, 10 loops each)
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>33.8 ms ± 372 μs per loop (mean ± std. dev. of 7 runs, 10 loops each)
 </pre></div>
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@@ -565,7 +565,7 @@ <h2>Gradient calculations<a class="headerlink" href="#gradient-calculations" tit
 </div>
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-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>258 ms ± 2.02 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>259 ms ± 1.29 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
 </pre></div>
 </div>
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diff --git a/dev/notebooks/solution.html b/dev/notebooks/solution.html
@@ -461,18 +461,7 @@ <h1>Mathematical description<a class="headerlink" href="#mathematical-descriptio
 The different solving methods of PyGOM is a subject for a <a class="reference internal" href="model_solver.html"><span class="doc">later chapter</span></a>, for now we introduce the two ways such systems may be viewed. Recall the model of the previous section:</p>
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-<div class="output traceback highlight-ipythontb notranslate"><div class="highlight"><pre><span></span><span class="gt">---------------------------------------------------------------------------</span>
-<span class="ne">ModuleNotFoundError</span><span class="g g-Whitespace">                       </span>Traceback (most recent call last)
-<span class="n">Cell</span> <span class="n">In</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">line</span> <span class="mi">2</span>
-<span class="g g-Whitespace">      </span><span class="mi">1</span> <span class="kn">from</span> <span class="nn">graphviz</span> <span class="kn">import</span> <span class="n">Digraph</span>
-<span class="ne">----&gt; </span><span class="mi">2</span> <span class="kn">import</span> <span class="nn">dot2tex</span>
-<span class="g g-Whitespace">      </span><span class="mi">5</span> <span class="n">dot</span> <span class="o">=</span> <span class="n">Digraph</span><span class="p">()</span>
-<span class="g g-Whitespace">      </span><span class="mi">7</span> <span class="n">dot</span><span class="o">.</span><span class="n">body</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="s1">&#39;rankdir=LR&#39;</span><span class="p">])</span>
-
-<span class="ne">ModuleNotFoundError</span>: No module named &#39;dot2tex&#39;
-</pre></div>
-</div>
-</div>
+<img alt="../_images/100dfe2f88e3fa1449c11d3977900cf7e920d6358f3b2dabae95b18183998271.svg" src="../_images/100dfe2f88e3fa1449c11d3977900cf7e920d6358f3b2dabae95b18183998271.svg" /></div>
 </div>
 <section id="ordinary-differential-equations">
 <h2>Ordinary Differential Equations<a class="headerlink" href="#ordinary-differential-equations" title="Permalink to this heading">#</a></h2>

diff --git a/dev/notebooks/unroll/unrollSimple.html b/dev/notebooks/unroll/unrollSimple.html
@@ -539,7 +539,7 @@ <h2>SIR with births and deaths<a class="headerlink" href="#sir-with-births-and-d
 </div>
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 <div class="output text_latex math notranslate nohighlight">
-\[\begin{split}\displaystyle \left[\begin{matrix}\frac{I S \beta}{I + R + S}\\I \gamma\\S \mu\\B R\\B I\\B S\\I \mu\\R \mu\end{matrix}\right]\end{split}\]</div>
+\[\begin{split}\displaystyle \left[\begin{matrix}\frac{I S \beta}{I + R + S}\\I \gamma\\S \mu\\B R\\B S\\B I\\I \mu\\R \mu\end{matrix}\right]\end{split}\]</div>
 </div>
 </div>
 <p>Birth and death processes are not between states, rather into and out of the system and so do not appear in the transition matrix.
@@ -553,7 +553,7 @@ <h2>SIR with births and deaths<a class="headerlink" href="#sir-with-births-and-d
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-<img alt="../../_images/54eec05bb58c7333e37407c6a701a5d259d0a7ddc7f289ec60e589f4a806c9cd.svg" src="../../_images/54eec05bb58c7333e37407c6a701a5d259d0a7ddc7f289ec60e589f4a806c9cd.svg" /></div>
+<img alt="../../_images/24960fa8dd243456d84e7f5efe4f77d696f06d90cfe794348a3a8a9ed4fda355.svg" src="../../_images/24960fa8dd243456d84e7f5efe4f77d696f06d90cfe794348a3a8a9ed4fda355.svg" /></div>
 </div>
 </section>
 <section id="sliar-epidemic-model">

diff --git a/dev/searchindex.js b/dev/searchindex.js