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34 <h1 class="logo"><a href="../index.html">EMULSION</a></h1>
38 <p class="blurb">Epidemiological Multi-Level Simulation Framework</p>
45 <h3>Navigation</h3>
46 <ul class="current">
47 <li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a><ul>
48 <li class="toctree-l2"><a class="reference internal" href="#requirements">Requirements</a></li>
49 <li class="toctree-l2"><a class="reference internal" href="#install-with-pip">Install with <code class="docutils literal notranslate"><span class="pre">pip</span></code></a></li>
50 <li class="toctree-l2"><a class="reference internal" href="#install-with-git">Install with <code class="docutils literal notranslate"><span class="pre">git</span></code></a></li>
51 <li class="toctree-l2"><a class="reference internal" href="#install-third-party-software">Install third-party software</a></li>
52 <li class="toctree-l2"><a class="reference internal" href="#test-your-installation">Test your installation</a></li>
53 </ul>
54 </li>
55 <li class="toctree-l1"><a class="reference internal" href="Getting_started.html">Getting started with EMULSION</a></li>
56 <li class="toctree-l1"><a class="reference internal" href="Modelling_principles.html">Modelling principles</a></li>
57 <li class="toctree-l1"><a class="reference internal" href="Modelling_language_basics.html">Modelling language (basics)</a></li>
58 <li class="toctree-l1"><a class="reference internal" href="Modelling_language_advanced.html">Modelling language (advanced)</a></li>
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61 <li class="toctree-l1"><a class="reference internal" href="License.html">License</a></li>
62 <li class="toctree-l1"><a class="reference internal" href="../emulsion_for_modellers.html">High-level functions for model designers</a></li>
63 <li class="toctree-l1"><a class="reference internal" href="../emulsion.html">emulsion package</a></li>
64 </ul>
66 <div class="relations">
67 <h3>Related Topics</h3>
68 <ul>
69   <li><a href="../index.html">Documentation overview</a><ul>
70       <li>Previous: <a href="../index.html" title="previous chapter">EMULSION Manual</a></li>
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93   <div class="section" id="installation">
94 <h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
95 <div class="section" id="requirements">
96 <h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">¶</a></h2>
97 <dl class="docutils">
98 <dt>System</dt>
99 <dd><p class="first">EMULSION has been tested with <strong>MacOS</strong> and <strong>Linux</strong>. This
100 installation procedure works for both.</p>
101 <p class="last">Also, in what follows, we assume you are working with a <strong>bash</strong>
102 shell. If you are not sure, typing: <code class="docutils literal notranslate"><span class="pre">echo</span> <span class="pre">$SHELL</span></code> should print
103 <code class="docutils literal notranslate"><span class="pre">/bin/bash</span></code>. Otherwise, please refer to the documentation of
104 your shell to adapt the commands below.</p>
105 </dd>
106 <dt>Language</dt>
107 <dd><p class="first">EMULSION is written in Python3 (version 3.6 or higher). In what
108 follows, we assume that <code class="docutils literal notranslate"><span class="pre">python3</span></code> and <code class="docutils literal notranslate"><span class="pre">pip3</span></code> refer to your
109 Python3 installation. If not, replace them by your own
110 configuration in the commands below.</p>
111 <p class="last">To install Python on your system, please consult <a class="reference external" href="https://www.python.org/downloads/">Python website</a></p>
112 </dd>
113 </dl>
114 </div>
115 <div class="section" id="install-with-pip">
116 <h2>Install with <code class="docutils literal notranslate"><span class="pre">pip</span></code><a class="headerlink" href="#install-with-pip" title="Permalink to this headline">¶</a></h2>
117 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo pip3 install emulsion
118 init_emulsion
119 <span class="nb">source</span> <span class="nv">$HOME</span>/.basrc
120 </pre></div>
121 </div>
122 <p>The second command (<code class="docutils literal notranslate"><span class="pre">init_emulsion</span></code>) initializes command-line
123 completion (available with a bash shell, under Linux or MacOS) allows
124 to use <code class="docutils literal notranslate"><span class="pre">TAB</span></code> key to get suggestions on what is expected (options,
125 files, parameters…) in the command.</p>
126 <p>When installing with <code class="docutils literal notranslate"><span class="pre">pip</span></code>, <a class="reference external" href="https://sourcesup.renater.fr/emulsion-public">documentation</a>
127 is provided on-line.</p>
128 </div>
129 <div class="section" id="install-with-git">
130 <h2>Install with <code class="docutils literal notranslate"><span class="pre">git</span></code><a class="headerlink" href="#install-with-git" title="Permalink to this headline">¶</a></h2>
131 <ol class="arabic">
132 <li><p class="first">Install (or update) required packages</p>
133 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo pip3 install numpy scipy matplotlib sympy pandas
134 sudo pip3 install networkx docopt jinja2 textx
135 sudo pip3 install sortedcontainers tqdm pyyaml
136 sudo pip3 install bokeh sqlalchemy
137 </pre></div>
138 </div>
139 </li>
140 <li><p class="first">Clone the EMULSION repository</p>
141 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git clone https://git.renater.fr/emulsion-public.git
142 <span class="nb">cd</span> emulsion-public
143 </pre></div>
144 </div>
145 </li>
146 <li><p class="first">Add the <code class="docutils literal notranslate"><span class="pre">src</span></code> directory to your <code class="docutils literal notranslate"><span class="pre">PYTHONPATH</span></code> environment
147 variable.</p>
148 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">echo</span> <span class="s2">&quot;export PYTHONPATH=</span><span class="k">$(</span><span class="nb">pwd</span><span class="k">)</span><span class="s2">/src&quot;</span> &gt;&gt;<span class="nv">$HOME</span>/.bashrc
149 </pre></div>
150 </div>
151 </li>
152 <li><p class="first">Install command-line completion (optional but very convenient).</p>
153 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">echo</span> <span class="s2">&quot;source </span><span class="k">$(</span><span class="nb">pwd</span><span class="k">)</span><span class="s2">/scripts/emulsion-completion.sh&quot;</span> &gt;&gt;<span class="nv">$HOME</span>/.bashrc
154 </pre></div>
155 </div>
156 <p>Command-line completion (available with a bash shell, under Linux
157 or MacOS) allows to use <code class="docutils literal notranslate"><span class="pre">TAB</span></code> key to get suggestions on what is
158 expected (options, files, parameters…) in the command.</p>
159 </li>
160 <li><p class="first">Create command <code class="docutils literal notranslate"><span class="pre">emulsion</span></code>:</p>
161 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">echo</span> <span class="s2">&quot;alias emulsion=&#39;python3 -m emulsion&#39;&quot;</span> &gt;&gt;<span class="nv">$HOME</span>/.bashrc
162 </pre></div>
163 </div>
164 </li>
165 <li><p class="first">Force the shell to update your init file:</p>
166 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">source</span> <span class="nv">$HOME</span>/.bashrc
167 </pre></div>
168 </div>
169 </li>
170 </ol>
171 </div>
172 <div class="section" id="install-third-party-software">
173 <h2>Install third-party software<a class="headerlink" href="#install-third-party-software" title="Permalink to this headline">¶</a></h2>
174 <p><a class="reference external" href="http://www.graphviz.org">Graphviz</a> is highly recommended
175 (otherwise, simulations will run but you will not be able to get the
176 nice diagrams representing model structure).</p>
177 <p>To install on Linux:</p>
178 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo apt install graphviz
179 </pre></div>
180 </div>
181 <p>To install on MacOS, use for instance <a class="reference external" href="https://brew.sh/">homebrew</a></p>
182 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>brew install graphviz
183 </pre></div>
184 </div>
185 </div>
186 <div class="section" id="test-your-installation">
187 <h2>Test your installation<a class="headerlink" href="#test-your-installation" title="Permalink to this headline">¶</a></h2>
188 <p>Download <strong>model examples</strong>
189 <a class="reference external" href="https://sourcesup.renater.fr/emulsion-public/models.zip">here.</a></p>
190 <p>Extract the archive, open a terminal in the <code class="docutils literal notranslate"><span class="pre">models</span></code> directory, then type:</p>
191 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> quickstart
192 emulsion run --plot quickstart.yaml --view-model --silent
193 </pre></div>
194 </div>
195 <p>This should produce the following output:</p>
196 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Simulation</span> <span class="n">level</span><span class="p">:</span> <span class="n">herd</span>
197 <span class="n">Generated</span> <span class="n">state</span> <span class="n">machine</span> <span class="n">diagram</span> <span class="n">img</span><span class="o">/</span><span class="n">Quickstart_age_group_machine</span><span class="o">.</span><span class="n">png</span>
198 <span class="n">Generated</span> <span class="n">state</span> <span class="n">machine</span> <span class="n">diagram</span> <span class="n">img</span><span class="o">/</span><span class="n">Quickstart_life_cycle_machine</span><span class="o">.</span><span class="n">png</span>
199 <span class="n">Generated</span> <span class="n">state</span> <span class="n">machine</span> <span class="n">diagram</span> <span class="n">img</span><span class="o">/</span><span class="n">Quickstart_health_state_machine</span><span class="o">.</span><span class="n">png</span>
200 <span class="mi">100</span><span class="o">%|*************************************************************|</span> <span class="mi">10</span><span class="o">/</span><span class="mi">10</span>
201 <span class="n">Simulation</span> <span class="n">finished</span> <span class="ow">in</span> <span class="mf">9.48</span> <span class="n">s</span>
202 <span class="n">Outputs</span> <span class="n">stored</span> <span class="ow">in</span> <span class="n">outputs</span><span class="o">/</span><span class="n">counts</span><span class="o">.</span><span class="n">csv</span>
203 <span class="n">Outputs</span> <span class="n">plot</span> <span class="ow">in</span> <span class="n">file</span><span class="p">:</span> <span class="n">img</span><span class="o">/</span><span class="n">Quickstart</span><span class="o">.</span><span class="n">html</span>
204 </pre></div>
205 </div>
206 <p>and the following figures should appear in your navigator:</p>
207 <div align="center" class="align-center"><object data="../_images/graphviz-92fc12dfc05ef7d71faa8575198ddd05ca7de496.svg" type="image/svg+xml">
208             <p class="warning">digraph {
209                 rankdir=LR;
210                 node[fontsize=16, fontname=Arial, shape=box, style=&quot;filled,rounded&quot;];
211                 edge[minlen=1.5, penwidth=1.5, tailtooltip=&quot;&quot;, headtooltip=&quot;&quot;];
213                 &quot;J&quot; [shape=&quot;Mrecord&quot;, label=&quot;{{\ J\ |&amp;#9670;}}&quot;, tooltip=&quot;J (Juvenile):
214         juvenile animals&quot;, fillcolor=orange, style=&quot;filled,rounded,bold&quot;] ;
215         &quot;A&quot; [shape=&quot;Mrecord&quot;, label=&quot;{{\ A\ |&amp;#9670;}}&quot;, tooltip=&quot;A (Adult):
216         adult animals&quot;, fillcolor=brown, style=&quot;filled,rounded&quot;] ;
217         &quot;J&quot; -&gt; &quot;A&quot; [label=&quot;proba: 1&quot;, labeltooltip=&quot;proba: 1&quot;, arrowtail=&quot;nonetee&quot;, arrowhead=&quot;normalnone&quot;, dir=both, tooltip=&quot;COND: GreaterThan(age, adult_age)&quot;, minlen=3, style=&quot;solid&quot;];
218 }</p></object>
219 </div>
220 <img alt="../_images/Quickstart_JA.png" class="align-left" src="../_images/Quickstart_JA.png" />
221 <div align="center" class="align-center"><object data="../_images/graphviz-bc851614e8a7cff2efb11362b96ee26808197fa4.svg" type="image/svg+xml">
222             <p class="warning">digraph {
223                 rankdir=LR;
224                 node[fontsize=16, fontname=Arial, shape=box, style=&quot;filled,rounded&quot;];
225                 edge[minlen=1.5, penwidth=1.5, tailtooltip=&quot;&quot;, headtooltip=&quot;&quot;];
227                 &quot;G&quot; [shape=&quot;Mrecord&quot;, label=&quot;G&amp;nbsp;&amp;#9719;&quot;, tooltip=&quot;G (Gestating):
228         state for gestating animals&quot;, fillcolor=green, style=&quot;filled,rounded&quot;] ;
229         &quot;NG&quot; [shape=&quot;Mrecord&quot;, label=&quot;NG&amp;nbsp;&amp;#9719;&quot;, tooltip=&quot;NG (NonGestating):
230         state for empty animals&quot;, fillcolor=cyan, style=&quot;filled,rounded,bold&quot;] ;
231         &quot;G&quot; -&gt; &quot;NG&quot; [label=&quot;proba: 1&quot;, labeltooltip=&quot;proba: 1&quot;, arrowtail=&quot;none&quot;, arrowhead=&quot;normalnonediamond&quot;, dir=both, tooltip=&quot;&quot;, minlen=3, style=&quot;solid&quot;];
232         &quot;G&quot; -&gt; &quot;NG&quot; [label=&quot;proba: daily_abortion&quot;, labeltooltip=&quot;daily_abortion [parameter]:
233         daily probability that an infected animal aborts during gestation       
234         1 - (1 - global_abortion)**(1/gestation_duration)&quot;, arrowtail=&quot;noneoinv&quot;, arrowhead=&quot;normalnonediamond&quot;, dir=both, tooltip=&quot;ESCAPE: is_I&quot;, minlen=3, style=&quot;solid&quot;];
235         &quot;NG&quot; -&gt; &quot;G&quot; [label=&quot;rate: reproduction&quot;, labeltooltip=&quot;reproduction [parameter]:
236         reproduction rate of the animals                                        
237         0.05&quot;, arrowtail=&quot;nonetee&quot;, arrowhead=&quot;normalnone&quot;, dir=both, tooltip=&quot;COND: is_A&quot;, minlen=3, style=&quot;solid&quot;];
238 }</p></object>
239 </div>
240 <img alt="../_images/Quickstart_GNG.png" class="align-left" src="../_images/Quickstart_GNG.png" />
241 <div align="center" class="align-center"><object data="../_images/graphviz-9af4d6f9e2d32ad0bebf692f5868037972ba622a.svg" type="image/svg+xml">
242             <p class="warning">digraph {
243                 rankdir=LR;
244                 node[fontsize=16, fontname=Arial, shape=box, style=&quot;filled,rounded&quot;];
245                 edge[minlen=1.5, penwidth=1.5, tailtooltip=&quot;&quot;, headtooltip=&quot;&quot;];
247                 &quot;M&quot; [shape=&quot;Mrecord&quot;, label=&quot;M&amp;nbsp;&amp;#9719;&quot;, tooltip=&quot;M (Maternal protection):
248         animal protected by maternal antibodies&quot;, fillcolor=cyan, style=&quot;filled,rounded&quot;] ;
249         &quot;S&quot; [shape=&quot;Mrecord&quot;, label=&quot;S&quot;, tooltip=&quot;S (Susceptible):
250         suceptible of becoming infectious&quot;, fillcolor=wheat, style=&quot;filled,rounded,bold&quot;] ;
251         &quot;E&quot; [shape=&quot;Mrecord&quot;, label=&quot;E&amp;nbsp;&amp;#9719;&quot;, tooltip=&quot;E (Exposed):
252         already infected but not yet able to transmit the disease&quot;, fillcolor=lightcoral, style=&quot;filled,rounded&quot;] ;
253         &quot;I&quot; [shape=&quot;Mrecord&quot;, label=&quot;I&quot;, tooltip=&quot;I (Infectious):
254         sick and able to transmit the disease&quot;, fillcolor=maroon, style=&quot;filled,rounded&quot;] ;
255         &quot;R&quot; [shape=&quot;Mrecord&quot;, label=&quot;R&quot;, tooltip=&quot;R (Resistant):
256         healthy again and resistant to infection&quot;, fillcolor=deepskyblue, style=&quot;filled,rounded&quot;] ;
257         &quot;Q&quot; [shape=&quot;Mrecord&quot;, label=&quot;Q&amp;nbsp;&amp;#9719;&quot;, tooltip=&quot;Q (Quarantine):
258         sick animals that are put aside for a while&quot;, fillcolor=green, style=&quot;filled,rounded&quot;] ;
259         &quot;D&quot; [shape=&quot;Mrecord&quot;, label=&quot;D&quot;, tooltip=&quot;D (Dead):
260         dead animals&quot;, fillcolor=white, style=&quot;filled,rounded,dotted&quot;] ;
261         &quot;E&quot; -&gt; &quot;D&quot; [label=&quot;rate: mortality_sick&quot;, labeltooltip=&quot;mortality_sick [parameter]:
262         mortality rate for sick animals (E / I / Q)
263         0.004&quot;, arrowtail=&quot;noneoinv&quot;, arrowhead=&quot;normalnone&quot;, dir=both, tooltip=&quot;ESCAPE: True&quot;, minlen=3, style=&quot;solid&quot;];
264         &quot;E&quot; -&gt; &quot;I&quot; [label=&quot;rate: α&quot;, labeltooltip=&quot;rate: α&quot;, arrowtail=&quot;none&quot;, arrowhead=&quot;normalnone&quot;, dir=both, tooltip=&quot;&quot;, minlen=3, style=&quot;solid&quot;];
265         &quot;I&quot; -&gt; &quot;D&quot; [label=&quot;rate: mortality_sick&quot;, labeltooltip=&quot;mortality_sick [parameter]:
266         mortality rate for sick animals (E / I / Q)
267         0.004&quot;, arrowtail=&quot;none&quot;, arrowhead=&quot;normalnone&quot;, dir=both, tooltip=&quot;&quot;, minlen=3, style=&quot;solid&quot;];
268         &quot;I&quot; -&gt; &quot;Q&quot; [label=&quot;rate: detection&quot;, labeltooltip=&quot;detection [parameter]:
269         rate at which animals are detected sick (falls to 0 if quarantine zone is full)
270         0.01*room_in_quarantine&quot;, arrowtail=&quot;noneodot&quot;, arrowhead=&quot;normalnone&quot;, dir=both, tooltip=&quot;WHEN: quarantine_period&quot;, minlen=3, style=&quot;solid&quot;];
271         &quot;I&quot; -&gt; &quot;R&quot; [label=&quot;rate: γ&quot;, labeltooltip=&quot;rate: γ&quot;, arrowtail=&quot;none&quot;, arrowhead=&quot;normalnone&quot;, dir=both, tooltip=&quot;&quot;, minlen=3, style=&quot;solid&quot;];
272         &quot;M&quot; -&gt; &quot;D&quot; [label=&quot;rate: mortality_healthy&quot;, labeltooltip=&quot;mortality_healthy [parameter]:
273         mortality rate for healthy animals
274         0.002&quot;, arrowtail=&quot;noneoinv&quot;, arrowhead=&quot;normalnone&quot;, dir=both, tooltip=&quot;ESCAPE: True&quot;, minlen=3, style=&quot;solid&quot;];
275         &quot;M&quot; -&gt; &quot;S&quot; [label=&quot;rate: ε&quot;, labeltooltip=&quot;rate: ε&quot;, arrowtail=&quot;none&quot;, arrowhead=&quot;normalnone&quot;, dir=both, tooltip=&quot;&quot;, minlen=3, style=&quot;solid&quot;];
276         &quot;Q&quot; -&gt; &quot;D&quot; [label=&quot;proba:      -δt⋅mortality_sick
277 1 - ℯ                  &quot;, labeltooltip=&quot;proba:      -δₜ⋅mortality_sick
278 1 - ℯ                  &quot;, arrowtail=&quot;noneoinv&quot;, arrowhead=&quot;normalnone&quot;, dir=both, tooltip=&quot;ESCAPE: True&quot;, minlen=3, style=&quot;solid&quot;];
279         &quot;Q&quot; -&gt; &quot;R&quot; [label=&quot;proba: 1&quot;, labeltooltip=&quot;proba: 1&quot;, arrowtail=&quot;none&quot;, arrowhead=&quot;normalnone&quot;, dir=both, tooltip=&quot;&quot;, minlen=3, style=&quot;solid&quot;];
280         &quot;R&quot; -&gt; &quot;D&quot; [label=&quot;rate: mortality_healthy&quot;, labeltooltip=&quot;mortality_healthy [parameter]:
281         mortality rate for healthy animals
282         0.002&quot;, arrowtail=&quot;none&quot;, arrowhead=&quot;normalnone&quot;, dir=both, tooltip=&quot;&quot;, minlen=3, style=&quot;solid&quot;];
283         &quot;R&quot; -&gt; &quot;S&quot; [label=&quot;rate: δ&quot;, labeltooltip=&quot;rate: δ&quot;, arrowtail=&quot;none&quot;, arrowhead=&quot;normalnone&quot;, dir=both, tooltip=&quot;&quot;, minlen=3, style=&quot;solid&quot;];
284         &quot;S&quot; -&gt; &quot;D&quot; [label=&quot;rate: mortality_healthy&quot;, labeltooltip=&quot;mortality_healthy [parameter]:
285         mortality rate for healthy animals
286         0.002&quot;, arrowtail=&quot;none&quot;, arrowhead=&quot;normalnone&quot;, dir=both, tooltip=&quot;&quot;, minlen=3, style=&quot;solid&quot;];
287         &quot;S&quot; -&gt; &quot;E&quot; [label=&quot;rate: f&quot;, labeltooltip=&quot;f [parameter]:
288         force of infection
289         beta * total_I / total_herd&quot;, arrowtail=&quot;none&quot;, arrowhead=&quot;normalnone&quot;, dir=both, tooltip=&quot;&quot;, minlen=3, style=&quot;solid&quot;];
290 }</p></object>
291 </div>
292 <img alt="../_images/Quickstart_MSEIRQ.png" class="align-left" src="../_images/Quickstart_MSEIRQ.png" />
293 <img alt="../_images/Quickstart_others.png" class="align-left" src="../_images/Quickstart_others.png" />
294 </div>
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