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<p id="t1" class="pln"><span class="n"><a href="#t1">1</a></span><span class="t"><span class="str">"""</span> </span><span class="r"></span></p>
<p id="t2" class="pln"><span class="n"><a href="#t2">2</a></span><span class="t"><span class="str">Generate contacts between people in the population, with many options possible</span> </span><span class="r"></span></p>
<p id="t3" class="pln"><span class="n"><a href="#t3">3</a></span><span class="t"><span class="str">"""</span> </span><span class="r"></span></p>
<p id="t4" class="pln"><span class="n"><a href="#t4">4</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t5" class="run"><span class="n"><a href="#t5">5</a></span><span class="t"><span class="key">import</span> <span class="nam">os</span> </span><span class="r"></span></p>
<p id="t6" class="run"><span class="n"><a href="#t6">6</a></span><span class="t"><span class="key">import</span> <span class="nam">numpy</span> <span class="key">as</span> <span class="nam">np</span> </span><span class="r"></span></p>
<p id="t7" class="run"><span class="n"><a href="#t7">7</a></span><span class="t"><span class="key">import</span> <span class="nam">pandas</span> <span class="key">as</span> <span class="nam">pd</span> </span><span class="r"></span></p>
<p id="t8" class="run"><span class="n"><a href="#t8">8</a></span><span class="t"><span class="key">import</span> <span class="nam">numba</span> <span class="key">as</span> <span class="nam">nb</span> </span><span class="r"></span></p>
<p id="t9" class="run"><span class="n"><a href="#t9">9</a></span><span class="t"><span class="key">import</span> <span class="nam">sciris</span> <span class="key">as</span> <span class="nam">sc</span> </span><span class="r"></span></p>
<p id="t10" class="run"><span class="n"><a href="#t10">10</a></span><span class="t"><span class="key">import</span> <span class="nam">networkx</span> <span class="key">as</span> <span class="nam">nx</span> </span><span class="r"></span></p>
<p id="t11" class="run"><span class="n"><a href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="op">.</span> <span class="key">import</span> <span class="nam">data_distributions</span> <span class="key">as</span> <span class="nam">spdata</span> </span><span class="r"></span></p>
<p id="t12" class="run"><span class="n"><a href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="op">.</span> <span class="key">import</span> <span class="nam">sampling</span> <span class="key">as</span> <span class="nam">spsamp</span> </span><span class="r"></span></p>
<p id="t13" class="run"><span class="n"><a href="#t13">13</a></span><span class="t"><span class="key">from</span> <span class="op">.</span> <span class="key">import</span> <span class="nam">base</span> <span class="key">as</span> <span class="nam">spb</span> </span><span class="r"></span></p>
<p id="t14" class="run"><span class="n"><a href="#t14">14</a></span><span class="t"><span class="key">from</span> <span class="op">.</span> <span class="key">import</span> <span class="nam">contact_networks</span> <span class="key">as</span> <span class="nam">spcnx</span> </span><span class="r"></span></p>
<p id="t15" class="run"><span class="n"><a href="#t15">15</a></span><span class="t"><span class="key">from</span> <span class="op">.</span> <span class="key">import</span> <span class="nam">read_write</span> <span class="key">as</span> <span class="nam">sprw</span> </span><span class="r"></span></p>
<p id="t16" class="run"><span class="n"><a href="#t16">16</a></span><span class="t"><span class="key">from</span> <span class="op">.</span><span class="nam">config</span> <span class="key">import</span> <span class="nam">datadir</span> </span><span class="r"></span></p>
<p id="t17" class="pln"><span class="n"><a href="#t17">17</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t18" class="pln"><span class="n"><a href="#t18">18</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t19" class="run"><span class="n"><a href="#t19">19</a></span><span class="t"><span class="key">def</span> <span class="nam">make_popdict</span><span class="op">(</span><span class="nam">n</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="nam">uids</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="nam">ages</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="nam">sexes</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="nam">location</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="nam">use_demography</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">id_len</span><span class="op">=</span><span class="num">16</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t20" class="pln"><span class="n"><a href="#t20">20</a></span><span class="t"> <span class="str">"""</span> </span><span class="r"></span></p>
<p id="t21" class="pln"><span class="n"><a href="#t21">21</a></span><span class="t"><span class="str"> Create a dictionary of n people with age, sex and loc keys</span> </span><span class="r"></span></p>
<p id="t22" class="pln"><span class="n"><a href="#t22">22</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t23" class="pln"><span class="n"><a href="#t23">23</a></span><span class="t"><span class="str"> Args:</span> </span><span class="r"></span></p>
<p id="t24" class="pln"><span class="n"><a href="#t24">24</a></span><span class="t"><span class="str"> n (int) : number of people</span> </span><span class="r"></span></p>
<p id="t25" class="pln"><span class="n"><a href="#t25">25</a></span><span class="t"><span class="str"> uids (list) : supplied uids of individuals</span> </span><span class="r"></span></p>
<p id="t26" class="pln"><span class="n"><a href="#t26">26</a></span><span class="t"><span class="str"> ages (list) : supplied ages of individuals</span> </span><span class="r"></span></p>
<p id="t27" class="pln"><span class="n"><a href="#t27">27</a></span><span class="t"><span class="str"> sexes (list) : supplied sexes of individuals</span> </span><span class="r"></span></p>
<p id="t28" class="pln"><span class="n"><a href="#t28">28</a></span><span class="t"><span class="str"> location (string) : name of the location</span> </span><span class="r"></span></p>
<p id="t29" class="pln"><span class="n"><a href="#t29">29</a></span><span class="t"><span class="str"> state_location (string) : name of the state the location is in</span> </span><span class="r"></span></p>
<p id="t30" class="pln"><span class="n"><a href="#t30">30</a></span><span class="t"><span class="str"> country_location (string) : name of the country the location is in</span> </span><span class="r"></span></p>
<p id="t31" class="pln"><span class="n"><a href="#t31">31</a></span><span class="t"><span class="str"> use_demography (bool) : If True, use demographic data</span> </span><span class="r"></span></p>
<p id="t32" class="pln"><span class="n"><a href="#t32">32</a></span><span class="t"><span class="str"> id_len (int) : length of the uid</span> </span><span class="r"></span></p>
<p id="t33" class="pln"><span class="n"><a href="#t33">33</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t34" class="pln"><span class="n"><a href="#t34">34</a></span><span class="t"><span class="str"> Returns:</span> </span><span class="r"></span></p>
<p id="t35" class="pln"><span class="n"><a href="#t35">35</a></span><span class="t"><span class="str"> A dictionary where keys are the uid of each person and the values are another dictionary containing values for other attributes of the person</span> </span><span class="r"></span></p>
<p id="t36" class="pln"><span class="n"><a href="#t36">36</a></span><span class="t"><span class="str"> """</span> </span><span class="r"></span></p>
<p id="t37" class="pln"><span class="n"><a href="#t37">37</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t38" class="run"><span class="n"><a href="#t38">38</a></span><span class="t"> <span class="nam">min_people</span> <span class="op">=</span> <span class="num">100</span> </span><span class="r"></span></p>
<p id="t39" class="pln"><span class="n"><a href="#t39">39</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t40" class="run"><span class="n"><a href="#t40">40</a></span><span class="t"> <span class="key">if</span> <span class="nam">location</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span> <span class="nam">location</span> <span class="op">=</span> <span class="str">'seattle_metro'</span> </span><span class="r"></span></p>
<p id="t41" class="run"><span class="n"><a href="#t41">41</a></span><span class="t"> <span class="key">if</span> <span class="nam">state_location</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span> <span class="nam">state_location</span> <span class="op">=</span> <span class="str">'Washington'</span> </span><span class="r"></span></p>
<p id="t42" class="pln"><span class="n"><a href="#t42">42</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t43" class="pln"><span class="n"><a href="#t43">43</a></span><span class="t"> <span class="com"># A list of UIDs was supplied as the first argument</span> </span><span class="r"></span></p>
<p id="t44" class="run"><span class="n"><a href="#t44">44</a></span><span class="t"> <span class="key">if</span> <span class="nam">uids</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span> <span class="com"># UIDs were supplied, use them</span> </span><span class="r"></span></p>
<p id="t45" class="run"><span class="n"><a href="#t45">45</a></span><span class="t"> <span class="nam">n</span> <span class="op">=</span> <span class="nam">len</span><span class="op">(</span><span class="nam">uids</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t46" class="pln"><span class="n"><a href="#t46">46</a></span><span class="t"> <span class="com"># uid_mapping = {uids[i]: i for i in range(len(uids))}</span> </span><span class="r"></span></p>
<p id="t47" class="run"><span class="n"><a href="#t47">47</a></span><span class="t"> <span class="key">try</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t48" class="run"><span class="n"><a href="#t48">48</a></span><span class="t"> <span class="nam">uid_mapping</span> <span class="op">=</span> <span class="op">{</span><span class="nam">uid</span><span class="op">:</span> <span class="nam">int</span><span class="op">(</span><span class="nam">uid</span><span class="op">)</span> <span class="key">for</span> <span class="nam">u</span><span class="op">,</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">enumerate</span><span class="op">(</span><span class="nam">uids</span><span class="op">)</span><span class="op">}</span> </span><span class="r"></span></p>
<p id="t49" class="mis show_mis"><span class="n"><a href="#t49">49</a></span><span class="t"> <span class="key">except</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t50" class="mis show_mis"><span class="n"><a href="#t50">50</a></span><span class="t"> <span class="nam">uid_mapping</span> <span class="op">=</span> <span class="op">{</span><span class="nam">uid</span><span class="op">:</span> <span class="nam">u</span> <span class="key">for</span> <span class="nam">u</span><span class="op">,</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">enumerate</span><span class="op">(</span><span class="nam">uids</span><span class="op">)</span><span class="op">}</span> <span class="com"># replacing uids for uid_mapping since uids might be strings</span> </span><span class="r"></span></p>
<p id="t51" class="pln"><span class="n"><a href="#t51">51</a></span><span class="t"> <span class="key">else</span><span class="op">:</span> <span class="com"># Not supplied, generate</span> </span><span class="r"></span></p>
<p id="t52" class="run"><span class="n"><a href="#t52">52</a></span><span class="t"> <span class="nam">n</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">n</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t53" class="pln"><span class="n"><a href="#t53">53</a></span><span class="t"> <span class="com"># default to using ints for ids from now on</span> </span><span class="r"></span></p>
<p id="t54" class="run"><span class="n"><a href="#t54">54</a></span><span class="t"> <span class="nam">uids</span> <span class="op">=</span> <span class="op">[</span><span class="nam">i</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">n</span><span class="op">)</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t55" class="run"><span class="n"><a href="#t55">55</a></span><span class="t"> <span class="nam">uid_mapping</span> <span class="op">=</span> <span class="op">{</span><span class="nam">i</span><span class="op">:</span> <span class="nam">i</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">n</span><span class="op">)</span><span class="op">}</span> </span><span class="r"></span></p>
<p id="t56" class="pln"><span class="n"><a href="#t56">56</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t57" class="pln"><span class="n"><a href="#t57">57</a></span><span class="t"> <span class="com"># using strings for uids</span> </span><span class="r"></span></p>
<p id="t58" class="pln"><span class="n"><a href="#t58">58</a></span><span class="t"> <span class="com"># uids = []</span> </span><span class="r"></span></p>
<p id="t59" class="pln"><span class="n"><a href="#t59">59</a></span><span class="t"> <span class="com"># for i in range(n):</span> </span><span class="r"></span></p>
<p id="t60" class="pln"><span class="n"><a href="#t60">60</a></span><span class="t"> <span class="com"># uids.append(sc.uuid(length=id_len))</span> </span><span class="r"></span></p>
<p id="t61" class="pln"><span class="n"><a href="#t61">61</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t62" class="pln"><span class="n"><a href="#t62">62</a></span><span class="t"> <span class="com"># Check that there are enough people</span> </span><span class="r"></span></p>
<p id="t63" class="run"><span class="n"><a href="#t63">63</a></span><span class="t"> <span class="key">if</span> <span class="nam">n</span> <span class="op"><</span> <span class="nam">min_people</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t64" class="mis show_mis"><span class="n"><a href="#t64">64</a></span><span class="t"> <span class="nam">print</span><span class="op">(</span><span class="str">f'Warning: with {n}<{min_people} people, contact matrices will be approximate'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t65" class="pln"><span class="n"><a href="#t65">65</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t66" class="pln"><span class="n"><a href="#t66">66</a></span><span class="t"> <span class="com"># Optionally take in either ages or sexes, too</span> </span><span class="r"></span></p>
<p id="t67" class="run"><span class="n"><a href="#t67">67</a></span><span class="t"> <span class="key">if</span> <span class="nam">ages</span> <span class="key">is</span> <span class="key">None</span> <span class="key">and</span> <span class="nam">sexes</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t68" class="run"><span class="n"><a href="#t68">68</a></span><span class="t"> <span class="key">if</span> <span class="nam">use_demography</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t69" class="mis show_mis"><span class="n"><a href="#t69">69</a></span><span class="t"> <span class="key">if</span> <span class="nam">country_location</span> <span class="op">!=</span> <span class="str">'usa'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t70" class="mis show_mis"><span class="n"><a href="#t70">70</a></span><span class="t"> <span class="nam">gen_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_age_n</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">n</span><span class="op">=</span><span class="nam">n</span><span class="op">,</span> <span class="nam">location</span><span class="op">=</span><span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">=</span><span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">=</span><span class="nam">country_location</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t71" class="mis show_mis"><span class="n"><a href="#t71">71</a></span><span class="t"> <span class="nam">gen_sexes</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">np</span><span class="op">.</span><span class="nam">random</span><span class="op">.</span><span class="nam">binomial</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">p</span><span class="op">=</span><span class="num">0.5</span><span class="op">,</span> <span class="nam">size</span><span class="op">=</span><span class="nam">n</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t72" class="pln"><span class="n"><a href="#t72">72</a></span><span class="t"> <span class="key">else</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t73" class="mis show_mis"><span class="n"><a href="#t73">73</a></span><span class="t"> <span class="key">if</span> <span class="nam">location</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span> <span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span> <span class="op">=</span> <span class="str">'seattle_metro'</span><span class="op">,</span> <span class="str">'Washington'</span> </span><span class="r"></span></p>
<p id="t74" class="mis show_mis"><span class="n"><a href="#t74">74</a></span><span class="t"> <span class="nam">gen_ages</span><span class="op">,</span> <span class="nam">gen_sexes</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_usa_age_sex_n</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">location</span><span class="op">=</span><span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">=</span><span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">=</span><span class="nam">country_location</span><span class="op">,</span> <span class="nam">n_people</span><span class="op">=</span><span class="nam">n</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t75" class="pln"><span class="n"><a href="#t75">75</a></span><span class="t"> <span class="key">else</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t76" class="pln"><span class="n"><a href="#t76">76</a></span><span class="t"> <span class="com"># if location is None:</span> </span><span class="r"></span></p>
<p id="t77" class="run"><span class="n"><a href="#t77">77</a></span><span class="t"> <span class="nam">gen_ages</span><span class="op">,</span> <span class="nam">gen_sexes</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_age_sex_n</span><span class="op">(</span><span class="key">None</span><span class="op">,</span> <span class="key">None</span><span class="op">,</span> <span class="key">None</span><span class="op">,</span> <span class="nam">n_people</span><span class="op">=</span><span class="nam">n</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t78" class="pln"><span class="n"><a href="#t78">78</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t79" class="pln"><span class="n"><a href="#t79">79</a></span><span class="t"> <span class="com"># you only have ages...</span> </span><span class="r"></span></p>
<p id="t80" class="run"><span class="n"><a href="#t80">80</a></span><span class="t"> <span class="key">elif</span> <span class="nam">ages</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span> <span class="key">and</span> <span class="nam">sexes</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t81" class="run"><span class="n"><a href="#t81">81</a></span><span class="t"> <span class="key">if</span> <span class="nam">country_location</span> <span class="op">==</span> <span class="str">'usa'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t82" class="mis show_mis"><span class="n"><a href="#t82">82</a></span><span class="t"> <span class="key">if</span> <span class="nam">location</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span> <span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span> <span class="op">=</span> <span class="str">'seattle_metro'</span><span class="op">,</span> <span class="str">'Washington'</span> </span><span class="r"></span></p>
<p id="t83" class="mis show_mis"><span class="n"><a href="#t83">83</a></span><span class="t"> <span class="nam">gen_ages</span><span class="op">,</span> <span class="nam">gen_sexes</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_usa_sex_n</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">ages</span><span class="op">,</span> <span class="nam">location</span><span class="op">=</span><span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">=</span><span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">=</span><span class="nam">country_location</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t84" class="pln"><span class="n"><a href="#t84">84</a></span><span class="t"> <span class="key">else</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t85" class="run"><span class="n"><a href="#t85">85</a></span><span class="t"> <span class="nam">gen_ages</span> <span class="op">=</span> <span class="nam">ages</span> </span><span class="r"></span></p>
<p id="t86" class="run"><span class="n"><a href="#t86">86</a></span><span class="t"> <span class="nam">gen_sexes</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">np</span><span class="op">.</span><span class="nam">random</span><span class="op">.</span><span class="nam">binomial</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">p</span><span class="op">=</span><span class="num">0.5</span><span class="op">,</span> <span class="nam">size</span><span class="op">=</span><span class="nam">n</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t87" class="pln"><span class="n"><a href="#t87">87</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t88" class="pln"><span class="n"><a href="#t88">88</a></span><span class="t"> <span class="com"># you only have sexes...</span> </span><span class="r"></span></p>
<p id="t89" class="run"><span class="n"><a href="#t89">89</a></span><span class="t"> <span class="key">elif</span> <span class="nam">ages</span> <span class="key">is</span> <span class="key">None</span> <span class="key">and</span> <span class="nam">sexes</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t90" class="mis show_mis"><span class="n"><a href="#t90">90</a></span><span class="t"> <span class="key">if</span> <span class="nam">country_location</span> <span class="op">==</span> <span class="str">'usa'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t91" class="mis show_mis"><span class="n"><a href="#t91">91</a></span><span class="t"> <span class="key">if</span> <span class="nam">location</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span> <span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span> <span class="op">=</span> <span class="str">'seattle_metro'</span><span class="op">,</span> <span class="str">'Washington'</span> </span><span class="r"></span></p>
<p id="t92" class="mis show_mis"><span class="n"><a href="#t92">92</a></span><span class="t"> <span class="nam">gen_ages</span><span class="op">,</span> <span class="nam">gen_sexes</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_usa_age_n</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">sexes</span><span class="op">,</span> <span class="nam">location</span><span class="op">=</span><span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">=</span><span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">=</span><span class="nam">country_location</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t93" class="pln"><span class="n"><a href="#t93">93</a></span><span class="t"> <span class="key">else</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t94" class="pln"><span class="n"><a href="#t94">94</a></span><span class="t"> <span class="com"># gen_sexes = sexes</span> </span><span class="r"></span></p>
<p id="t95" class="pln"><span class="n"><a href="#t95">95</a></span><span class="t"> <span class="com"># gen_ages = sp.get_age_n(datadir,n=n,location=location,state_location=state_location,country_location=country_location)</span> </span><span class="r"></span></p>
<p id="t96" class="mis show_mis"><span class="n"><a href="#t96">96</a></span><span class="t"> <span class="key">raise</span> <span class="nam">NotImplementedError</span><span class="op">(</span><span class="str">'Currently, only locations in the US are supported'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t97" class="pln"><span class="n"><a href="#t97">97</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t98" class="pln"><span class="n"><a href="#t98">98</a></span><span class="t"> <span class="com"># randomize your generated ages and sexes</span> </span><span class="r"></span></p>
<p id="t99" class="run"><span class="n"><a href="#t99">99</a></span><span class="t"> <span class="key">if</span> <span class="nam">ages</span> <span class="key">is</span> <span class="key">None</span> <span class="key">or</span> <span class="nam">sexes</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t100" class="run"><span class="n"><a href="#t100">100</a></span><span class="t"> <span class="nam">random_inds</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">random</span><span class="op">.</span><span class="nam">permutation</span><span class="op">(</span><span class="nam">n</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t101" class="run"><span class="n"><a href="#t101">101</a></span><span class="t"> <span class="nam">ages</span> <span class="op">=</span> <span class="op">[</span><span class="nam">gen_ages</span><span class="op">[</span><span class="nam">r</span><span class="op">]</span> <span class="key">for</span> <span class="nam">r</span> <span class="key">in</span> <span class="nam">random_inds</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t102" class="run"><span class="n"><a href="#t102">102</a></span><span class="t"> <span class="nam">sexes</span> <span class="op">=</span> <span class="op">[</span><span class="nam">gen_sexes</span><span class="op">[</span><span class="nam">r</span><span class="op">]</span> <span class="key">for</span> <span class="nam">r</span> <span class="key">in</span> <span class="nam">random_inds</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t103" class="pln"><span class="n"><a href="#t103">103</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t104" class="pln"><span class="n"><a href="#t104">104</a></span><span class="t"> <span class="com"># you have both ages and sexes so we'll just populate that for you...</span> </span><span class="r"></span></p>
<p id="t105" class="run"><span class="n"><a href="#t105">105</a></span><span class="t"> <span class="nam">popdict</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span> </span><span class="r"></span></p>
<p id="t106" class="run"><span class="n"><a href="#t106">106</a></span><span class="t"> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">enumerate</span><span class="op">(</span><span class="nam">uids</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t107" class="run"><span class="n"><a href="#t107">107</a></span><span class="t"> <span class="nam">u</span> <span class="op">=</span> <span class="nam">uid_mapping</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t108" class="run"><span class="n"><a href="#t108">108</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span> </span><span class="r"></span></p>
<p id="t109" class="run"><span class="n"><a href="#t109">109</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'age'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">ages</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t110" class="run"><span class="n"><a href="#t110">110</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'sex'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">sexes</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t111" class="run"><span class="n"><a href="#t111">111</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'loc'</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span> </span><span class="r"></span></p>
<p id="t112" class="run"><span class="n"><a href="#t112">112</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span> <span class="op">=</span> <span class="op">{</span><span class="str">'M'</span><span class="op">:</span> <span class="nam">set</span><span class="op">(</span><span class="op">)</span><span class="op">}</span> </span><span class="r"></span></p>
<p id="t113" class="pln"><span class="n"><a href="#t113">113</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t114" class="run"><span class="n"><a href="#t114">114</a></span><span class="t"> <span class="key">return</span> <span class="nam">popdict</span> </span><span class="r"></span></p>
<p id="t115" class="pln"><span class="n"><a href="#t115">115</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t116" class="pln"><span class="n"><a href="#t116">116</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t117" class="run"><span class="n"><a href="#t117">117</a></span><span class="t"><span class="key">def</span> <span class="nam">make_contacts_generic</span><span class="op">(</span><span class="nam">popdict</span><span class="op">,</span> <span class="nam">network_distr_args</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t118" class="pln"><span class="n"><a href="#t118">118</a></span><span class="t"> <span class="str">"""</span> </span><span class="r"></span></p>
<p id="t119" class="pln"><span class="n"><a href="#t119">119</a></span><span class="t"><span class="str"> Create contact network regardless of age, according to network distribution properties. Can be used by webapp.</span> </span><span class="r"></span></p>
<p id="t120" class="pln"><span class="n"><a href="#t120">120</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t121" class="pln"><span class="n"><a href="#t121">121</a></span><span class="t"><span class="str"> Args:</span> </span><span class="r"></span></p>
<p id="t122" class="pln"><span class="n"><a href="#t122">122</a></span><span class="t"><span class="str"> popdict (dict) : dictionary of all individuals</span> </span><span class="r"></span></p>
<p id="t123" class="pln"><span class="n"><a href="#t123">123</a></span><span class="t"><span class="str"> network_distr_args (dict): network distribution parameters dictionary for average_degree, network_type, and directionality</span> </span><span class="r"></span></p>
<p id="t124" class="pln"><span class="n"><a href="#t124">124</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t125" class="pln"><span class="n"><a href="#t125">125</a></span><span class="t"><span class="str"> Returns:</span> </span><span class="r"></span></p>
<p id="t126" class="pln"><span class="n"><a href="#t126">126</a></span><span class="t"><span class="str"> A dictionary of individuals with contacts drawn from given network distribution parameters.</span> </span><span class="r"></span></p>
<p id="t127" class="pln"><span class="n"><a href="#t127">127</a></span><span class="t"><span class="str"> """</span> </span><span class="r"></span></p>
<p id="t128" class="pln"><span class="n"><a href="#t128">128</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t129" class="run"><span class="n"><a href="#t129">129</a></span><span class="t"> <span class="nam">n_contacts</span> <span class="op">=</span> <span class="nam">network_distr_args</span><span class="op">[</span><span class="str">'average_degree'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t130" class="run"><span class="n"><a href="#t130">130</a></span><span class="t"> <span class="nam">network_type</span> <span class="op">=</span> <span class="nam">network_distr_args</span><span class="op">[</span><span class="str">'network_type'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t131" class="run"><span class="n"><a href="#t131">131</a></span><span class="t"> <span class="nam">directed</span> <span class="op">=</span> <span class="nam">network_distr_args</span><span class="op">[</span><span class="str">'directed'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t132" class="pln"><span class="n"><a href="#t132">132</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t133" class="run"><span class="n"><a href="#t133">133</a></span><span class="t"> <span class="nam">uids</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">.</span><span class="nam">keys</span><span class="op">(</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t134" class="run"><span class="n"><a href="#t134">134</a></span><span class="t"> <span class="nam">uids</span> <span class="op">=</span> <span class="op">[</span><span class="nam">uid</span> <span class="key">for</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">uids</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t135" class="pln"><span class="n"><a href="#t135">135</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t136" class="pln"><span class="n"><a href="#t136">136</a></span><span class="t"> <span class="com"># if isinstance(uids[0], str):</span> </span><span class="r"></span></p>
<p id="t137" class="pln"><span class="n"><a href="#t137">137</a></span><span class="t"> <span class="com"># uid_mapping = {uid: u for u, uid in enumerate(uids)}</span> </span><span class="r"></span></p>
<p id="t138" class="pln"><span class="n"><a href="#t138">138</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t139" class="pln"><span class="n"><a href="#t139">139</a></span><span class="t"> <span class="com"># elif isinstance(uids[0], int):</span> </span><span class="r"></span></p>
<p id="t140" class="pln"><span class="n"><a href="#t140">140</a></span><span class="t"> <span class="com"># uid_mapping = {i: i for i in range(len(uids))}</span> </span><span class="r"></span></p>
<p id="t141" class="pln"><span class="n"><a href="#t141">141</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t142" class="run"><span class="n"><a href="#t142">142</a></span><span class="t"> <span class="nam">N</span> <span class="op">=</span> <span class="nam">len</span><span class="op">(</span><span class="nam">popdict</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t143" class="pln"><span class="n"><a href="#t143">143</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t144" class="run"><span class="n"><a href="#t144">144</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t145" class="run"><span class="n"><a href="#t145">145</a></span><span class="t"> <span class="nam">p</span> <span class="op">=</span> <span class="nam">float</span><span class="op">(</span><span class="nam">n_contacts</span><span class="op">)</span><span class="op">/</span><span class="nam">N</span> </span><span class="r"></span></p>
<p id="t146" class="pln"><span class="n"><a href="#t146">146</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t147" class="run"><span class="n"><a href="#t147">147</a></span><span class="t"> <span class="nam">G</span> <span class="op">=</span> <span class="nam">nx</span><span class="op">.</span><span class="nam">erdos_renyi_graph</span><span class="op">(</span><span class="nam">N</span><span class="op">,</span> <span class="nam">p</span><span class="op">,</span> <span class="nam">directed</span><span class="op">=</span><span class="nam">directed</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t148" class="pln"><span class="n"><a href="#t148">148</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t149" class="run"><span class="n"><a href="#t149">149</a></span><span class="t"> <span class="nam">A</span> <span class="op">=</span> <span class="op">[</span><span class="nam">a</span> <span class="key">for</span> <span class="nam">a</span> <span class="key">in</span> <span class="nam">G</span><span class="op">.</span><span class="nam">adjacency</span><span class="op">(</span><span class="op">)</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t150" class="pln"><span class="n"><a href="#t150">150</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t151" class="run"><span class="n"><a href="#t151">151</a></span><span class="t"> <span class="key">for</span> <span class="nam">n</span><span class="op">,</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">enumerate</span><span class="op">(</span><span class="nam">uids</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t152" class="run"><span class="n"><a href="#t152">152</a></span><span class="t"> <span class="nam">targets</span> <span class="op">=</span> <span class="op">[</span><span class="nam">t</span> <span class="key">for</span> <span class="nam">t</span> <span class="key">in</span> <span class="nam">A</span><span class="op">[</span><span class="nam">n</span><span class="op">]</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">.</span><span class="nam">keys</span><span class="op">(</span><span class="op">)</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t153" class="run"><span class="n"><a href="#t153">153</a></span><span class="t"> <span class="nam">target_uids</span> <span class="op">=</span> <span class="op">[</span><span class="nam">uids</span><span class="op">[</span><span class="nam">target</span><span class="op">]</span> <span class="key">for</span> <span class="nam">target</span> <span class="key">in</span> <span class="nam">targets</span><span class="op">]</span> <span class="com"># if using uids which may be strings or ints</span> </span><span class="r"></span></p>
<p id="t154" class="run"><span class="n"><a href="#t154">154</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'M'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">set</span><span class="op">(</span><span class="nam">target_uids</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t155" class="pln"><span class="n"><a href="#t155">155</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t156" class="run"><span class="n"><a href="#t156">156</a></span><span class="t"> <span class="key">return</span> <span class="nam">popdict</span> </span><span class="r"></span></p>
<p id="t157" class="pln"><span class="n"><a href="#t157">157</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t158" class="pln"><span class="n"><a href="#t158">158</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t159" class="run"><span class="n"><a href="#t159">159</a></span><span class="t"><span class="key">def</span> <span class="nam">make_contacts_without_social_layers_152</span><span class="op">(</span><span class="nam">popdict</span><span class="op">,</span> <span class="nam">n_contacts_dic</span><span class="op">,</span> <span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">,</span> <span class="nam">sheet_name</span><span class="op">,</span> <span class="nam">network_distr_args</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t160" class="pln"><span class="n"><a href="#t160">160</a></span><span class="t"> <span class="str">"""</span> </span><span class="r"></span></p>
<p id="t161" class="pln"><span class="n"><a href="#t161">161</a></span><span class="t"><span class="str"> Create contact network according to overall age-mixing contact matrices. Does not capture clustering or microstructure,</span> </span><span class="r"></span></p>
<p id="t162" class="pln"><span class="n"><a href="#t162">162</a></span><span class="t"><span class="str"> therefore exact households, schools, or workplaces are not created. However, this does separate agents according to their</span> </span><span class="r"></span></p>
<p id="t163" class="pln"><span class="n"><a href="#t163">163</a></span><span class="t"><span class="str"> age and gives them contacts likely for their age. For all ages, the average number of contacts is constant with this</span> </span><span class="r"></span></p>
<p id="t164" class="pln"><span class="n"><a href="#t164">164</a></span><span class="t"><span class="str"> method, although location specific data may prove this to not be true.</span> </span><span class="r"></span></p>
<p id="t165" class="pln"><span class="n"><a href="#t165">165</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t166" class="pln"><span class="n"><a href="#t166">166</a></span><span class="t"><span class="str"> Args:</span> </span><span class="r"></span></p>
<p id="t167" class="pln"><span class="n"><a href="#t167">167</a></span><span class="t"><span class="str"> popdict (dict) : dictionary of all individuals</span> </span><span class="r"></span></p>
<p id="t168" class="pln"><span class="n"><a href="#t168">168</a></span><span class="t"><span class="str"> n_contacts_dic (dict) : number of contacts to draw on average by setting</span> </span><span class="r"></span></p>
<p id="t169" class="pln"><span class="n"><a href="#t169">169</a></span><span class="t"><span class="str"> location (string) : name of the location</span> </span><span class="r"></span></p>
<p id="t170" class="pln"><span class="n"><a href="#t170">170</a></span><span class="t"><span class="str"> state_location (string) : name of the state the location is in</span> </span><span class="r"></span></p>
<p id="t171" class="pln"><span class="n"><a href="#t171">171</a></span><span class="t"><span class="str"> country_location (string) : name of the country the location is in</span> </span><span class="r"></span></p>
<p id="t172" class="pln"><span class="n"><a href="#t172">172</a></span><span class="t"><span class="str"> sheet_name (string) : name of the sheet in the excel file with contact patterns</span> </span><span class="r"></span></p>
<p id="t173" class="pln"><span class="n"><a href="#t173">173</a></span><span class="t"><span class="str"> network_distr_args (dict) : network distribution parameters dictionary for average_degree, network_type, and directionality, can also include powerlaw exponents,</span> </span><span class="r"></span></p>
<p id="t174" class="pln"><span class="n"><a href="#t174">174</a></span><span class="t"><span class="str"> block sizes (re: SBMs), clustering distribution, or other properties needed to generate network structures. Checkout</span> </span><span class="r"></span></p>
<p id="t175" class="pln"><span class="n"><a href="#t175">175</a></span><span class="t"><span class="str"> https://networkx.github.io/documentation/stable/reference/generators.html#module-networkx.generators for what's possible</span> </span><span class="r"></span></p>
<p id="t176" class="pln"><span class="n"><a href="#t176">176</a></span><span class="t"><span class="str"> Default 'network_type' is 'poisson_degree' for Erdos-Renyi random graphs in large n limit.</span> </span><span class="r"></span></p>
<p id="t177" class="pln"><span class="n"><a href="#t177">177</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t178" class="pln"><span class="n"><a href="#t178">178</a></span><span class="t"><span class="str"> Returns:</span> </span><span class="r"></span></p>
<p id="t179" class="pln"><span class="n"><a href="#t179">179</a></span><span class="t"><span class="str"> A dictionary of individuals with attributes, including their age and the ids of their contacts drawn from given network distribution parameters and the ages of contacts drawn according to overall age mixing data.</span> </span><span class="r"></span></p>
<p id="t180" class="pln"><span class="n"><a href="#t180">180</a></span><span class="t"><span class="str"> A single social setting or layer of contacts.</span> </span><span class="r"></span></p>
<p id="t181" class="pln"><span class="n"><a href="#t181">181</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t182" class="pln"><span class="n"><a href="#t182">182</a></span><span class="t"><span class="str"> """</span> </span><span class="r"></span></p>
<p id="t183" class="pln"><span class="n"><a href="#t183">183</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t184" class="run"><span class="n"><a href="#t184">184</a></span><span class="t"> <span class="nam">uids_by_age_dic</span> <span class="op">=</span> <span class="nam">spb</span><span class="op">.</span><span class="nam">get_uids_by_age_dic</span><span class="op">(</span><span class="nam">popdict</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t185" class="run"><span class="n"><a href="#t185">185</a></span><span class="t"> <span class="nam">age_brackets</span> <span class="op">=</span> <span class="nam">spdata</span><span class="op">.</span><span class="nam">get_census_age_brackets</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">=</span><span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">=</span><span class="nam">country_location</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t186" class="run"><span class="n"><a href="#t186">186</a></span><span class="t"> <span class="nam">num_agebrackets</span> <span class="op">=</span> <span class="nam">len</span><span class="op">(</span><span class="nam">age_brackets</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t187" class="run"><span class="n"><a href="#t187">187</a></span><span class="t"> <span class="nam">age_by_brackets_dic</span> <span class="op">=</span> <span class="nam">spb</span><span class="op">.</span><span class="nam">get_age_by_brackets_dic</span><span class="op">(</span><span class="nam">age_brackets</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t188" class="pln"><span class="n"><a href="#t188">188</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t189" class="run"><span class="n"><a href="#t189">189</a></span><span class="t"> <span class="nam">age_mixing_matrix_dic</span> <span class="op">=</span> <span class="nam">spdata</span><span class="op">.</span><span class="nam">get_contact_matrix_dic</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">sheet_name</span><span class="op">=</span><span class="nam">sheet_name</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t190" class="run"><span class="n"><a href="#t190">190</a></span><span class="t"> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="str">'M'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">spb</span><span class="op">.</span><span class="nam">combine_matrices</span><span class="op">(</span><span class="nam">age_mixing_matrix_dic</span><span class="op">,</span> <span class="nam">n_contacts_dic</span><span class="op">,</span> <span class="nam">num_agebrackets</span><span class="op">)</span> <span class="com"># may need to normalize matrices before applying this method to K. Prem et al matrices because of the difference in what the raw matrices represent</span> </span><span class="r"></span></p>
<p id="t191" class="pln"><span class="n"><a href="#t191">191</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t192" class="run"><span class="n"><a href="#t192">192</a></span><span class="t"> <span class="nam">n_contacts</span> <span class="op">=</span> <span class="nam">network_distr_args</span><span class="op">[</span><span class="str">'average_degree'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t193" class="run"><span class="n"><a href="#t193">193</a></span><span class="t"> <span class="nam">directed</span> <span class="op">=</span> <span class="nam">network_distr_args</span><span class="op">[</span><span class="str">'directed'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t194" class="run"><span class="n"><a href="#t194">194</a></span><span class="t"> <span class="nam">network_type</span> <span class="op">=</span> <span class="nam">network_distr_args</span><span class="op">[</span><span class="str">'network_type'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t195" class="pln"><span class="n"><a href="#t195">195</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t196" class="run"><span class="n"><a href="#t196">196</a></span><span class="t"> <span class="nam">k</span> <span class="op">=</span> <span class="str">'M'</span> </span><span class="r"></span></p>
<p id="t197" class="run"><span class="n"><a href="#t197">197</a></span><span class="t"> <span class="key">if</span> <span class="nam">directed</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t198" class="mis show_mis"><span class="n"><a href="#t198">198</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t199" class="mis show_mis"><span class="n"><a href="#t199">199</a></span><span class="t"> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t200" class="mis show_mis"><span class="n"><a href="#t200">200</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t201" class="mis show_mis"><span class="n"><a href="#t201">201</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">[</span><span class="str">'age'</span><span class="op">]</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t202" class="mis show_mis"><span class="n"><a href="#t202">202</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t203" class="pln"><span class="n"><a href="#t203">203</a></span><span class="t"> <span class="key">else</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t204" class="run"><span class="n"><a href="#t204">204</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t205" class="run"><span class="n"><a href="#t205">205</a></span><span class="t"> <span class="nam">n_contacts</span> <span class="op">=</span> <span class="nam">n_contacts</span><span class="op">/</span><span class="num">2</span> </span><span class="r"></span></p>
<p id="t206" class="run"><span class="n"><a href="#t206">206</a></span><span class="t"> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t207" class="run"><span class="n"><a href="#t207">207</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t208" class="run"><span class="n"><a href="#t208">208</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">[</span><span class="str">'age'</span><span class="op">]</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t209" class="run"><span class="n"><a href="#t209">209</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t210" class="run"><span class="n"><a href="#t210">210</a></span><span class="t"> <span class="key">for</span> <span class="nam">c</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t211" class="run"><span class="n"><a href="#t211">211</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">c</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">add</span><span class="op">(</span><span class="nam">i</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t212" class="pln"><span class="n"><a href="#t212">212</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t213" class="run"><span class="n"><a href="#t213">213</a></span><span class="t"> <span class="key">return</span> <span class="nam">popdict</span> </span><span class="r"></span></p>
<p id="t214" class="pln"><span class="n"><a href="#t214">214</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t215" class="pln"><span class="n"><a href="#t215">215</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t216" class="run"><span class="n"><a href="#t216">216</a></span><span class="t"><span class="key">def</span> <span class="nam">make_contacts_with_social_layers_152</span><span class="op">(</span><span class="nam">popdict</span><span class="op">,</span> <span class="nam">n_contacts_dic</span><span class="op">,</span> <span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">,</span> <span class="nam">sheet_name</span><span class="op">,</span> <span class="nam">activity_args</span><span class="op">,</span> <span class="nam">network_distr_args</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t217" class="pln"><span class="n"><a href="#t217">217</a></span><span class="t"> <span class="str">"""</span> </span><span class="r"></span></p>
<p id="t218" class="pln"><span class="n"><a href="#t218">218</a></span><span class="t"><span class="str"> Create contact network according to overall age-mixing contact matrices. Does not capture clustering or microstructure,</span> </span><span class="r"></span></p>
<p id="t219" class="pln"><span class="n"><a href="#t219">219</a></span><span class="t"><span class="str"> therefore exact households, schools, or workplaces are not created. However, this does separate agents according to their</span> </span><span class="r"></span></p>
<p id="t220" class="pln"><span class="n"><a href="#t220">220</a></span><span class="t"><span class="str"> age and gives them contacts likely for their age specified by the social settings they are likely to participate in.</span> </span><span class="r"></span></p>
<p id="t221" class="pln"><span class="n"><a href="#t221">221</a></span><span class="t"><span class="str"> For all ages, the average number of contacts is constant with this method, although location specific data very wel may</span> </span><span class="r"></span></p>
<p id="t222" class="pln"><span class="n"><a href="#t222">222</a></span><span class="t"><span class="str"> prove this to not be true. In general, college students may also be workers, however here they are only students and we</span> </span><span class="r"></span></p>
<p id="t223" class="pln"><span class="n"><a href="#t223">223</a></span><span class="t"><span class="str"> assume that any of their contacts in the work environment are likely to look like their contacts at school.</span> </span><span class="r"></span></p>
<p id="t224" class="pln"><span class="n"><a href="#t224">224</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t225" class="pln"><span class="n"><a href="#t225">225</a></span><span class="t"><span class="str"> Essentially recreates an age-specific compartmental model's concept of contacts but for an agent based modeling framework.</span> </span><span class="r"></span></p>
<p id="t226" class="pln"><span class="n"><a href="#t226">226</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t227" class="pln"><span class="n"><a href="#t227">227</a></span><span class="t"><span class="str"> Args:</span> </span><span class="r"></span></p>
<p id="t228" class="pln"><span class="n"><a href="#t228">228</a></span><span class="t"><span class="str"> popdict (dict) : dictionary of all individuals</span> </span><span class="r"></span></p>
<p id="t229" class="pln"><span class="n"><a href="#t229">229</a></span><span class="t"><span class="str"> n_contacts_dic (dict) : number of contacts to draw on average by setting</span> </span><span class="r"></span></p>
<p id="t230" class="pln"><span class="n"><a href="#t230">230</a></span><span class="t"><span class="str"> location (string) : name of the location</span> </span><span class="r"></span></p>
<p id="t231" class="pln"><span class="n"><a href="#t231">231</a></span><span class="t"><span class="str"> state_location (string) : name of the state the location is in</span> </span><span class="r"></span></p>
<p id="t232" class="pln"><span class="n"><a href="#t232">232</a></span><span class="t"><span class="str"> country_location (string) : name of the country the location is in</span> </span><span class="r"></span></p>
<p id="t233" class="pln"><span class="n"><a href="#t233">233</a></span><span class="t"><span class="str"> sheet_name (string) : name of the sheet in the excel file with contact patterns</span> </span><span class="r"></span></p>
<p id="t234" class="pln"><span class="n"><a href="#t234">234</a></span><span class="t"><span class="str"> activity_args (dict) : dictionary of age bounds for participating in different activities like going to school or working, also student-teacher ratio</span> </span><span class="r"></span></p>
<p id="t235" class="pln"><span class="n"><a href="#t235">235</a></span><span class="t"><span class="str"> network_distr_args (dict) : network distribution parameters dictionary for average_degree, network_type, and directionality, can also include powerlaw exponents,</span> </span><span class="r"></span></p>
<p id="t236" class="pln"><span class="n"><a href="#t236">236</a></span><span class="t"><span class="str"> block sizes (re: SBMs), clustering distribution, or other properties needed to generate network structures. Checkout</span> </span><span class="r"></span></p>
<p id="t237" class="pln"><span class="n"><a href="#t237">237</a></span><span class="t"><span class="str"> https://networkx.github.io/documentation/stable/reference/generators.html#module-networkx.generators for what's possible</span> </span><span class="r"></span></p>
<p id="t238" class="pln"><span class="n"><a href="#t238">238</a></span><span class="t"><span class="str"> Default 'network_type' is 'poisson_degree' for Erdos-Renyi random graphs in large n limit.</span> </span><span class="r"></span></p>
<p id="t239" class="pln"><span class="n"><a href="#t239">239</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t240" class="pln"><span class="n"><a href="#t240">240</a></span><span class="t"><span class="str"> Returns:</span> </span><span class="r"></span></p>
<p id="t241" class="pln"><span class="n"><a href="#t241">241</a></span><span class="t"><span class="str"> A dictionary of individuals with contacts with attributes, including their age and the ids of their contacts drawn from given network distribution parameters and the ages of contacts drawn according to age mixing data.</span> </span><span class="r"></span></p>
<p id="t242" class="pln"><span class="n"><a href="#t242">242</a></span><span class="t"><span class="str"> Multiple social settings or layers so contacts are listed for different layers.</span> </span><span class="r"></span></p>
<p id="t243" class="pln"><span class="n"><a href="#t243">243</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t244" class="pln"><span class="n"><a href="#t244">244</a></span><span class="t"><span class="str"> """</span> </span><span class="r"></span></p>
<p id="t245" class="pln"><span class="n"><a href="#t245">245</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t246" class="run"><span class="n"><a href="#t246">246</a></span><span class="t"> <span class="nam">uids_by_age_dic</span> <span class="op">=</span> <span class="nam">spb</span><span class="op">.</span><span class="nam">get_uids_by_age_dic</span><span class="op">(</span><span class="nam">popdict</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t247" class="run"><span class="n"><a href="#t247">247</a></span><span class="t"> <span class="nam">age_brackets</span> <span class="op">=</span> <span class="nam">spdata</span><span class="op">.</span><span class="nam">get_census_age_brackets</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">=</span><span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">=</span><span class="nam">country_location</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t248" class="run"><span class="n"><a href="#t248">248</a></span><span class="t"> <span class="nam">num_agebrackets</span> <span class="op">=</span> <span class="nam">len</span><span class="op">(</span><span class="nam">age_brackets</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t249" class="run"><span class="n"><a href="#t249">249</a></span><span class="t"> <span class="nam">age_by_brackets_dic</span> <span class="op">=</span> <span class="nam">spb</span><span class="op">.</span><span class="nam">get_age_by_brackets_dic</span><span class="op">(</span><span class="nam">age_brackets</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t250" class="pln"><span class="n"><a href="#t250">250</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t251" class="run"><span class="n"><a href="#t251">251</a></span><span class="t"> <span class="nam">age_mixing_matrix_dic</span> <span class="op">=</span> <span class="nam">spdata</span><span class="op">.</span><span class="nam">get_contact_matrix_dic</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">sheet_name</span><span class="op">=</span><span class="nam">sheet_name</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t252" class="run"><span class="n"><a href="#t252">252</a></span><span class="t"> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="str">'M'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">spb</span><span class="op">.</span><span class="nam">combine_matrices</span><span class="op">(</span><span class="nam">age_mixing_matrix_dic</span><span class="op">,</span> <span class="nam">n_contacts_dic</span><span class="op">,</span> <span class="nam">num_agebrackets</span><span class="op">)</span> <span class="com"># may need to normalize matrices before applying this method to K. Prem et al matrices because of the difference in what the raw matrices represent</span> </span><span class="r"></span></p>
<p id="t253" class="pln"><span class="n"><a href="#t253">253</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t254" class="run"><span class="n"><a href="#t254">254</a></span><span class="t"> <span class="nam">directed</span> <span class="op">=</span> <span class="nam">network_distr_args</span><span class="op">[</span><span class="str">'directed'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t255" class="run"><span class="n"><a href="#t255">255</a></span><span class="t"> <span class="nam">network_type</span> <span class="op">=</span> <span class="nam">network_distr_args</span><span class="op">[</span><span class="str">'network_type'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t256" class="pln"><span class="n"><a href="#t256">256</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t257" class="pln"><span class="n"><a href="#t257">257</a></span><span class="t"> <span class="com"># currently not set to capture school enrollment rates or work enrollment rates</span> </span><span class="r"></span></p>
<p id="t258" class="run"><span class="n"><a href="#t258">258</a></span><span class="t"> <span class="nam">student_n_dic</span> <span class="op">=</span> <span class="nam">sc</span><span class="op">.</span><span class="nam">dcp</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t259" class="run"><span class="n"><a href="#t259">259</a></span><span class="t"> <span class="nam">non_student_n_dic</span> <span class="op">=</span> <span class="nam">sc</span><span class="op">.</span><span class="nam">dcp</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t260" class="pln"><span class="n"><a href="#t260">260</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t261" class="pln"><span class="n"><a href="#t261">261</a></span><span class="t"> <span class="com"># this might not be needed because students will choose their teachers, but if directed then this makes teachers point to students as well</span> </span><span class="r"></span></p>
<p id="t262" class="run"><span class="n"><a href="#t262">262</a></span><span class="t"> <span class="nam">n_students</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">[</span><span class="nam">len</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">[</span><span class="nam">a</span><span class="op">]</span><span class="op">)</span> <span class="key">for</span> <span class="nam">a</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_age_min'</span><span class="op">]</span><span class="op">,</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_age_max'</span><span class="op">]</span><span class="op">+</span><span class="num">1</span><span class="op">)</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t263" class="run"><span class="n"><a href="#t263">263</a></span><span class="t"> <span class="nam">n_workers</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">[</span><span class="nam">len</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">[</span><span class="nam">a</span><span class="op">]</span><span class="op">)</span> <span class="key">for</span> <span class="nam">a</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">activity_args</span><span class="op">[</span><span class="str">'worker_age_min'</span><span class="op">]</span><span class="op">,</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'worker_age_max'</span><span class="op">]</span><span class="op">+</span><span class="num">1</span><span class="op">)</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t264" class="run"><span class="n"><a href="#t264">264</a></span><span class="t"> <span class="nam">n_teachers</span> <span class="op">=</span> <span class="nam">n_students</span><span class="op">/</span><span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_teacher_ratio'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t265" class="run"><span class="n"><a href="#t265">265</a></span><span class="t"> <span class="nam">teachers_school_weight</span> <span class="op">=</span> <span class="nam">n_teachers</span><span class="op">/</span><span class="nam">n_workers</span> </span><span class="r"></span></p>
<p id="t266" class="pln"><span class="n"><a href="#t266">266</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t267" class="run"><span class="n"><a href="#t267">267</a></span><span class="t"> <span class="nam">student_n_dic</span><span class="op">[</span><span class="str">'W'</span><span class="op">]</span> <span class="op">=</span> <span class="num">0</span> </span><span class="r"></span></p>
<p id="t268" class="run"><span class="n"><a href="#t268">268</a></span><span class="t"> <span class="nam">non_student_n_dic</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">teachers_school_weight</span> <span class="com"># make some teachers</span> </span><span class="r"></span></p>
<p id="t269" class="pln"><span class="n"><a href="#t269">269</a></span><span class="t"> <span class="com"># 5 categories as defined by activity_args:</span> </span><span class="r"></span></p>
<p id="t270" class="pln"><span class="n"><a href="#t270">270</a></span><span class="t"> <span class="com"># infants & toddlers : H, C</span> </span><span class="r"></span></p>
<p id="t271" class="pln"><span class="n"><a href="#t271">271</a></span><span class="t"> <span class="com"># school-aged students : H, S, C</span> </span><span class="r"></span></p>
<p id="t272" class="pln"><span class="n"><a href="#t272">272</a></span><span class="t"> <span class="com"># college-aged students / workers : H, S, W, C</span> </span><span class="r"></span></p>
<p id="t273" class="pln"><span class="n"><a href="#t273">273</a></span><span class="t"> <span class="com"># non-student workers : H, W, C</span> </span><span class="r"></span></p>
<p id="t274" class="pln"><span class="n"><a href="#t274">274</a></span><span class="t"> <span class="com"># retired elderly : H, C - some may be workers too but it's low. directed means they won't have contacts in the workplace, but undirected means they will at least a little.</span> </span><span class="r"></span></p>
<p id="t275" class="pln"><span class="n"><a href="#t275">275</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t276" class="pln"><span class="n"><a href="#t276">276</a></span><span class="t"> <span class="com"># will follow degree distribution well</span> </span><span class="r"></span></p>
<p id="t277" class="run"><span class="n"><a href="#t277">277</a></span><span class="t"> <span class="key">for</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t278" class="run"><span class="n"><a href="#t278">278</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="nam">n_contacts_dic</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t279" class="run"><span class="n"><a href="#t279">279</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">set</span><span class="op">(</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t280" class="pln"><span class="n"><a href="#t280">280</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t281" class="run"><span class="n"><a href="#t281">281</a></span><span class="t"> <span class="key">if</span> <span class="nam">directed</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t282" class="pln"><span class="n"><a href="#t282">282</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t283" class="mis show_mis"><span class="n"><a href="#t283">283</a></span><span class="t"> <span class="key">for</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t284" class="mis show_mis"><span class="n"><a href="#t284">284</a></span><span class="t"> <span class="nam">age</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'age'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t285" class="mis show_mis"><span class="n"><a href="#t285">285</a></span><span class="t"> <span class="key">if</span> <span class="nam">age</span> <span class="op"><</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_age_min'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t286" class="mis show_mis"><span class="n"><a href="#t286">286</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t287" class="mis show_mis"><span class="n"><a href="#t287">287</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t288" class="mis show_mis"><span class="n"><a href="#t288">288</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t289" class="mis show_mis"><span class="n"><a href="#t289">289</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t290" class="mis show_mis"><span class="n"><a href="#t290">290</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t291" class="pln"><span class="n"><a href="#t291">291</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t292" class="mis show_mis"><span class="n"><a href="#t292">292</a></span><span class="t"> <span class="key">elif</span> <span class="nam">age</span> <span class="op">>=</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_age_min'</span><span class="op">]</span> <span class="key">and</span> <span class="nam">age</span> <span class="op"><</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_age_max'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t293" class="mis show_mis"><span class="n"><a href="#t293">293</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'S'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t294" class="mis show_mis"><span class="n"><a href="#t294">294</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t295" class="mis show_mis"><span class="n"><a href="#t295">295</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t296" class="mis show_mis"><span class="n"><a href="#t296">296</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t297" class="mis show_mis"><span class="n"><a href="#t297">297</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t298" class="pln"><span class="n"><a href="#t298">298</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t299" class="mis show_mis"><span class="n"><a href="#t299">299</a></span><span class="t"> <span class="key">elif</span> <span class="nam">age</span> <span class="op">>=</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'college_age_min'</span><span class="op">]</span> <span class="key">and</span> <span class="nam">age</span> <span class="op"><</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'college_age_max'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t300" class="mis show_mis"><span class="n"><a href="#t300">300</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'S'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t301" class="mis show_mis"><span class="n"><a href="#t301">301</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t302" class="mis show_mis"><span class="n"><a href="#t302">302</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t303" class="mis show_mis"><span class="n"><a href="#t303">303</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t304" class="mis show_mis"><span class="n"><a href="#t304">304</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t305" class="pln"><span class="n"><a href="#t305">305</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t306" class="mis show_mis"><span class="n"><a href="#t306">306</a></span><span class="t"> <span class="key">elif</span> <span class="nam">age</span> <span class="op">>=</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'worker_age_min'</span><span class="op">]</span> <span class="key">and</span> <span class="nam">age</span> <span class="op"><</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'worker_age_max'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t307" class="mis show_mis"><span class="n"><a href="#t307">307</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'S'</span><span class="op">,</span> <span class="str">'W'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t308" class="mis show_mis"><span class="n"><a href="#t308">308</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t309" class="mis show_mis"><span class="n"><a href="#t309">309</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">non_student_n_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t310" class="mis show_mis"><span class="n"><a href="#t310">310</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t311" class="mis show_mis"><span class="n"><a href="#t311">311</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t312" class="pln"><span class="n"><a href="#t312">312</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t313" class="mis show_mis"><span class="n"><a href="#t313">313</a></span><span class="t"> <span class="key">elif</span> <span class="nam">age</span> <span class="op">>=</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'worker_age_max'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t314" class="mis show_mis"><span class="n"><a href="#t314">314</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t315" class="mis show_mis"><span class="n"><a href="#t315">315</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t316" class="mis show_mis"><span class="n"><a href="#t316">316</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t317" class="mis show_mis"><span class="n"><a href="#t317">317</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t318" class="mis show_mis"><span class="n"><a href="#t318">318</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t319" class="pln"><span class="n"><a href="#t319">319</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t320" class="pln"><span class="n"><a href="#t320">320</a></span><span class="t"> <span class="key">else</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t321" class="run"><span class="n"><a href="#t321">321</a></span><span class="t"> <span class="key">for</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t322" class="run"><span class="n"><a href="#t322">322</a></span><span class="t"> <span class="nam">age</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'age'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t323" class="run"><span class="n"><a href="#t323">323</a></span><span class="t"> <span class="key">if</span> <span class="nam">age</span> <span class="op"><</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_age_min'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t324" class="run"><span class="n"><a href="#t324">324</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t325" class="run"><span class="n"><a href="#t325">325</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t326" class="run"><span class="n"><a href="#t326">326</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">/</span><span class="num">2</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t327" class="run"><span class="n"><a href="#t327">327</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t328" class="run"><span class="n"><a href="#t328">328</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t329" class="run"><span class="n"><a href="#t329">329</a></span><span class="t"> <span class="key">for</span> <span class="nam">c</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t330" class="run"><span class="n"><a href="#t330">330</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">c</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">add</span><span class="op">(</span><span class="nam">uid</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t331" class="pln"><span class="n"><a href="#t331">331</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t332" class="run"><span class="n"><a href="#t332">332</a></span><span class="t"> <span class="key">elif</span> <span class="nam">age</span> <span class="op">>=</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_age_min'</span><span class="op">]</span> <span class="key">and</span> <span class="nam">age</span> <span class="op"><</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_age_max'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t333" class="run"><span class="n"><a href="#t333">333</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'S'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t334" class="run"><span class="n"><a href="#t334">334</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t335" class="run"><span class="n"><a href="#t335">335</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">/</span><span class="num">2</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t336" class="run"><span class="n"><a href="#t336">336</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t337" class="run"><span class="n"><a href="#t337">337</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t338" class="run"><span class="n"><a href="#t338">338</a></span><span class="t"> <span class="key">for</span> <span class="nam">c</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t339" class="run"><span class="n"><a href="#t339">339</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">c</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">add</span><span class="op">(</span><span class="nam">uid</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t340" class="pln"><span class="n"><a href="#t340">340</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t341" class="run"><span class="n"><a href="#t341">341</a></span><span class="t"> <span class="key">elif</span> <span class="nam">age</span> <span class="op">>=</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'college_age_min'</span><span class="op">]</span> <span class="key">and</span> <span class="nam">age</span> <span class="op"><</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'college_age_max'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t342" class="run"><span class="n"><a href="#t342">342</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'S'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t343" class="run"><span class="n"><a href="#t343">343</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t344" class="run"><span class="n"><a href="#t344">344</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">/</span><span class="num">2</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t345" class="run"><span class="n"><a href="#t345">345</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t346" class="run"><span class="n"><a href="#t346">346</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t347" class="run"><span class="n"><a href="#t347">347</a></span><span class="t"> <span class="key">for</span> <span class="nam">c</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t348" class="run"><span class="n"><a href="#t348">348</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">c</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">add</span><span class="op">(</span><span class="nam">uid</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t349" class="pln"><span class="n"><a href="#t349">349</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t350" class="run"><span class="n"><a href="#t350">350</a></span><span class="t"> <span class="key">elif</span> <span class="nam">age</span> <span class="op">>=</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'worker_age_min'</span><span class="op">]</span> <span class="key">and</span> <span class="nam">age</span> <span class="op"><</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'worker_age_max'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t351" class="run"><span class="n"><a href="#t351">351</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'W'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t352" class="run"><span class="n"><a href="#t352">352</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t353" class="run"><span class="n"><a href="#t353">353</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">non_student_n_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">/</span><span class="num">2</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t354" class="run"><span class="n"><a href="#t354">354</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t355" class="run"><span class="n"><a href="#t355">355</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t356" class="run"><span class="n"><a href="#t356">356</a></span><span class="t"> <span class="key">for</span> <span class="nam">c</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t357" class="run"><span class="n"><a href="#t357">357</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">c</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">add</span><span class="op">(</span><span class="nam">uid</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t358" class="pln"><span class="n"><a href="#t358">358</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t359" class="run"><span class="n"><a href="#t359">359</a></span><span class="t"> <span class="key">elif</span> <span class="nam">age</span> <span class="op">>=</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'worker_age_max'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t360" class="run"><span class="n"><a href="#t360">360</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t361" class="run"><span class="n"><a href="#t361">361</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t362" class="run"><span class="n"><a href="#t362">362</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">/</span><span class="num">2</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t363" class="run"><span class="n"><a href="#t363">363</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t364" class="run"><span class="n"><a href="#t364">364</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t365" class="run"><span class="n"><a href="#t365">365</a></span><span class="t"> <span class="key">for</span> <span class="nam">c</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t366" class="run"><span class="n"><a href="#t366">366</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">c</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">add</span><span class="op">(</span><span class="nam">uid</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t367" class="pln"><span class="n"><a href="#t367">367</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t368" class="run"><span class="n"><a href="#t368">368</a></span><span class="t"> <span class="key">return</span> <span class="nam">popdict</span> </span><span class="r"></span></p>
<p id="t369" class="pln"><span class="n"><a href="#t369">369</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t370" class="pln"><span class="n"><a href="#t370">370</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t371" class="run"><span class="n"><a href="#t371">371</a></span><span class="t"><span class="key">def</span> <span class="nam">make_contacts_without_social_layers_and_sex</span><span class="op">(</span><span class="nam">popdict</span><span class="op">,</span> <span class="nam">n_contacts_dic</span><span class="op">,</span> <span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">,</span> <span class="nam">sheet_name</span><span class="op">,</span> <span class="nam">network_distr_args</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t372" class="pln"><span class="n"><a href="#t372">372</a></span><span class="t"> <span class="str">"""</span> </span><span class="r"></span></p>
<p id="t373" class="pln"><span class="n"><a href="#t373">373</a></span><span class="t"><span class="str"> Create contact network according to overall age-mixing contact matrices for the US. Does not capture clustering or microstructure, therefore</span> </span><span class="r"></span></p>
<p id="t374" class="pln"><span class="n"><a href="#t374">374</a></span><span class="t"><span class="str"> exact households, schools, or workplaces are not created. However, this does separate agents according to their age and gives them contacts</span> </span><span class="r"></span></p>
<p id="t375" class="pln"><span class="n"><a href="#t375">375</a></span><span class="t"><span class="str"> likely for their age. For all ages, the average number of contacts is constant, although location specific data may prove this to not be true.</span> </span><span class="r"></span></p>
<p id="t376" class="pln"><span class="n"><a href="#t376">376</a></span><span class="t"><span class="str"> Individuals also have a sex, though this in general does not have an impact on their contact patterns.</span> </span><span class="r"></span></p>
<p id="t377" class="pln"><span class="n"><a href="#t377">377</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t378" class="pln"><span class="n"><a href="#t378">378</a></span><span class="t"><span class="str"> Args:</span> </span><span class="r"></span></p>
<p id="t379" class="pln"><span class="n"><a href="#t379">379</a></span><span class="t"><span class="str"> popdict (dict) : dictionary of all individuals</span> </span><span class="r"></span></p>
<p id="t380" class="pln"><span class="n"><a href="#t380">380</a></span><span class="t"><span class="str"> n_contacts_dic (dict) : number of contacts to draw on average by setting</span> </span><span class="r"></span></p>
<p id="t381" class="pln"><span class="n"><a href="#t381">381</a></span><span class="t"><span class="str"> location (string) : name of the location</span> </span><span class="r"></span></p>
<p id="t382" class="pln"><span class="n"><a href="#t382">382</a></span><span class="t"><span class="str"> state_location (string) : name of the state the location is in</span> </span><span class="r"></span></p>
<p id="t383" class="pln"><span class="n"><a href="#t383">383</a></span><span class="t"><span class="str"> country_location (string) : name of the country the location is in</span> </span><span class="r"></span></p>
<p id="t384" class="pln"><span class="n"><a href="#t384">384</a></span><span class="t"><span class="str"> sheet_name (string) : name of the sheet in the excel file with contact patterns</span> </span><span class="r"></span></p>
<p id="t385" class="pln"><span class="n"><a href="#t385">385</a></span><span class="t"><span class="str"> network_distr_args (dict) : network distribution parameters dictionary for average_degree, network_type, and directionality, can also include powerlaw exponents,</span> </span><span class="r"></span></p>
<p id="t386" class="pln"><span class="n"><a href="#t386">386</a></span><span class="t"><span class="str"> block sizes (re: SBMs), clustering distribution, or other properties needed to generate network structures. Checkout</span> </span><span class="r"></span></p>
<p id="t387" class="pln"><span class="n"><a href="#t387">387</a></span><span class="t"><span class="str"> https://networkx.github.io/documentation/stable/reference/generators.html#module-networkx.generators for what's possible</span> </span><span class="r"></span></p>
<p id="t388" class="pln"><span class="n"><a href="#t388">388</a></span><span class="t"><span class="str"> Default 'network_type' is 'poisson_degree' for Erdos-Renyi random graphs in large n limit.</span> </span><span class="r"></span></p>
<p id="t389" class="pln"><span class="n"><a href="#t389">389</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t390" class="pln"><span class="n"><a href="#t390">390</a></span><span class="t"><span class="str"> Returns:</span> </span><span class="r"></span></p>
<p id="t391" class="pln"><span class="n"><a href="#t391">391</a></span><span class="t"><span class="str"> A dictionary of individuals with attributes, including their age and the ids of their contacts drawn from given network distribution parameters and the ages of contacts drawn according to overall age mixing data.</span> </span><span class="r"></span></p>
<p id="t392" class="pln"><span class="n"><a href="#t392">392</a></span><span class="t"><span class="str"> A single social setting or layer of contacts.</span> </span><span class="r"></span></p>
<p id="t393" class="pln"><span class="n"><a href="#t393">393</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t394" class="pln"><span class="n"><a href="#t394">394</a></span><span class="t"><span class="str"> """</span> </span><span class="r"></span></p>
<p id="t395" class="pln"><span class="n"><a href="#t395">395</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t396" class="pln"><span class="n"><a href="#t396">396</a></span><span class="t"> <span class="com"># using a single contact matrix combined from the other settings available</span> </span><span class="r"></span></p>
<p id="t397" class="mis show_mis"><span class="n"><a href="#t397">397</a></span><span class="t"> <span class="nam">uids_by_age_dic</span> <span class="op">=</span> <span class="nam">spb</span><span class="op">.</span><span class="nam">get_uids_by_age_dic</span><span class="op">(</span><span class="nam">popdict</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t398" class="mis show_mis"><span class="n"><a href="#t398">398</a></span><span class="t"> <span class="nam">age_brackets</span> <span class="op">=</span> <span class="nam">spdata</span><span class="op">.</span><span class="nam">get_census_age_brackets</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">=</span><span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">=</span><span class="nam">country_location</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t399" class="mis show_mis"><span class="n"><a href="#t399">399</a></span><span class="t"> <span class="nam">age_by_brackets_dic</span> <span class="op">=</span> <span class="nam">spb</span><span class="op">.</span><span class="nam">get_age_by_brackets_dic</span><span class="op">(</span><span class="nam">age_brackets</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t400" class="mis show_mis"><span class="n"><a href="#t400">400</a></span><span class="t"> <span class="nam">num_agebrackets</span> <span class="op">=</span> <span class="nam">len</span><span class="op">(</span><span class="nam">age_brackets</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t401" class="pln"><span class="n"><a href="#t401">401</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t402" class="mis show_mis"><span class="n"><a href="#t402">402</a></span><span class="t"> <span class="nam">age_mixing_matrix_dic</span> <span class="op">=</span> <span class="nam">spdata</span><span class="op">.</span><span class="nam">get_contact_matrix_dic</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">sheet_name</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t403" class="mis show_mis"><span class="n"><a href="#t403">403</a></span><span class="t"> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="str">'M'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">spb</span><span class="op">.</span><span class="nam">combine_matrices</span><span class="op">(</span><span class="nam">age_mixing_matrix_dic</span><span class="op">,</span> <span class="nam">n_contacts_dic</span><span class="op">,</span> <span class="nam">num_agebrackets</span><span class="op">)</span> <span class="com"># may need to normalize matrices before applying this method to K. Prem et al matrices because of the difference in what the raw matrices represent</span> </span><span class="r"></span></p>
<p id="t404" class="pln"><span class="n"><a href="#t404">404</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t405" class="mis show_mis"><span class="n"><a href="#t405">405</a></span><span class="t"> <span class="nam">n_contacts</span> <span class="op">=</span> <span class="nam">network_distr_args</span><span class="op">[</span><span class="str">'average_degree'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t406" class="mis show_mis"><span class="n"><a href="#t406">406</a></span><span class="t"> <span class="nam">directed</span> <span class="op">=</span> <span class="nam">network_distr_args</span><span class="op">[</span><span class="str">'directed'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t407" class="mis show_mis"><span class="n"><a href="#t407">407</a></span><span class="t"> <span class="nam">network_type</span> <span class="op">=</span> <span class="nam">network_distr_args</span><span class="op">[</span><span class="str">'network_type'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t408" class="pln"><span class="n"><a href="#t408">408</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t409" class="mis show_mis"><span class="n"><a href="#t409">409</a></span><span class="t"> <span class="nam">k</span> <span class="op">=</span> <span class="str">'M'</span> </span><span class="r"></span></p>
<p id="t410" class="pln"><span class="n"><a href="#t410">410</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t411" class="mis show_mis"><span class="n"><a href="#t411">411</a></span><span class="t"> <span class="key">if</span> <span class="nam">directed</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t412" class="mis show_mis"><span class="n"><a href="#t412">412</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t413" class="mis show_mis"><span class="n"><a href="#t413">413</a></span><span class="t"> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t414" class="mis show_mis"><span class="n"><a href="#t414">414</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t415" class="mis show_mis"><span class="n"><a href="#t415">415</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">[</span><span class="str">'age'</span><span class="op">]</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t416" class="mis show_mis"><span class="n"><a href="#t416">416</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t417" class="pln"><span class="n"><a href="#t417">417</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t418" class="pln"><span class="n"><a href="#t418">418</a></span><span class="t"> <span class="key">else</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t419" class="mis show_mis"><span class="n"><a href="#t419">419</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t420" class="mis show_mis"><span class="n"><a href="#t420">420</a></span><span class="t"> <span class="nam">n_contacts</span> <span class="op">=</span> <span class="nam">n_contacts</span><span class="op">/</span><span class="num">2</span> </span><span class="r"></span></p>
<p id="t421" class="mis show_mis"><span class="n"><a href="#t421">421</a></span><span class="t"> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t422" class="mis show_mis"><span class="n"><a href="#t422">422</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t423" class="mis show_mis"><span class="n"><a href="#t423">423</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">[</span><span class="str">'age'</span><span class="op">]</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t424" class="mis show_mis"><span class="n"><a href="#t424">424</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t425" class="mis show_mis"><span class="n"><a href="#t425">425</a></span><span class="t"> <span class="key">for</span> <span class="nam">c</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t426" class="mis show_mis"><span class="n"><a href="#t426">426</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">c</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">add</span><span class="op">(</span><span class="nam">i</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t427" class="pln"><span class="n"><a href="#t427">427</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t428" class="mis show_mis"><span class="n"><a href="#t428">428</a></span><span class="t"> <span class="key">return</span> <span class="nam">popdict</span> </span><span class="r"></span></p>
<p id="t429" class="pln"><span class="n"><a href="#t429">429</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t430" class="pln"><span class="n"><a href="#t430">430</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t431" class="run"><span class="n"><a href="#t431">431</a></span><span class="t"><span class="key">def</span> <span class="nam">make_contacts_with_social_layers_and_sex</span><span class="op">(</span><span class="nam">popdict</span><span class="op">,</span> <span class="nam">n_contacts_dic</span><span class="op">,</span> <span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">,</span> <span class="nam">sheet_name</span><span class="op">,</span> <span class="nam">activity_args</span><span class="op">,</span> <span class="nam">network_distr_args</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t432" class="pln"><span class="n"><a href="#t432">432</a></span><span class="t"> <span class="str">"""</span> </span><span class="r"></span></p>
<p id="t433" class="pln"><span class="n"><a href="#t433">433</a></span><span class="t"><span class="str"> Create contact network according to overall age-mixing contact matrices for the US.</span> </span><span class="r"></span></p>
<p id="t434" class="pln"><span class="n"><a href="#t434">434</a></span><span class="t"><span class="str"> Does not capture clustering or microstructure, therefore exact households, schools, or workplaces are not created.</span> </span><span class="r"></span></p>
<p id="t435" class="pln"><span class="n"><a href="#t435">435</a></span><span class="t"><span class="str"> However, this does separate agents according to their age and gives them contacts likely for their age specified by</span> </span><span class="r"></span></p>
<p id="t436" class="pln"><span class="n"><a href="#t436">436</a></span><span class="t"><span class="str"> the social settings they are likely to participate in. College students may also be workers, however here they are</span> </span><span class="r"></span></p>
<p id="t437" class="pln"><span class="n"><a href="#t437">437</a></span><span class="t"><span class="str"> only students and we assume that any of their contacts in the work environment are likely to look like their contacts at school.</span> </span><span class="r"></span></p>
<p id="t438" class="pln"><span class="n"><a href="#t438">438</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t439" class="pln"><span class="n"><a href="#t439">439</a></span><span class="t"><span class="str"> Args:</span> </span><span class="r"></span></p>
<p id="t440" class="pln"><span class="n"><a href="#t440">440</a></span><span class="t"><span class="str"> popdict (dict) : dictionary of all individuals</span> </span><span class="r"></span></p>
<p id="t441" class="pln"><span class="n"><a href="#t441">441</a></span><span class="t"><span class="str"> n_contacts_dic (dict) : number of contacts to draw on average by setting</span> </span><span class="r"></span></p>
<p id="t442" class="pln"><span class="n"><a href="#t442">442</a></span><span class="t"><span class="str"> location (string) : name of the location</span> </span><span class="r"></span></p>
<p id="t443" class="pln"><span class="n"><a href="#t443">443</a></span><span class="t"><span class="str"> state_location (string) : name of the state the location is in</span> </span><span class="r"></span></p>
<p id="t444" class="pln"><span class="n"><a href="#t444">444</a></span><span class="t"><span class="str"> country_location (string) : name of the country the location is in</span> </span><span class="r"></span></p>
<p id="t445" class="pln"><span class="n"><a href="#t445">445</a></span><span class="t"><span class="str"> sheet_name (string) : name of the sheet in the excel file with contact patterns</span> </span><span class="r"></span></p>
<p id="t446" class="pln"><span class="n"><a href="#t446">446</a></span><span class="t"><span class="str"> activity_args (dict) : dictionary of age bounds for participating in different activities like going to school or working, also student-teacher ratio</span> </span><span class="r"></span></p>
<p id="t447" class="pln"><span class="n"><a href="#t447">447</a></span><span class="t"><span class="str"> network_distr_args (dict) : network distribution parameters dictionary for average_degree, network_type, and directionality, can also include powerlaw exponents,</span> </span><span class="r"></span></p>
<p id="t448" class="pln"><span class="n"><a href="#t448">448</a></span><span class="t"><span class="str"> block sizes (re: SBMs), clustering distribution, or other properties needed to generate network structures. Checkout</span> </span><span class="r"></span></p>
<p id="t449" class="pln"><span class="n"><a href="#t449">449</a></span><span class="t"><span class="str"> https://networkx.github.io/documentation/stable/reference/generators.html#module-networkx.generators for what's possible</span> </span><span class="r"></span></p>
<p id="t450" class="pln"><span class="n"><a href="#t450">450</a></span><span class="t"><span class="str"> Default 'network_type' is 'poisson_degree' for Erdos-Renyi random graphs in large n limit.</span> </span><span class="r"></span></p>
<p id="t451" class="pln"><span class="n"><a href="#t451">451</a></span><span class="t"><span class="str"> Returns:</span> </span><span class="r"></span></p>
<p id="t452" class="pln"><span class="n"><a href="#t452">452</a></span><span class="t"><span class="str"> A dictionary of individuals with attributes, including their age and the ids of their contacts drawn from given network distribution parameters and the ages of contacts drawn according to age mixing data.</span> </span><span class="r"></span></p>
<p id="t453" class="pln"><span class="n"><a href="#t453">453</a></span><span class="t"><span class="str"> Multiple social settings or layers so contacts are listed for different layers.</span> </span><span class="r"></span></p>
<p id="t454" class="pln"><span class="n"><a href="#t454">454</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t455" class="pln"><span class="n"><a href="#t455">455</a></span><span class="t"><span class="str"> """</span> </span><span class="r"></span></p>
<p id="t456" class="pln"><span class="n"><a href="#t456">456</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t457" class="pln"><span class="n"><a href="#t457">457</a></span><span class="t"> <span class="com"># use a contact matrix dictionary and n_contacts_dic for the average number of contacts in each layer</span> </span><span class="r"></span></p>
<p id="t458" class="run"><span class="n"><a href="#t458">458</a></span><span class="t"> <span class="nam">uids_by_age_dic</span> <span class="op">=</span> <span class="nam">spb</span><span class="op">.</span><span class="nam">get_uids_by_age_dic</span><span class="op">(</span><span class="nam">popdict</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t459" class="pln"><span class="n"><a href="#t459">459</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t460" class="run"><span class="n"><a href="#t460">460</a></span><span class="t"> <span class="nam">age_brackets</span> <span class="op">=</span> <span class="nam">spdata</span><span class="op">.</span><span class="nam">get_census_age_brackets</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">=</span><span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">=</span><span class="nam">country_location</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t461" class="run"><span class="n"><a href="#t461">461</a></span><span class="t"> <span class="nam">age_by_brackets_dic</span> <span class="op">=</span> <span class="nam">spb</span><span class="op">.</span><span class="nam">get_age_by_brackets_dic</span><span class="op">(</span><span class="nam">age_brackets</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t462" class="pln"><span class="n"><a href="#t462">462</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t463" class="run"><span class="n"><a href="#t463">463</a></span><span class="t"> <span class="nam">age_mixing_matrix_dic</span> <span class="op">=</span> <span class="nam">spdata</span><span class="op">.</span><span class="nam">get_contact_matrix_dic</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">sheet_name</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t464" class="pln"><span class="n"><a href="#t464">464</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t465" class="run"><span class="n"><a href="#t465">465</a></span><span class="t"> <span class="nam">directed</span> <span class="op">=</span> <span class="nam">network_distr_args</span><span class="op">[</span><span class="str">'directed'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t466" class="run"><span class="n"><a href="#t466">466</a></span><span class="t"> <span class="nam">network_type</span> <span class="op">=</span> <span class="nam">network_distr_args</span><span class="op">[</span><span class="str">'network_type'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t467" class="pln"><span class="n"><a href="#t467">467</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t468" class="run"><span class="n"><a href="#t468">468</a></span><span class="t"> <span class="nam">student_n_dic</span> <span class="op">=</span> <span class="nam">sc</span><span class="op">.</span><span class="nam">dcp</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t469" class="run"><span class="n"><a href="#t469">469</a></span><span class="t"> <span class="nam">non_student_n_dic</span> <span class="op">=</span> <span class="nam">sc</span><span class="op">.</span><span class="nam">dcp</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t470" class="pln"><span class="n"><a href="#t470">470</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t471" class="pln"><span class="n"><a href="#t471">471</a></span><span class="t"> <span class="com"># this might not be needed because students will choose their teachers, but if directed then this makes teachers point to students as well</span> </span><span class="r"></span></p>
<p id="t472" class="run"><span class="n"><a href="#t472">472</a></span><span class="t"> <span class="nam">n_students</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">[</span><span class="nam">len</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">[</span><span class="nam">a</span><span class="op">]</span><span class="op">)</span> <span class="key">for</span> <span class="nam">a</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_age_min'</span><span class="op">]</span><span class="op">,</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_age_max'</span><span class="op">]</span><span class="op">+</span><span class="num">1</span><span class="op">)</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t473" class="run"><span class="n"><a href="#t473">473</a></span><span class="t"> <span class="nam">n_workers</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="op">[</span><span class="nam">len</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">[</span><span class="nam">a</span><span class="op">]</span><span class="op">)</span> <span class="key">for</span> <span class="nam">a</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">activity_args</span><span class="op">[</span><span class="str">'worker_age_min'</span><span class="op">]</span><span class="op">,</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'worker_age_max'</span><span class="op">]</span><span class="op">+</span><span class="num">1</span><span class="op">)</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t474" class="run"><span class="n"><a href="#t474">474</a></span><span class="t"> <span class="nam">n_teachers</span> <span class="op">=</span> <span class="nam">n_students</span><span class="op">/</span><span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_teacher_ratio'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t475" class="run"><span class="n"><a href="#t475">475</a></span><span class="t"> <span class="nam">teachers_school_weight</span> <span class="op">=</span> <span class="nam">n_teachers</span><span class="op">/</span><span class="nam">n_workers</span> </span><span class="r"></span></p>
<p id="t476" class="pln"><span class="n"><a href="#t476">476</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t477" class="run"><span class="n"><a href="#t477">477</a></span><span class="t"> <span class="nam">student_n_dic</span><span class="op">[</span><span class="str">'W'</span><span class="op">]</span> <span class="op">=</span> <span class="num">0</span> </span><span class="r"></span></p>
<p id="t478" class="run"><span class="n"><a href="#t478">478</a></span><span class="t"> <span class="nam">non_student_n_dic</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">teachers_school_weight</span> <span class="com"># make some teachers</span> </span><span class="r"></span></p>
<p id="t479" class="pln"><span class="n"><a href="#t479">479</a></span><span class="t"> <span class="com"># 5 categories :</span> </span><span class="r"></span></p>
<p id="t480" class="pln"><span class="n"><a href="#t480">480</a></span><span class="t"> <span class="com"># infants & toddlers : H, C</span> </span><span class="r"></span></p>
<p id="t481" class="pln"><span class="n"><a href="#t481">481</a></span><span class="t"> <span class="com"># school-aged students : H, S, C</span> </span><span class="r"></span></p>
<p id="t482" class="pln"><span class="n"><a href="#t482">482</a></span><span class="t"> <span class="com"># college-aged students / workers : H, S, W, C</span> </span><span class="r"></span></p>
<p id="t483" class="pln"><span class="n"><a href="#t483">483</a></span><span class="t"> <span class="com"># non-student workers : H, W, C</span> </span><span class="r"></span></p>
<p id="t484" class="pln"><span class="n"><a href="#t484">484</a></span><span class="t"> <span class="com"># retired elderly : H, C - some may be workers too but it's low. directed means they won't have contacts in the workplace, but undirected means they will at least a little.</span> </span><span class="r"></span></p>
<p id="t485" class="pln"><span class="n"><a href="#t485">485</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t486" class="pln"><span class="n"><a href="#t486">486</a></span><span class="t"> <span class="com"># will follow degree distribution well</span> </span><span class="r"></span></p>
<p id="t487" class="run"><span class="n"><a href="#t487">487</a></span><span class="t"> <span class="key">for</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t488" class="run"><span class="n"><a href="#t488">488</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="nam">n_contacts_dic</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t489" class="run"><span class="n"><a href="#t489">489</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">set</span><span class="op">(</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t490" class="pln"><span class="n"><a href="#t490">490</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t491" class="run"><span class="n"><a href="#t491">491</a></span><span class="t"> <span class="key">if</span> <span class="nam">directed</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t492" class="pln"><span class="n"><a href="#t492">492</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t493" class="mis show_mis"><span class="n"><a href="#t493">493</a></span><span class="t"> <span class="key">for</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t494" class="mis show_mis"><span class="n"><a href="#t494">494</a></span><span class="t"> <span class="nam">age</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'age'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t495" class="mis show_mis"><span class="n"><a href="#t495">495</a></span><span class="t"> <span class="key">if</span> <span class="nam">age</span> <span class="op"><</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_age_min'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t496" class="mis show_mis"><span class="n"><a href="#t496">496</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t497" class="mis show_mis"><span class="n"><a href="#t497">497</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t498" class="mis show_mis"><span class="n"><a href="#t498">498</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t499" class="mis show_mis"><span class="n"><a href="#t499">499</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t500" class="mis show_mis"><span class="n"><a href="#t500">500</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t501" class="pln"><span class="n"><a href="#t501">501</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t502" class="mis show_mis"><span class="n"><a href="#t502">502</a></span><span class="t"> <span class="key">elif</span> <span class="nam">age</span> <span class="op">>=</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_age_min'</span><span class="op">]</span> <span class="key">and</span> <span class="nam">age</span> <span class="op"><</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_age_max'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t503" class="mis show_mis"><span class="n"><a href="#t503">503</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'S'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t504" class="mis show_mis"><span class="n"><a href="#t504">504</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t505" class="mis show_mis"><span class="n"><a href="#t505">505</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t506" class="mis show_mis"><span class="n"><a href="#t506">506</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t507" class="mis show_mis"><span class="n"><a href="#t507">507</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t508" class="pln"><span class="n"><a href="#t508">508</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t509" class="mis show_mis"><span class="n"><a href="#t509">509</a></span><span class="t"> <span class="key">elif</span> <span class="nam">age</span> <span class="op">>=</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'college_age_min'</span><span class="op">]</span> <span class="key">and</span> <span class="nam">age</span> <span class="op"><</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'college_age_max'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t510" class="mis show_mis"><span class="n"><a href="#t510">510</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'S'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t511" class="mis show_mis"><span class="n"><a href="#t511">511</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t512" class="pln"><span class="n"><a href="#t512">512</a></span><span class="t"> <span class="com"># people at school and work? how??? college students going to school might actually look like their work environments anyways so for now this is just going to have schools and no work</span> </span><span class="r"></span></p>
<p id="t513" class="mis show_mis"><span class="n"><a href="#t513">513</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t514" class="mis show_mis"><span class="n"><a href="#t514">514</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t515" class="mis show_mis"><span class="n"><a href="#t515">515</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t516" class="pln"><span class="n"><a href="#t516">516</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t517" class="mis show_mis"><span class="n"><a href="#t517">517</a></span><span class="t"> <span class="key">elif</span> <span class="nam">age</span> <span class="op">>=</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'worker_age_min'</span><span class="op">]</span> <span class="key">and</span> <span class="nam">age</span> <span class="op"><</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'worker_age_max'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t518" class="mis show_mis"><span class="n"><a href="#t518">518</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'S'</span><span class="op">,</span> <span class="str">'W'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t519" class="mis show_mis"><span class="n"><a href="#t519">519</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t520" class="mis show_mis"><span class="n"><a href="#t520">520</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">non_student_n_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t521" class="mis show_mis"><span class="n"><a href="#t521">521</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t522" class="mis show_mis"><span class="n"><a href="#t522">522</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t523" class="pln"><span class="n"><a href="#t523">523</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t524" class="mis show_mis"><span class="n"><a href="#t524">524</a></span><span class="t"> <span class="key">elif</span> <span class="nam">age</span> <span class="op">>=</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'worker_age_max'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t525" class="mis show_mis"><span class="n"><a href="#t525">525</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t526" class="mis show_mis"><span class="n"><a href="#t526">526</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t527" class="mis show_mis"><span class="n"><a href="#t527">527</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t528" class="mis show_mis"><span class="n"><a href="#t528">528</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t529" class="mis show_mis"><span class="n"><a href="#t529">529</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t530" class="pln"><span class="n"><a href="#t530">530</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t531" class="pln"><span class="n"><a href="#t531">531</a></span><span class="t"> <span class="key">else</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t532" class="run"><span class="n"><a href="#t532">532</a></span><span class="t"> <span class="key">for</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t533" class="run"><span class="n"><a href="#t533">533</a></span><span class="t"> <span class="nam">age</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'age'</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t534" class="run"><span class="n"><a href="#t534">534</a></span><span class="t"> <span class="key">if</span> <span class="nam">age</span> <span class="op"><</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_age_min'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t535" class="run"><span class="n"><a href="#t535">535</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t536" class="run"><span class="n"><a href="#t536">536</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t537" class="run"><span class="n"><a href="#t537">537</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">/</span><span class="num">2</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t538" class="run"><span class="n"><a href="#t538">538</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t539" class="run"><span class="n"><a href="#t539">539</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t540" class="run"><span class="n"><a href="#t540">540</a></span><span class="t"> <span class="key">for</span> <span class="nam">c</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t541" class="run"><span class="n"><a href="#t541">541</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">c</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">add</span><span class="op">(</span><span class="nam">uid</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t542" class="pln"><span class="n"><a href="#t542">542</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t543" class="run"><span class="n"><a href="#t543">543</a></span><span class="t"> <span class="key">elif</span> <span class="nam">age</span> <span class="op">>=</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_age_min'</span><span class="op">]</span> <span class="key">and</span> <span class="nam">age</span> <span class="op"><</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'student_age_max'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t544" class="run"><span class="n"><a href="#t544">544</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'S'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t545" class="run"><span class="n"><a href="#t545">545</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t546" class="run"><span class="n"><a href="#t546">546</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">/</span><span class="num">2</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t547" class="run"><span class="n"><a href="#t547">547</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t548" class="run"><span class="n"><a href="#t548">548</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t549" class="run"><span class="n"><a href="#t549">549</a></span><span class="t"> <span class="key">for</span> <span class="nam">c</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t550" class="run"><span class="n"><a href="#t550">550</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">c</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">add</span><span class="op">(</span><span class="nam">uid</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t551" class="pln"><span class="n"><a href="#t551">551</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t552" class="run"><span class="n"><a href="#t552">552</a></span><span class="t"> <span class="key">elif</span> <span class="nam">age</span> <span class="op">>=</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'college_age_min'</span><span class="op">]</span> <span class="key">and</span> <span class="nam">age</span> <span class="op"><</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'college_age_max'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t553" class="run"><span class="n"><a href="#t553">553</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'S'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t554" class="run"><span class="n"><a href="#t554">554</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t555" class="run"><span class="n"><a href="#t555">555</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">/</span><span class="num">2</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t556" class="run"><span class="n"><a href="#t556">556</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t557" class="run"><span class="n"><a href="#t557">557</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t558" class="run"><span class="n"><a href="#t558">558</a></span><span class="t"> <span class="key">for</span> <span class="nam">c</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t559" class="run"><span class="n"><a href="#t559">559</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">c</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">add</span><span class="op">(</span><span class="nam">uid</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t560" class="pln"><span class="n"><a href="#t560">560</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t561" class="run"><span class="n"><a href="#t561">561</a></span><span class="t"> <span class="key">elif</span> <span class="nam">age</span> <span class="op">>=</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'worker_age_min'</span><span class="op">]</span> <span class="key">and</span> <span class="nam">age</span> <span class="op"><</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'worker_age_max'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t562" class="run"><span class="n"><a href="#t562">562</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'W'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t563" class="run"><span class="n"><a href="#t563">563</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t564" class="run"><span class="n"><a href="#t564">564</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">non_student_n_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">/</span><span class="num">2</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t565" class="run"><span class="n"><a href="#t565">565</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t566" class="run"><span class="n"><a href="#t566">566</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t567" class="run"><span class="n"><a href="#t567">567</a></span><span class="t"> <span class="key">for</span> <span class="nam">c</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t568" class="run"><span class="n"><a href="#t568">568</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">c</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">add</span><span class="op">(</span><span class="nam">uid</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t569" class="pln"><span class="n"><a href="#t569">569</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t570" class="run"><span class="n"><a href="#t570">570</a></span><span class="t"> <span class="key">elif</span> <span class="nam">age</span> <span class="op">>=</span> <span class="nam">activity_args</span><span class="op">[</span><span class="str">'worker_age_max'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t571" class="run"><span class="n"><a href="#t571">571</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t572" class="run"><span class="n"><a href="#t572">572</a></span><span class="t"> <span class="key">if</span> <span class="nam">network_type</span> <span class="op">==</span> <span class="str">'poisson_degree'</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t573" class="run"><span class="n"><a href="#t573">573</a></span><span class="t"> <span class="nam">nc</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">pt</span><span class="op">(</span><span class="nam">n_contacts_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">/</span><span class="num">2</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t574" class="run"><span class="n"><a href="#t574">574</a></span><span class="t"> <span class="nam">contact_ages</span> <span class="op">=</span> <span class="nam">spsamp</span><span class="op">.</span><span class="nam">sample_n_contact_ages_with_matrix</span><span class="op">(</span><span class="nam">nc</span><span class="op">,</span> <span class="nam">age</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">,</span> <span class="nam">age_mixing_matrix_dic</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t575" class="run"><span class="n"><a href="#t575">575</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">spsamp</span><span class="op">.</span><span class="nam">get_n_contact_ids_by_age</span><span class="op">(</span><span class="nam">uids_by_age_dic</span><span class="op">,</span> <span class="nam">contact_ages</span><span class="op">,</span> <span class="nam">age_brackets</span><span class="op">,</span> <span class="nam">age_by_brackets_dic</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t576" class="run"><span class="n"><a href="#t576">576</a></span><span class="t"> <span class="key">for</span> <span class="nam">c</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t577" class="run"><span class="n"><a href="#t577">577</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">c</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span><span class="op">.</span><span class="nam">add</span><span class="op">(</span><span class="nam">uid</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t578" class="pln"><span class="n"><a href="#t578">578</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t579" class="run"><span class="n"><a href="#t579">579</a></span><span class="t"> <span class="key">return</span> <span class="nam">popdict</span> </span><span class="r"></span></p>
<p id="t580" class="pln"><span class="n"><a href="#t580">580</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t581" class="pln"><span class="n"><a href="#t581">581</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t582" class="run"><span class="n"><a href="#t582">582</a></span><span class="t"><span class="key">def</span> <span class="nam">rehydrate</span><span class="op">(</span><span class="nam">data</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t583" class="pln"><span class="n"><a href="#t583">583</a></span><span class="t"> <span class="str">"""</span> </span><span class="r"></span></p>
<p id="t584" class="pln"><span class="n"><a href="#t584">584</a></span><span class="t"><span class="str"> Populate popdict with uids, ages and contacts from generated microstructure data</span> </span><span class="r"></span></p>
<p id="t585" class="pln"><span class="n"><a href="#t585">585</a></span><span class="t"><span class="str"> that was saved to data object</span> </span><span class="r"></span></p>
<p id="t586" class="pln"><span class="n"><a href="#t586">586</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t587" class="pln"><span class="n"><a href="#t587">587</a></span><span class="t"><span class="str"> Args:</span> </span><span class="r"></span></p>
<p id="t588" class="pln"><span class="n"><a href="#t588">588</a></span><span class="t"><span class="str"> data (pop object)</span> </span><span class="r"></span></p>
<p id="t589" class="pln"><span class="n"><a href="#t589">589</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t590" class="pln"><span class="n"><a href="#t590">590</a></span><span class="t"><span class="str"> Returns:</span> </span><span class="r"></span></p>
<p id="t591" class="pln"><span class="n"><a href="#t591">591</a></span><span class="t"><span class="str"> Popdict (sc.objdict)</span> </span><span class="r"></span></p>
<p id="t592" class="pln"><span class="n"><a href="#t592">592</a></span><span class="t"><span class="str"> """</span> </span><span class="r"></span></p>
<p id="t593" class="mis show_mis"><span class="n"><a href="#t593">593</a></span><span class="t"> <span class="nam">popdict</span> <span class="op">=</span> <span class="nam">sc</span><span class="op">.</span><span class="nam">dcp</span><span class="op">(</span><span class="nam">data</span><span class="op">[</span><span class="str">'popdict'</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t594" class="mis show_mis"><span class="n"><a href="#t594">594</a></span><span class="t"> <span class="nam">mapping</span> <span class="op">=</span> <span class="op">{</span><span class="str">'H'</span><span class="op">:</span> <span class="str">'households'</span><span class="op">,</span> <span class="str">'S'</span><span class="op">:</span> <span class="str">'schools'</span><span class="op">,</span> <span class="str">'W'</span><span class="op">:</span> <span class="str">'workplaces'</span><span class="op">}</span> </span><span class="r"></span></p>
<p id="t595" class="mis show_mis"><span class="n"><a href="#t595">595</a></span><span class="t"> <span class="key">for</span> <span class="nam">key</span><span class="op">,</span> <span class="nam">label</span> <span class="key">in</span> <span class="nam">mapping</span><span class="op">.</span><span class="nam">items</span><span class="op">(</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t596" class="mis show_mis"><span class="n"><a href="#t596">596</a></span><span class="t"> <span class="key">for</span> <span class="nam">r</span> <span class="key">in</span> <span class="nam">data</span><span class="op">[</span><span class="nam">label</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t597" class="mis show_mis"><span class="n"><a href="#t597">597</a></span><span class="t"> <span class="key">for</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">r</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t598" class="mis show_mis"><span class="n"><a href="#t598">598</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">key</span><span class="op">]</span> <span class="op">=</span> <span class="nam">set</span><span class="op">(</span><span class="nam">r</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t599" class="mis show_mis"><span class="n"><a href="#t599">599</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">key</span><span class="op">]</span><span class="op">.</span><span class="nam">remove</span><span class="op">(</span><span class="nam">uid</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t600" class="pln"><span class="n"><a href="#t600">600</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t601" class="mis show_mis"><span class="n"><a href="#t601">601</a></span><span class="t"> <span class="key">return</span> <span class="nam">popdict</span> </span><span class="r"></span></p>
<p id="t602" class="pln"><span class="n"><a href="#t602">602</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t603" class="pln"><span class="n"><a href="#t603">603</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t604" class="run"><span class="n"><a href="#t604">604</a></span><span class="t"><span class="key">def</span> <span class="nam">save_synthpop</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">contacts</span><span class="op">,</span> <span class="nam">location</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t605" class="pln"><span class="n"><a href="#t605">605</a></span><span class="t"> <span class="str">"""</span> </span><span class="r"></span></p>
<p id="t606" class="pln"><span class="n"><a href="#t606">606</a></span><span class="t"><span class="str"> Save pop data object to file.</span> </span><span class="r"></span></p>
<p id="t607" class="pln"><span class="n"><a href="#t607">607</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t608" class="pln"><span class="n"><a href="#t608">608</a></span><span class="t"><span class="str"> Args:</span> </span><span class="r"></span></p>
<p id="t609" class="pln"><span class="n"><a href="#t609">609</a></span><span class="t"><span class="str"> datadir (string) : file path to the data directory</span> </span><span class="r"></span></p>
<p id="t610" class="pln"><span class="n"><a href="#t610">610</a></span><span class="t"><span class="str"> contacts (dict) : dictionary of people with contacts</span> </span><span class="r"></span></p>
<p id="t611" class="pln"><span class="n"><a href="#t611">611</a></span><span class="t"><span class="str"> location (string) : name of the location</span> </span><span class="r"></span></p>
<p id="t612" class="pln"><span class="n"><a href="#t612">612</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t613" class="pln"><span class="n"><a href="#t613">613</a></span><span class="t"><span class="str"> Returns:</span> </span><span class="r"></span></p>
<p id="t614" class="pln"><span class="n"><a href="#t614">614</a></span><span class="t"><span class="str"> None</span> </span><span class="r"></span></p>
<p id="t615" class="pln"><span class="n"><a href="#t615">615</a></span><span class="t"><span class="str"> """</span> </span><span class="r"></span></p>
<p id="t616" class="pln"><span class="n"><a href="#t616">616</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t617" class="mis show_mis"><span class="n"><a href="#t617">617</a></span><span class="t"> <span class="nam">filename</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">location</span> <span class="op">+</span> <span class="str">'_synthpop_'</span> <span class="op">+</span> <span class="nam">str</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">contacts</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span> <span class="str">'.pop'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t618" class="mis show_mis"><span class="n"><a href="#t618">618</a></span><span class="t"> <span class="nam">sc</span><span class="op">.</span><span class="nam">saveobj</span><span class="op">(</span><span class="nam">filename</span><span class="op">=</span><span class="nam">filename</span><span class="op">,</span> <span class="nam">obj</span><span class="op">=</span><span class="nam">contacts</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t619" class="pln"><span class="n"><a href="#t619">619</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t620" class="pln"><span class="n"><a href="#t620">620</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t621" class="run"><span class="n"><a href="#t621">621</a></span><span class="t"><span class="key">def</span> <span class="nam">create_reduced_contacts_with_group_types</span><span class="op">(</span><span class="nam">popdict</span><span class="op">,</span> <span class="nam">group_1</span><span class="op">,</span> <span class="nam">group_2</span><span class="op">,</span> <span class="nam">setting</span><span class="op">,</span> <span class="nam">average_degree</span><span class="op">=</span><span class="num">20</span><span class="op">,</span> <span class="nam">p_matrix</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="nam">force_cross_edges</span><span class="op">=</span><span class="key">True</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t622" class="pln"><span class="n"><a href="#t622">622</a></span><span class="t"> <span class="str">"""</span> </span><span class="r"></span></p>
<p id="t623" class="pln"><span class="n"><a href="#t623">623</a></span><span class="t"><span class="str"> Create contacts between members of group 1 and group 2, fixing the average degree, and the</span> </span><span class="r"></span></p>
<p id="t624" class="pln"><span class="n"><a href="#t624">624</a></span><span class="t"><span class="str"> probability of an edge between any two groups controlled by p_matrix if provided.</span> </span><span class="r"></span></p>
<p id="t625" class="pln"><span class="n"><a href="#t625">625</a></span><span class="t"><span class="str"> Forces inter group edge for each individual in group 1 with force_cross_groups equal to True.</span> </span><span class="r"></span></p>
<p id="t626" class="pln"><span class="n"><a href="#t626">626</a></span><span class="t"><span class="str"> This means not everyone in group 2 will have a contact with group 1.</span> </span><span class="r"></span></p>
<p id="t627" class="pln"><span class="n"><a href="#t627">627</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t628" class="pln"><span class="n"><a href="#t628">628</a></span><span class="t"><span class="str"> The members of group 1 and group 2 should be distinct and non-overlapping.</span> </span><span class="r"></span></p>
<p id="t629" class="pln"><span class="n"><a href="#t629">629</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t630" class="pln"><span class="n"><a href="#t630">630</a></span><span class="t"><span class="str"> Args:</span> </span><span class="r"></span></p>
<p id="t631" class="pln"><span class="n"><a href="#t631">631</a></span><span class="t"><span class="str"> group_1 (list) : list of ids for group 1</span> </span><span class="r"></span></p>
<p id="t632" class="pln"><span class="n"><a href="#t632">632</a></span><span class="t"><span class="str"> group_2 (list) : list of ids for group 2</span> </span><span class="r"></span></p>
<p id="t633" class="pln"><span class="n"><a href="#t633">633</a></span><span class="t"><span class="str"> average_degree (int) : average degree across group 1 and 2</span> </span><span class="r"></span></p>
<p id="t634" class="pln"><span class="n"><a href="#t634">634</a></span><span class="t"><span class="str"> p_matrix (np.ndarray) : probability matrix for edges between any two groups</span> </span><span class="r"></span></p>
<p id="t635" class="pln"><span class="n"><a href="#t635">635</a></span><span class="t"><span class="str"> force_cross_groups (bool) : If True, force each individual to have at least one contact with a member from the other group</span> </span><span class="r"></span></p>
<p id="t636" class="pln"><span class="n"><a href="#t636">636</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t637" class="pln"><span class="n"><a href="#t637">637</a></span><span class="t"><span class="str"> Returns:</span> </span><span class="r"></span></p>
<p id="t638" class="pln"><span class="n"><a href="#t638">638</a></span><span class="t"><span class="str"> Popdict with edges added for nodes in the two groups.</span> </span><span class="r"></span></p>
<p id="t639" class="pln"><span class="n"><a href="#t639">639</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t640" class="pln"><span class="n"><a href="#t640">640</a></span><span class="t"><span class="str"> Notes:</span> </span><span class="r"></span></p>
<p id="t641" class="pln"><span class="n"><a href="#t641">641</a></span><span class="t"><span class="str"> This method uses the Stochastic Block Model algorithm to generate contacts both between nodes in different groups</span> </span><span class="r"></span></p>
<p id="t642" class="pln"><span class="n"><a href="#t642">642</a></span><span class="t"><span class="str"> and for nodes within the same group. In the current version, fixing the average degree and p_matrix, the matrix of probabilities</span> </span><span class="r"></span></p>
<p id="t643" class="pln"><span class="n"><a href="#t643">643</a></span><span class="t"><span class="str"> for edges between any two groups is not supported. Future versions may add support for this.</span> </span><span class="r"></span></p>
<p id="t644" class="pln"><span class="n"><a href="#t644">644</a></span><span class="t"><span class="str"> """</span> </span><span class="r"></span></p>
<p id="t645" class="pln"><span class="n"><a href="#t645">645</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t646" class="run"><span class="n"><a href="#t646">646</a></span><span class="t"> <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">group_1</span><span class="op">)</span> <span class="op">==</span> <span class="num">0</span> <span class="key">or</span> <span class="nam">len</span><span class="op">(</span><span class="nam">group_2</span><span class="op">)</span> <span class="op">==</span> <span class="num">0</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t647" class="mis show_mis"><span class="n"><a href="#t647">647</a></span><span class="t"> <span class="nam">errormsg</span> <span class="op">=</span> <span class="str">f'This method requires that both groups are populated. If one of the two groups has size 0, then consider using the synthpops.trim_contacts() method, or checking that the groups provided to this method are correct.'</span> </span><span class="r"></span></p>
<p id="t648" class="mis show_mis"><span class="n"><a href="#t648">648</a></span><span class="t"> <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="nam">errormsg</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t649" class="pln"><span class="n"><a href="#t649">649</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t650" class="run"><span class="n"><a href="#t650">650</a></span><span class="t"> <span class="key">if</span> <span class="nam">average_degree</span> <span class="op"><</span> <span class="num">2</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t651" class="mis show_mis"><span class="n"><a href="#t651">651</a></span><span class="t"> <span class="nam">errormsg</span> <span class="op">=</span> <span class="str">f'This method is likely to create disconnected graphs with average_degree < 2. In order to keep the group connected, use a higher average_degree for nodes across the two groups.'</span> </span><span class="r"></span></p>
<p id="t652" class="mis show_mis"><span class="n"><a href="#t652">652</a></span><span class="t"> <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="nam">errormsg</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t653" class="pln"><span class="n"><a href="#t653">653</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t654" class="run"><span class="n"><a href="#t654">654</a></span><span class="t"> <span class="nam">r1</span> <span class="op">=</span> <span class="op">[</span><span class="nam">int</span><span class="op">(</span><span class="nam">i</span><span class="op">)</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">group_1</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t655" class="run"><span class="n"><a href="#t655">655</a></span><span class="t"> <span class="nam">r2</span> <span class="op">=</span> <span class="op">[</span><span class="nam">int</span><span class="op">(</span><span class="nam">i</span><span class="op">)</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">group_2</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t656" class="pln"><span class="n"><a href="#t656">656</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t657" class="run"><span class="n"><a href="#t657">657</a></span><span class="t"> <span class="nam">n1</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">np</span><span class="op">.</span><span class="nam">arange</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">r1</span><span class="op">)</span><span class="op">)</span><span class="op">.</span><span class="nam">astype</span><span class="op">(</span><span class="nam">int</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t658" class="run"><span class="n"><a href="#t658">658</a></span><span class="t"> <span class="nam">n2</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">np</span><span class="op">.</span><span class="nam">arange</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">r1</span><span class="op">)</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">r1</span><span class="op">)</span><span class="op">+</span><span class="nam">len</span><span class="op">(</span><span class="nam">r2</span><span class="op">)</span><span class="op">)</span><span class="op">.</span><span class="nam">astype</span><span class="op">(</span><span class="nam">int</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t659" class="pln"><span class="n"><a href="#t659">659</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t660" class="run"><span class="n"><a href="#t660">660</a></span><span class="t"> <span class="nam">group</span> <span class="op">=</span> <span class="nam">r1</span> <span class="op">+</span> <span class="nam">r2</span> </span><span class="r"></span></p>
<p id="t661" class="run"><span class="n"><a href="#t661">661</a></span><span class="t"> <span class="nam">sizes</span> <span class="op">=</span> <span class="op">[</span><span class="nam">len</span><span class="op">(</span><span class="nam">r1</span><span class="op">)</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">r2</span><span class="op">)</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t662" class="pln"><span class="n"><a href="#t662">662</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t663" class="run"><span class="n"><a href="#t663">663</a></span><span class="t"> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">popdict</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t664" class="run"><span class="n"><a href="#t664">664</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">.</span><span class="nam">setdefault</span><span class="op">(</span><span class="nam">setting</span><span class="op">,</span> <span class="nam">set</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t665" class="pln"><span class="n"><a href="#t665">665</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t666" class="pln"><span class="n"><a href="#t666">666</a></span><span class="t"> <span class="com"># group is less than the average degree, so return a fully connected graph instead</span> </span><span class="r"></span></p>
<p id="t667" class="run"><span class="n"><a href="#t667">667</a></span><span class="t"> <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">group</span><span class="op">)</span> <span class="op"><=</span> <span class="nam">average_degree</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t668" class="mis show_mis"><span class="n"><a href="#t668">668</a></span><span class="t"> <span class="nam">G</span> <span class="op">=</span> <span class="nam">nx</span><span class="op">.</span><span class="nam">complete_graph</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">group</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t669" class="pln"><span class="n"><a href="#t669">669</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t670" class="pln"><span class="n"><a href="#t670">670</a></span><span class="t"> <span class="com"># group 2 is less than 2 people so everyone in group 1 must be connected to that lone group 2 individual, create a fully connected graph then remove some edges at random to preserve the degree distribution</span> </span><span class="r"></span></p>
<p id="t671" class="run"><span class="n"><a href="#t671">671</a></span><span class="t"> <span class="key">elif</span> <span class="nam">len</span><span class="op">(</span><span class="nam">group_2</span><span class="op">)</span> <span class="op"><</span> <span class="num">2</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t672" class="mis show_mis"><span class="n"><a href="#t672">672</a></span><span class="t"> <span class="nam">G</span> <span class="op">=</span> <span class="nam">nx</span><span class="op">.</span><span class="nam">complete_graph</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">group</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t673" class="mis show_mis"><span class="n"><a href="#t673">673</a></span><span class="t"> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">n1</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t674" class="mis show_mis"><span class="n"><a href="#t674">674</a></span><span class="t"> <span class="nam">group_1_neighbors</span> <span class="op">=</span> <span class="op">[</span><span class="nam">j</span> <span class="key">for</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">G</span><span class="op">.</span><span class="nam">neighbors</span><span class="op">(</span><span class="nam">i</span><span class="op">)</span> <span class="key">if</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">n1</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t675" class="pln"><span class="n"><a href="#t675">675</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t676" class="pln"><span class="n"><a href="#t676">676</a></span><span class="t"> <span class="com"># if the person's degree is too high, cut out some contacts</span> </span><span class="r"></span></p>
<p id="t677" class="mis show_mis"><span class="n"><a href="#t677">677</a></span><span class="t"> <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">group_1_neighbors</span><span class="op">)</span> <span class="op">></span> <span class="nam">average_degree</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t678" class="mis show_mis"><span class="n"><a href="#t678">678</a></span><span class="t"> <span class="nam">ncut</span> <span class="op">=</span> <span class="nam">len</span><span class="op">(</span><span class="nam">group_1_neighbors</span><span class="op">)</span> <span class="op">-</span> <span class="nam">average_degree</span> <span class="com"># rough number to cut</span> </span><span class="r"></span></p>
<p id="t679" class="pln"><span class="n"><a href="#t679">679</a></span><span class="t"> <span class="com"># ncut = spsamp.pt(ncut) # sample from poisson that number</span> </span><span class="r"></span></p>
<p id="t680" class="pln"><span class="n"><a href="#t680">680</a></span><span class="t"> <span class="com"># ncut = min(len(group_1_neighbors), ncut) # make sure the number isn't greater than the people available to cut</span> </span><span class="r"></span></p>
<p id="t681" class="mis show_mis"><span class="n"><a href="#t681">681</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">ncut</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t682" class="mis show_mis"><span class="n"><a href="#t682">682</a></span><span class="t"> <span class="nam">j</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">random</span><span class="op">.</span><span class="nam">choice</span><span class="op">(</span><span class="nam">group_1_neighbors</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t683" class="mis show_mis"><span class="n"><a href="#t683">683</a></span><span class="t"> <span class="nam">G</span><span class="op">.</span><span class="nam">remove_edge</span><span class="op">(</span><span class="nam">i</span><span class="op">,</span> <span class="nam">j</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t684" class="mis show_mis"><span class="n"><a href="#t684">684</a></span><span class="t"> <span class="nam">group_1_neighbors</span><span class="op">.</span><span class="nam">remove</span><span class="op">(</span><span class="nam">j</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t685" class="pln"><span class="n"><a href="#t685">685</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t686" class="pln"><span class="n"><a href="#t686">686</a></span><span class="t"> <span class="key">else</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t687" class="run"><span class="n"><a href="#t687">687</a></span><span class="t"> <span class="nam">share_k_matrix</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">ones</span><span class="op">(</span><span class="op">(</span><span class="num">2</span><span class="op">,</span> <span class="num">2</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t688" class="run"><span class="n"><a href="#t688">688</a></span><span class="t"> <span class="nam">share_k_matrix</span> <span class="op">*=</span> <span class="nam">average_degree</span><span class="op">/</span><span class="nam">np</span><span class="op">.</span><span class="nam">sum</span><span class="op">(</span><span class="nam">sizes</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t689" class="pln"><span class="n"><a href="#t689">689</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t690" class="run"><span class="n"><a href="#t690">690</a></span><span class="t"> <span class="key">if</span> <span class="nam">p_matrix</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t691" class="run"><span class="n"><a href="#t691">691</a></span><span class="t"> <span class="nam">p_matrix</span> <span class="op">=</span> <span class="nam">share_k_matrix</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t692" class="pln"><span class="n"><a href="#t692">692</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t693" class="pln"><span class="n"><a href="#t693">693</a></span><span class="t"> <span class="com"># create a graph with edges within each groups and between members of different groups using the probability matrix</span> </span><span class="r"></span></p>
<p id="t694" class="run"><span class="n"><a href="#t694">694</a></span><span class="t"> <span class="nam">G</span> <span class="op">=</span> <span class="nam">nx</span><span class="op">.</span><span class="nam">stochastic_block_model</span><span class="op">(</span><span class="nam">sizes</span><span class="op">,</span> <span class="nam">p_matrix</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t695" class="pln"><span class="n"><a href="#t695">695</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t696" class="pln"><span class="n"><a href="#t696">696</a></span><span class="t"> <span class="com"># how many people in group 2 have connections they could cut to preserve the degree distribution</span> </span><span class="r"></span></p>
<p id="t697" class="run"><span class="n"><a href="#t697">697</a></span><span class="t"> <span class="nam">group_2_to_group_2_connections</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t698" class="run"><span class="n"><a href="#t698">698</a></span><span class="t"> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">n2</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t699" class="run"><span class="n"><a href="#t699">699</a></span><span class="t"> <span class="nam">group_2_neighbors</span> <span class="op">=</span> <span class="op">[</span><span class="nam">j</span> <span class="key">for</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">G</span><span class="op">.</span><span class="nam">neighbors</span><span class="op">(</span><span class="nam">i</span><span class="op">)</span> <span class="key">if</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">n2</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t700" class="run"><span class="n"><a href="#t700">700</a></span><span class="t"> <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">group_2_neighbors</span><span class="op">)</span> <span class="op">></span> <span class="num">0</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t701" class="run"><span class="n"><a href="#t701">701</a></span><span class="t"> <span class="nam">group_2_to_group_2_connections</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">i</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t702" class="pln"><span class="n"><a href="#t702">702</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t703" class="pln"><span class="n"><a href="#t703">703</a></span><span class="t"> <span class="com"># there are no people in group 2 who can remove edges to other group 2 people, so instead, just add edges</span> </span><span class="r"></span></p>
<p id="t704" class="run"><span class="n"><a href="#t704">704</a></span><span class="t"> <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">group_2_to_group_2_connections</span><span class="op">)</span> <span class="op">==</span> <span class="num">0</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t705" class="mis show_mis"><span class="n"><a href="#t705">705</a></span><span class="t"> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">n1</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t706" class="mis show_mis"><span class="n"><a href="#t706">706</a></span><span class="t"> <span class="nam">group_2_neighbors</span> <span class="op">=</span> <span class="op">[</span><span class="nam">j</span> <span class="key">for</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">G</span><span class="op">.</span><span class="nam">neighbors</span><span class="op">(</span><span class="nam">i</span><span class="op">)</span> <span class="key">if</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">n2</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t707" class="pln"><span class="n"><a href="#t707">707</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t708" class="pln"><span class="n"><a href="#t708">708</a></span><span class="t"> <span class="com"># need to add a contact in group 2</span> </span><span class="r"></span></p>
<p id="t709" class="mis show_mis"><span class="n"><a href="#t709">709</a></span><span class="t"> <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">group_2_neighbors</span><span class="op">)</span> <span class="op">==</span> <span class="num">0</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t710" class="pln"><span class="n"><a href="#t710">710</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t711" class="mis show_mis"><span class="n"><a href="#t711">711</a></span><span class="t"> <span class="nam">random_group_2_j</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">random</span><span class="op">.</span><span class="nam">choice</span><span class="op">(</span><span class="nam">n2</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t712" class="mis show_mis"><span class="n"><a href="#t712">712</a></span><span class="t"> <span class="nam">G</span><span class="op">.</span><span class="nam">add_edge</span><span class="op">(</span><span class="nam">i</span><span class="op">,</span> <span class="nam">random_group_2_j</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t713" class="pln"><span class="n"><a href="#t713">713</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t714" class="pln"><span class="n"><a href="#t714">714</a></span><span class="t"> <span class="com"># some in group 2 have contacts to remove to preserve the degree distribution</span> </span><span class="r"></span></p>
<p id="t715" class="pln"><span class="n"><a href="#t715">715</a></span><span class="t"> <span class="key">else</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t716" class="run"><span class="n"><a href="#t716">716</a></span><span class="t"> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">n1</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t717" class="run"><span class="n"><a href="#t717">717</a></span><span class="t"> <span class="nam">group_2_neighbors</span> <span class="op">=</span> <span class="op">[</span><span class="nam">j</span> <span class="key">for</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">G</span><span class="op">.</span><span class="nam">neighbors</span><span class="op">(</span><span class="nam">i</span><span class="op">)</span> <span class="key">if</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">n2</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t718" class="pln"><span class="n"><a href="#t718">718</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t719" class="pln"><span class="n"><a href="#t719">719</a></span><span class="t"> <span class="com"># increase the degree of the node in group 1, while decreasing the degree of a member of group 2 at random</span> </span><span class="r"></span></p>
<p id="t720" class="run"><span class="n"><a href="#t720">720</a></span><span class="t"> <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">group_2_neighbors</span><span class="op">)</span> <span class="op">==</span> <span class="num">0</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t721" class="pln"><span class="n"><a href="#t721">721</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t722" class="run"><span class="n"><a href="#t722">722</a></span><span class="t"> <span class="nam">random_group_2_j</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">random</span><span class="op">.</span><span class="nam">choice</span><span class="op">(</span><span class="nam">n2</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t723" class="run"><span class="n"><a href="#t723">723</a></span><span class="t"> <span class="nam">random_group_2_neighbors</span> <span class="op">=</span> <span class="op">[</span><span class="nam">ii</span> <span class="key">for</span> <span class="nam">ii</span> <span class="key">in</span> <span class="nam">G</span><span class="op">.</span><span class="nam">neighbors</span><span class="op">(</span><span class="nam">random_group_2_j</span><span class="op">)</span> <span class="key">if</span> <span class="nam">ii</span> <span class="key">in</span> <span class="nam">n2</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t724" class="pln"><span class="n"><a href="#t724">724</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t725" class="pln"><span class="n"><a href="#t725">725</a></span><span class="t"> <span class="com"># add an edge to random_group_2_j</span> </span><span class="r"></span></p>
<p id="t726" class="run"><span class="n"><a href="#t726">726</a></span><span class="t"> <span class="nam">G</span><span class="op">.</span><span class="nam">add_edge</span><span class="op">(</span><span class="nam">i</span><span class="op">,</span> <span class="nam">random_group_2_j</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t727" class="pln"><span class="n"><a href="#t727">727</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t728" class="pln"><span class="n"><a href="#t728">728</a></span><span class="t"> <span class="com"># if the group 2 person has an edge they can cut to their own group, remove it</span> </span><span class="r"></span></p>
<p id="t729" class="run"><span class="n"><a href="#t729">729</a></span><span class="t"> <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">random_group_2_neighbors</span><span class="op">)</span> <span class="op">></span> <span class="num">0</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t730" class="mis show_mis"><span class="n"><a href="#t730">730</a></span><span class="t"> <span class="nam">random_group_2_neighbor_cut</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">random</span><span class="op">.</span><span class="nam">choice</span><span class="op">(</span><span class="nam">random_group_2_neighbors</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t731" class="mis show_mis"><span class="n"><a href="#t731">731</a></span><span class="t"> <span class="nam">G</span><span class="op">.</span><span class="nam">remove_edge</span><span class="op">(</span><span class="nam">random_group_2_j</span><span class="op">,</span> <span class="nam">random_group_2_neighbor_cut</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t732" class="pln"><span class="n"><a href="#t732">732</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t733" class="run"><span class="n"><a href="#t733">733</a></span><span class="t"> <span class="nam">E</span> <span class="op">=</span> <span class="nam">G</span><span class="op">.</span><span class="nam">edges</span><span class="op">(</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t734" class="run"><span class="n"><a href="#t734">734</a></span><span class="t"> <span class="key">for</span> <span class="nam">e</span> <span class="key">in</span> <span class="nam">E</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t735" class="run"><span class="n"><a href="#t735">735</a></span><span class="t"> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="op">=</span> <span class="nam">e</span> </span><span class="r"></span></p>
<p id="t736" class="pln"><span class="n"><a href="#t736">736</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t737" class="run"><span class="n"><a href="#t737">737</a></span><span class="t"> <span class="nam">id_i</span> <span class="op">=</span> <span class="nam">group</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t738" class="run"><span class="n"><a href="#t738">738</a></span><span class="t"> <span class="nam">id_j</span> <span class="op">=</span> <span class="nam">group</span><span class="op">[</span><span class="nam">j</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t739" class="pln"><span class="n"><a href="#t739">739</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t740" class="run"><span class="n"><a href="#t740">740</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">id_i</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">setting</span><span class="op">]</span><span class="op">.</span><span class="nam">add</span><span class="op">(</span><span class="nam">id_j</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t741" class="run"><span class="n"><a href="#t741">741</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">id_j</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">setting</span><span class="op">]</span><span class="op">.</span><span class="nam">add</span><span class="op">(</span><span class="nam">id_i</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t742" class="pln"><span class="n"><a href="#t742">742</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t743" class="run"><span class="n"><a href="#t743">743</a></span><span class="t"> <span class="key">return</span> <span class="nam">popdict</span> </span><span class="r"></span></p>
<p id="t744" class="pln"><span class="n"><a href="#t744">744</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t745" class="pln"><span class="n"><a href="#t745">745</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t746" class="run"><span class="n"><a href="#t746">746</a></span><span class="t"><span class="key">def</span> <span class="nam">make_contacts_from_microstructure</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">,</span> <span class="nam">n</span><span class="op">,</span> <span class="nam">with_industry_code</span><span class="op">=</span><span class="key">False</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t747" class="pln"><span class="n"><a href="#t747">747</a></span><span class="t"> <span class="str">"""</span> </span><span class="r"></span></p>
<p id="t748" class="pln"><span class="n"><a href="#t748">748</a></span><span class="t"><span class="str"> Make a popdict from synthetic household, school, and workplace files with uids. If with_industry_code is True, then individuals</span> </span><span class="r"></span></p>
<p id="t749" class="pln"><span class="n"><a href="#t749">749</a></span><span class="t"><span class="str"> will have a workplace industry code as well (default value is -1 to represent that this data is unavailable). Currently, industry</span> </span><span class="r"></span></p>
<p id="t750" class="pln"><span class="n"><a href="#t750">750</a></span><span class="t"><span class="str"> codes are only available to assign to populations within the US.</span> </span><span class="r"></span></p>
<p id="t751" class="pln"><span class="n"><a href="#t751">751</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t752" class="pln"><span class="n"><a href="#t752">752</a></span><span class="t"><span class="str"> Args:</span> </span><span class="r"></span></p>
<p id="t753" class="pln"><span class="n"><a href="#t753">753</a></span><span class="t"><span class="str"> datadir (string) : file path to the data directory</span> </span><span class="r"></span></p>
<p id="t754" class="pln"><span class="n"><a href="#t754">754</a></span><span class="t"><span class="str"> location (string) : name of the location</span> </span><span class="r"></span></p>
<p id="t755" class="pln"><span class="n"><a href="#t755">755</a></span><span class="t"><span class="str"> state_location (string) : name of the state the location is in</span> </span><span class="r"></span></p>
<p id="t756" class="pln"><span class="n"><a href="#t756">756</a></span><span class="t"><span class="str"> country_location (string) : name of the country the location is in</span> </span><span class="r"></span></p>
<p id="t757" class="pln"><span class="n"><a href="#t757">757</a></span><span class="t"><span class="str"> n (int) : number of people in the population</span> </span><span class="r"></span></p>
<p id="t758" class="pln"><span class="n"><a href="#t758">758</a></span><span class="t"><span class="str"> with_industry_code (bool) : If True, assign workplace industry code read in from cached file</span> </span><span class="r"></span></p>
<p id="t759" class="pln"><span class="n"><a href="#t759">759</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t760" class="pln"><span class="n"><a href="#t760">760</a></span><span class="t"><span class="str"> Returns:</span> </span><span class="r"></span></p>
<p id="t761" class="pln"><span class="n"><a href="#t761">761</a></span><span class="t"><span class="str"> A popdict of people with attributes. Dictionary keys are the IDs of individuals in the population and the values are a dictionary</span> </span><span class="r"></span></p>
<p id="t762" class="pln"><span class="n"><a href="#t762">762</a></span><span class="t"><span class="str"> for each individual with their attributes, such as age, household ID (hhid), school ID (scid), workplace ID (wpid), workplace</span> </span><span class="r"></span></p>
<p id="t763" class="pln"><span class="n"><a href="#t763">763</a></span><span class="t"><span class="str"> industry code (wpindcode) if available, and the IDs of their contacts in different layers. Different layers available are</span> </span><span class="r"></span></p>
<p id="t764" class="pln"><span class="n"><a href="#t764">764</a></span><span class="t"><span class="str"> households ('H'), schools ('S'), and workplaces ('W'). Contacts in these layers are clustered and thus form a network composed of</span> </span><span class="r"></span></p>
<p id="t765" class="pln"><span class="n"><a href="#t765">765</a></span><span class="t"><span class="str"> groups of people interacting with each other. For example, all household members are contacts of each other, and everyone in the</span> </span><span class="r"></span></p>
<p id="t766" class="pln"><span class="n"><a href="#t766">766</a></span><span class="t"><span class="str"> same school is considered a contact of each other.</span> </span><span class="r"></span></p>
<p id="t767" class="pln"><span class="n"><a href="#t767">767</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t768" class="pln"><span class="n"><a href="#t768">768</a></span><span class="t"><span class="str"> Notes:</span> </span><span class="r"></span></p>
<p id="t769" class="pln"><span class="n"><a href="#t769">769</a></span><span class="t"><span class="str"> Methods to trim large groups of contacts down to better approximate a sense of close contacts (such as classroom sizes or</span> </span><span class="r"></span></p>
<p id="t770" class="pln"><span class="n"><a href="#t770">770</a></span><span class="t"><span class="str"> smaller work groups are available via sp.trim_contacts() - see below).</span> </span><span class="r"></span></p>
<p id="t771" class="pln"><span class="n"><a href="#t771">771</a></span><span class="t"><span class="str"> """</span> </span><span class="r"></span></p>
<p id="t772" class="run"><span class="n"><a href="#t772">772</a></span><span class="t"> <span class="nam">folder_name</span> <span class="op">=</span> <span class="str">'contact_networks'</span> </span><span class="r"></span></p>
<p id="t773" class="run"><span class="n"><a href="#t773">773</a></span><span class="t"> <span class="nam">file_path</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="str">'demographics'</span><span class="op">,</span> <span class="str">'contact_matrices_152_countries'</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">,</span> <span class="nam">folder_name</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t774" class="pln"><span class="n"><a href="#t774">774</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t775" class="run"><span class="n"><a href="#t775">775</a></span><span class="t"> <span class="nam">households_by_uid_path</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">file_path</span><span class="op">,</span> <span class="nam">location</span> <span class="op">+</span> <span class="str">'_'</span> <span class="op">+</span> <span class="nam">str</span><span class="op">(</span><span class="nam">n</span><span class="op">)</span> <span class="op">+</span> <span class="str">'_synthetic_households_with_uids.dat'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t776" class="pln"><span class="n"><a href="#t776">776</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t777" class="run"><span class="n"><a href="#t777">777</a></span><span class="t"> <span class="key">if</span> <span class="nam">with_industry_code</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t778" class="mis show_mis"><span class="n"><a href="#t778">778</a></span><span class="t"> <span class="nam">workplaces_by_uid_path</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">file_path</span><span class="op">,</span> <span class="nam">location</span> <span class="op">+</span> <span class="str">'_'</span> <span class="op">+</span> <span class="nam">str</span><span class="op">(</span><span class="nam">n</span><span class="op">)</span> <span class="op">+</span> <span class="str">'_synthetic_workplaces_by_industry_with_uids.dat'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t779" class="mis show_mis"><span class="n"><a href="#t779">779</a></span><span class="t"> <span class="nam">workplaces_by_industry_code_path</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">file_path</span><span class="op">,</span> <span class="nam">location</span> <span class="op">+</span> <span class="str">'_'</span> <span class="op">+</span> <span class="nam">str</span><span class="op">(</span><span class="nam">n</span><span class="op">)</span> <span class="op">+</span> <span class="str">'_synthetic_workplaces_by_industry_codes.dat'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t780" class="pln"><span class="n"><a href="#t780">780</a></span><span class="t"> <span class="key">else</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t781" class="run"><span class="n"><a href="#t781">781</a></span><span class="t"> <span class="nam">workplaces_by_uid_path</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">file_path</span><span class="op">,</span> <span class="nam">location</span> <span class="op">+</span> <span class="str">'_'</span> <span class="op">+</span> <span class="nam">str</span><span class="op">(</span><span class="nam">n</span><span class="op">)</span> <span class="op">+</span> <span class="str">'_synthetic_workplaces_with_uids.dat'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t782" class="run"><span class="n"><a href="#t782">782</a></span><span class="t"> <span class="nam">schools_by_uid_path</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">file_path</span><span class="op">,</span> <span class="nam">location</span> <span class="op">+</span> <span class="str">'_'</span> <span class="op">+</span> <span class="nam">str</span><span class="op">(</span><span class="nam">n</span><span class="op">)</span> <span class="op">+</span> <span class="str">'_synthetic_schools_with_uids.dat'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t783" class="run"><span class="n"><a href="#t783">783</a></span><span class="t"> <span class="nam">teachers_by_uid_path</span> <span class="op">=</span> <span class="nam">os</span><span class="op">.</span><span class="nam">path</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">file_path</span><span class="op">,</span> <span class="nam">location</span> <span class="op">+</span> <span class="str">'_'</span> <span class="op">+</span> <span class="nam">str</span><span class="op">(</span><span class="nam">n</span><span class="op">)</span> <span class="op">+</span> <span class="str">'_synthetic_teachers_with_uids.dat'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t784" class="pln"><span class="n"><a href="#t784">784</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t785" class="pln"><span class="n"><a href="#t785">785</a></span><span class="t"><span class="com"># <<<<<<< HEAD</span> </span><span class="r"></span></p>
<p id="t786" class="run"><span class="n"><a href="#t786">786</a></span><span class="t"> <span class="nam">age_by_uid_dic</span> <span class="op">=</span> <span class="nam">sprw</span><span class="op">.</span><span class="nam">read_in_age_by_uid</span><span class="op">(</span><span class="nam">datadir</span><span class="op">,</span> <span class="nam">location</span><span class="op">,</span> <span class="nam">state_location</span><span class="op">,</span> <span class="nam">country_location</span><span class="op">,</span> <span class="nam">folder_name</span><span class="op">,</span> <span class="nam">n</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t787" class="pln"><span class="n"><a href="#t787">787</a></span><span class="t"><span class="com"># =======</span> </span><span class="r"></span></p>
<p id="t788" class="pln"><span class="n"><a href="#t788">788</a></span><span class="t"> <span class="com"># age_by_uid_dic = sprw.read_in_age_by_uid(datadir, location, country_location, state_location, 'contact_networks', n)</span> </span><span class="r"></span></p>
<p id="t789" class="pln"><span class="n"><a href="#t789">789</a></span><span class="t"><span class="com"># >>>>>>> origin/mf/update-saved-pop-fixes</span> </span><span class="r"></span></p>
<p id="t790" class="run"><span class="n"><a href="#t790">790</a></span><span class="t"> <span class="nam">uids</span> <span class="op">=</span> <span class="nam">age_by_uid_dic</span><span class="op">.</span><span class="nam">keys</span><span class="op">(</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t791" class="run"><span class="n"><a href="#t791">791</a></span><span class="t"> <span class="nam">uids</span> <span class="op">=</span> <span class="op">[</span><span class="nam">uid</span> <span class="key">for</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">uids</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t792" class="pln"><span class="n"><a href="#t792">792</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t793" class="pln"><span class="n"><a href="#t793">793</a></span><span class="t"> <span class="com"># uid are strings or ints</span> </span><span class="r"></span></p>
<p id="t794" class="run"><span class="n"><a href="#t794">794</a></span><span class="t"> <span class="key">if</span> <span class="nam">isinstance</span><span class="op">(</span><span class="nam">uids</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">,</span> <span class="nam">str</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t795" class="mis show_mis"><span class="n"><a href="#t795">795</a></span><span class="t"> <span class="nam">uid_mapping</span> <span class="op">=</span> <span class="op">{</span><span class="nam">uid</span><span class="op">:</span> <span class="nam">u</span> <span class="key">for</span> <span class="nam">u</span><span class="op">,</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">enumerate</span><span class="op">(</span><span class="nam">uids</span><span class="op">)</span><span class="op">}</span> </span><span class="r"></span></p>
<p id="t796" class="run"><span class="n"><a href="#t796">796</a></span><span class="t"> <span class="key">elif</span> <span class="nam">isinstance</span><span class="op">(</span><span class="nam">uids</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">integer</span><span class="op">)</span> <span class="key">or</span> <span class="nam">isinstance</span><span class="op">(</span><span class="nam">uids</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">,</span> <span class="nam">int</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t797" class="run"><span class="n"><a href="#t797">797</a></span><span class="t"> <span class="nam">uid_mapping</span> <span class="op">=</span> <span class="op">{</span><span class="nam">u</span><span class="op">:</span> <span class="nam">u</span> <span class="key">for</span> <span class="nam">u</span> <span class="key">in</span> <span class="nam">uids</span><span class="op">}</span> </span><span class="r"></span></p>
<p id="t798" class="pln"><span class="n"><a href="#t798">798</a></span><span class="t"> <span class="key">else</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t799" class="mis show_mis"><span class="n"><a href="#t799">799</a></span><span class="t"> <span class="nam">errormsg</span> <span class="op">=</span> <span class="str">f'Agent IDs should be either a string or an integer. The IDs being read in do not match either of those types. Please check that the data files being read in are correct.'</span> </span><span class="r"></span></p>
<p id="t800" class="mis show_mis"><span class="n"><a href="#t800">800</a></span><span class="t"> <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="nam">errormsg</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t801" class="pln"><span class="n"><a href="#t801">801</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t802" class="pln"><span class="n"><a href="#t802">802</a></span><span class="t"> <span class="com"># you have ages but not sexes so we'll just populate that for you at random</span> </span><span class="r"></span></p>
<p id="t803" class="run"><span class="n"><a href="#t803">803</a></span><span class="t"> <span class="nam">popdict</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span> </span><span class="r"></span></p>
<p id="t804" class="run"><span class="n"><a href="#t804">804</a></span><span class="t"> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">enumerate</span><span class="op">(</span><span class="nam">uids</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t805" class="run"><span class="n"><a href="#t805">805</a></span><span class="t"> <span class="nam">u</span> <span class="op">=</span> <span class="nam">uid_mapping</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t806" class="run"><span class="n"><a href="#t806">806</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span> </span><span class="r"></span></p>
<p id="t807" class="run"><span class="n"><a href="#t807">807</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'age'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">age_by_uid_dic</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t808" class="run"><span class="n"><a href="#t808">808</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'sex'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">random</span><span class="op">.</span><span class="nam">binomial</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">p</span><span class="op">=</span><span class="num">0.5</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t809" class="run"><span class="n"><a href="#t809">809</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'loc'</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span> </span><span class="r"></span></p>
<p id="t810" class="run"><span class="n"><a href="#t810">810</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span> <span class="op">=</span> <span class="op">{</span><span class="op">}</span> </span><span class="r"></span></p>
<p id="t811" class="run"><span class="n"><a href="#t811">811</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'hhid'</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span> </span><span class="r"></span></p>
<p id="t812" class="run"><span class="n"><a href="#t812">812</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'scid'</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span> </span><span class="r"></span></p>
<p id="t813" class="run"><span class="n"><a href="#t813">813</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'sc_student'</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span> </span><span class="r"></span></p>
<p id="t814" class="run"><span class="n"><a href="#t814">814</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'sc_teacher'</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span> </span><span class="r"></span></p>
<p id="t815" class="run"><span class="n"><a href="#t815">815</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'wpid'</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span> </span><span class="r"></span></p>
<p id="t816" class="run"><span class="n"><a href="#t816">816</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'wpindcode'</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span> </span><span class="r"></span></p>
<p id="t817" class="run"><span class="n"><a href="#t817">817</a></span><span class="t"> <span class="key">for</span> <span class="nam">k</span> <span class="key">in</span> <span class="op">[</span><span class="str">'H'</span><span class="op">,</span> <span class="str">'S'</span><span class="op">,</span> <span class="str">'W'</span><span class="op">,</span> <span class="str">'C'</span><span class="op">]</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t818" class="run"><span class="n"><a href="#t818">818</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="nam">k</span><span class="op">]</span> <span class="op">=</span> <span class="nam">set</span><span class="op">(</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t819" class="pln"><span class="n"><a href="#t819">819</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t820" class="run"><span class="n"><a href="#t820">820</a></span><span class="t"> <span class="nam">fh</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">households_by_uid_path</span><span class="op">,</span> <span class="str">'r'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t821" class="run"><span class="n"><a href="#t821">821</a></span><span class="t"> <span class="nam">fs</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">schools_by_uid_path</span><span class="op">,</span> <span class="str">'r'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t822" class="run"><span class="n"><a href="#t822">822</a></span><span class="t"> <span class="nam">ft</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">teachers_by_uid_path</span><span class="op">,</span> <span class="str">'r'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t823" class="run"><span class="n"><a href="#t823">823</a></span><span class="t"> <span class="nam">fw</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">workplaces_by_uid_path</span><span class="op">,</span> <span class="str">'r'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t824" class="pln"><span class="n"><a href="#t824">824</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t825" class="run"><span class="n"><a href="#t825">825</a></span><span class="t"> <span class="key">if</span> <span class="nam">with_industry_code</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t826" class="mis show_mis"><span class="n"><a href="#t826">826</a></span><span class="t"> <span class="nam">fi</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">workplaces_by_industry_code_path</span><span class="op">,</span> <span class="str">'r'</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t827" class="mis show_mis"><span class="n"><a href="#t827">827</a></span><span class="t"> <span class="nam">workplaces_by_industry_codes</span> <span class="op">=</span> <span class="nam">np</span><span class="op">.</span><span class="nam">loadtxt</span><span class="op">(</span><span class="nam">fi</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t828" class="mis show_mis"><span class="n"><a href="#t828">828</a></span><span class="t"> <span class="nam">fi</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t829" class="pln"><span class="n"><a href="#t829">829</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t830" class="pln"><span class="n"><a href="#t830">830</a></span><span class="t"> <span class="com"># map uids to ints in the popdict created</span> </span><span class="r"></span></p>
<p id="t831" class="run"><span class="n"><a href="#t831">831</a></span><span class="t"> <span class="key">if</span> <span class="nam">isinstance</span><span class="op">(</span><span class="nam">uids</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">,</span> <span class="nam">str</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t832" class="pln"><span class="n"><a href="#t832">832</a></span><span class="t"> <span class="com"># read in home contacts</span> </span><span class="r"></span></p>
<p id="t833" class="mis show_mis"><span class="n"><a href="#t833">833</a></span><span class="t"> <span class="key">for</span> <span class="nam">nh</span><span class="op">,</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">enumerate</span><span class="op">(</span><span class="nam">fh</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t834" class="mis show_mis"><span class="n"><a href="#t834">834</a></span><span class="t"> <span class="nam">r</span> <span class="op">=</span> <span class="nam">line</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t835" class="mis show_mis"><span class="n"><a href="#t835">835</a></span><span class="t"> <span class="nam">household</span> <span class="op">=</span> <span class="op">[</span><span class="nam">uid_mapping</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span> <span class="key">for</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">r</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t836" class="pln"><span class="n"><a href="#t836">836</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t837" class="mis show_mis"><span class="n"><a href="#t837">837</a></span><span class="t"> <span class="key">for</span> <span class="nam">u</span> <span class="key">in</span> <span class="nam">household</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t838" class="mis show_mis"><span class="n"><a href="#t838">838</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'H'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">set</span><span class="op">(</span><span class="nam">household</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t839" class="mis show_mis"><span class="n"><a href="#t839">839</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'H'</span><span class="op">]</span><span class="op">.</span><span class="nam">remove</span><span class="op">(</span><span class="nam">u</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t840" class="mis show_mis"><span class="n"><a href="#t840">840</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'hhid'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">nh</span> </span><span class="r"></span></p>
<p id="t841" class="pln"><span class="n"><a href="#t841">841</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t842" class="pln"><span class="n"><a href="#t842">842</a></span><span class="t"> <span class="com"># read in school contacts</span> </span><span class="r"></span></p>
<p id="t843" class="mis show_mis"><span class="n"><a href="#t843">843</a></span><span class="t"> <span class="key">for</span> <span class="nam">ns</span><span class="op">,</span> <span class="op">(</span><span class="nam">line1</span><span class="op">,</span> <span class="nam">line2</span><span class="op">)</span> <span class="key">in</span> <span class="nam">enumerate</span><span class="op">(</span><span class="nam">zip</span><span class="op">(</span><span class="nam">fs</span><span class="op">,</span> <span class="nam">ft</span><span class="op">)</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t844" class="mis show_mis"><span class="n"><a href="#t844">844</a></span><span class="t"> <span class="nam">r1</span> <span class="op">=</span> <span class="nam">line1</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t845" class="mis show_mis"><span class="n"><a href="#t845">845</a></span><span class="t"> <span class="nam">r2</span> <span class="op">=</span> <span class="nam">line2</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t846" class="pln"><span class="n"><a href="#t846">846</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t847" class="mis show_mis"><span class="n"><a href="#t847">847</a></span><span class="t"> <span class="nam">students</span> <span class="op">=</span> <span class="op">[</span><span class="nam">uid_mapping</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span> <span class="key">for</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">r1</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t848" class="mis show_mis"><span class="n"><a href="#t848">848</a></span><span class="t"> <span class="nam">teachers</span> <span class="op">=</span> <span class="op">[</span><span class="nam">uid_mapping</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span> <span class="key">for</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">r2</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t849" class="pln"><span class="n"><a href="#t849">849</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t850" class="pln"><span class="n"><a href="#t850">850</a></span><span class="t"> <span class="com"># for uid in school:</span> </span><span class="r"></span></p>
<p id="t851" class="mis show_mis"><span class="n"><a href="#t851">851</a></span><span class="t"> <span class="key">for</span> <span class="nam">u</span> <span class="key">in</span> <span class="nam">students</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t852" class="mis show_mis"><span class="n"><a href="#t852">852</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">set</span><span class="op">(</span><span class="nam">students</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t853" class="mis show_mis"><span class="n"><a href="#t853">853</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">set</span><span class="op">(</span><span class="nam">teachers</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t854" class="mis show_mis"><span class="n"><a href="#t854">854</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span><span class="op">.</span><span class="nam">remove</span><span class="op">(</span><span class="nam">u</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t855" class="mis show_mis"><span class="n"><a href="#t855">855</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'scid'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">ns</span> </span><span class="r"></span></p>
<p id="t856" class="mis show_mis"><span class="n"><a href="#t856">856</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'sc_student'</span><span class="op">]</span> <span class="op">=</span> <span class="num">1</span> </span><span class="r"></span></p>
<p id="t857" class="pln"><span class="n"><a href="#t857">857</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t858" class="mis show_mis"><span class="n"><a href="#t858">858</a></span><span class="t"> <span class="key">for</span> <span class="nam">u</span> <span class="key">in</span> <span class="nam">teachers</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t859" class="mis show_mis"><span class="n"><a href="#t859">859</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">set</span><span class="op">(</span><span class="nam">students</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t860" class="mis show_mis"><span class="n"><a href="#t860">860</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">set</span><span class="op">(</span><span class="nam">teachers</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t861" class="mis show_mis"><span class="n"><a href="#t861">861</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span><span class="op">.</span><span class="nam">remove</span><span class="op">(</span><span class="nam">u</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t862" class="mis show_mis"><span class="n"><a href="#t862">862</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'scid'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">ns</span> </span><span class="r"></span></p>
<p id="t863" class="mis show_mis"><span class="n"><a href="#t863">863</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'sc_teacher'</span><span class="op">]</span> <span class="op">=</span> <span class="num">1</span> </span><span class="r"></span></p>
<p id="t864" class="pln"><span class="n"><a href="#t864">864</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t865" class="pln"><span class="n"><a href="#t865">865</a></span><span class="t"> <span class="com"># read in workplace contacts</span> </span><span class="r"></span></p>
<p id="t866" class="mis show_mis"><span class="n"><a href="#t866">866</a></span><span class="t"> <span class="key">for</span> <span class="nam">nw</span><span class="op">,</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">enumerate</span><span class="op">(</span><span class="nam">fw</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t867" class="mis show_mis"><span class="n"><a href="#t867">867</a></span><span class="t"> <span class="nam">r</span> <span class="op">=</span> <span class="nam">line</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t868" class="mis show_mis"><span class="n"><a href="#t868">868</a></span><span class="t"> <span class="nam">workplace</span> <span class="op">=</span> <span class="op">[</span><span class="nam">uid_mapping</span><span class="op">[</span><span class="nam">uid</span><span class="op">]</span> <span class="key">for</span> <span class="nam">uid</span> <span class="key">in</span> <span class="nam">r</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t869" class="pln"><span class="n"><a href="#t869">869</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t870" class="mis show_mis"><span class="n"><a href="#t870">870</a></span><span class="t"> <span class="key">for</span> <span class="nam">u</span> <span class="key">in</span> <span class="nam">workplace</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t871" class="mis show_mis"><span class="n"><a href="#t871">871</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'W'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">set</span><span class="op">(</span><span class="nam">workplace</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t872" class="mis show_mis"><span class="n"><a href="#t872">872</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'W'</span><span class="op">]</span><span class="op">.</span><span class="nam">remove</span><span class="op">(</span><span class="nam">u</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t873" class="mis show_mis"><span class="n"><a href="#t873">873</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'wpid'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">nw</span> </span><span class="r"></span></p>
<p id="t874" class="mis show_mis"><span class="n"><a href="#t874">874</a></span><span class="t"> <span class="key">if</span> <span class="nam">with_industry_code</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t875" class="mis show_mis"><span class="n"><a href="#t875">875</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'wpindcode'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">workplaces_by_industry_codes</span><span class="op">[</span><span class="nam">nw</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t876" class="pln"><span class="n"><a href="#t876">876</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t877" class="pln"><span class="n"><a href="#t877">877</a></span><span class="t"> <span class="com"># uids are ints so no need to do any mapping</span> </span><span class="r"></span></p>
<p id="t878" class="pln"><span class="n"><a href="#t878">878</a></span><span class="t"> <span class="com"># elif isinstance(uids[0], int) or isinstance(uids[0], np.int64):</span> </span><span class="r"></span></p>
<p id="t879" class="run"><span class="n"><a href="#t879">879</a></span><span class="t"> <span class="key">elif</span> <span class="nam">isinstance</span><span class="op">(</span><span class="nam">uids</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">,</span> <span class="nam">np</span><span class="op">.</span><span class="nam">integer</span><span class="op">)</span> <span class="key">or</span> <span class="nam">isinstance</span><span class="op">(</span><span class="nam">uids</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">,</span> <span class="nam">int</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t880" class="pln"><span class="n"><a href="#t880">880</a></span><span class="t"> <span class="com"># read in home contacts</span> </span><span class="r"></span></p>
<p id="t881" class="run"><span class="n"><a href="#t881">881</a></span><span class="t"> <span class="key">for</span> <span class="nam">nh</span><span class="op">,</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">enumerate</span><span class="op">(</span><span class="nam">fh</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t882" class="run"><span class="n"><a href="#t882">882</a></span><span class="t"> <span class="nam">r</span> <span class="op">=</span> <span class="nam">line</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t883" class="run"><span class="n"><a href="#t883">883</a></span><span class="t"> <span class="nam">home</span> <span class="op">=</span> <span class="op">[</span><span class="nam">int</span><span class="op">(</span><span class="nam">u</span><span class="op">)</span> <span class="key">for</span> <span class="nam">u</span> <span class="key">in</span> <span class="nam">r</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t884" class="pln"><span class="n"><a href="#t884">884</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t885" class="run"><span class="n"><a href="#t885">885</a></span><span class="t"> <span class="key">for</span> <span class="nam">u</span> <span class="key">in</span> <span class="nam">home</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t886" class="run"><span class="n"><a href="#t886">886</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'H'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">set</span><span class="op">(</span><span class="nam">home</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t887" class="run"><span class="n"><a href="#t887">887</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'H'</span><span class="op">]</span><span class="op">.</span><span class="nam">remove</span><span class="op">(</span><span class="nam">u</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t888" class="run"><span class="n"><a href="#t888">888</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'hhid'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">nh</span> </span><span class="r"></span></p>
<p id="t889" class="pln"><span class="n"><a href="#t889">889</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t890" class="pln"><span class="n"><a href="#t890">890</a></span><span class="t"> <span class="com"># read in school contacts</span> </span><span class="r"></span></p>
<p id="t891" class="run"><span class="n"><a href="#t891">891</a></span><span class="t"> <span class="key">for</span> <span class="nam">ns</span><span class="op">,</span> <span class="op">(</span><span class="nam">line1</span><span class="op">,</span> <span class="nam">line2</span><span class="op">)</span> <span class="key">in</span> <span class="nam">enumerate</span><span class="op">(</span><span class="nam">zip</span><span class="op">(</span><span class="nam">fs</span><span class="op">,</span> <span class="nam">ft</span><span class="op">)</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t892" class="run"><span class="n"><a href="#t892">892</a></span><span class="t"> <span class="nam">r1</span> <span class="op">=</span> <span class="nam">line1</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t893" class="run"><span class="n"><a href="#t893">893</a></span><span class="t"> <span class="nam">r2</span> <span class="op">=</span> <span class="nam">line2</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t894" class="pln"><span class="n"><a href="#t894">894</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t895" class="run"><span class="n"><a href="#t895">895</a></span><span class="t"> <span class="nam">students</span> <span class="op">=</span> <span class="op">[</span><span class="nam">int</span><span class="op">(</span><span class="nam">u</span><span class="op">)</span> <span class="key">for</span> <span class="nam">u</span> <span class="key">in</span> <span class="nam">r1</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t896" class="run"><span class="n"><a href="#t896">896</a></span><span class="t"> <span class="nam">teachers</span> <span class="op">=</span> <span class="op">[</span><span class="nam">int</span><span class="op">(</span><span class="nam">u</span><span class="op">)</span> <span class="key">for</span> <span class="nam">u</span> <span class="key">in</span> <span class="nam">r2</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t897" class="pln"><span class="n"><a href="#t897">897</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t898" class="run"><span class="n"><a href="#t898">898</a></span><span class="t"> <span class="key">for</span> <span class="nam">u</span> <span class="key">in</span> <span class="nam">students</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t899" class="run"><span class="n"><a href="#t899">899</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">set</span><span class="op">(</span><span class="nam">students</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t900" class="run"><span class="n"><a href="#t900">900</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">set</span><span class="op">(</span><span class="nam">teachers</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t901" class="run"><span class="n"><a href="#t901">901</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span><span class="op">.</span><span class="nam">remove</span><span class="op">(</span><span class="nam">u</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t902" class="run"><span class="n"><a href="#t902">902</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'scid'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">ns</span> </span><span class="r"></span></p>
<p id="t903" class="run"><span class="n"><a href="#t903">903</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'sc_student'</span><span class="op">]</span> <span class="op">=</span> <span class="num">1</span> </span><span class="r"></span></p>
<p id="t904" class="pln"><span class="n"><a href="#t904">904</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t905" class="run"><span class="n"><a href="#t905">905</a></span><span class="t"> <span class="key">for</span> <span class="nam">u</span> <span class="key">in</span> <span class="nam">teachers</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t906" class="run"><span class="n"><a href="#t906">906</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">set</span><span class="op">(</span><span class="nam">students</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t907" class="run"><span class="n"><a href="#t907">907</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span><span class="op">.</span><span class="nam">union</span><span class="op">(</span><span class="nam">set</span><span class="op">(</span><span class="nam">teachers</span><span class="op">)</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t908" class="run"><span class="n"><a href="#t908">908</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'S'</span><span class="op">]</span><span class="op">.</span><span class="nam">remove</span><span class="op">(</span><span class="nam">u</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t909" class="run"><span class="n"><a href="#t909">909</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'scid'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">ns</span> </span><span class="r"></span></p>
<p id="t910" class="run"><span class="n"><a href="#t910">910</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'sc_teacher'</span><span class="op">]</span> <span class="op">=</span> <span class="num">1</span> </span><span class="r"></span></p>
<p id="t911" class="pln"><span class="n"><a href="#t911">911</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t912" class="pln"><span class="n"><a href="#t912">912</a></span><span class="t"> <span class="com"># read in workplace contacts</span> </span><span class="r"></span></p>
<p id="t913" class="run"><span class="n"><a href="#t913">913</a></span><span class="t"> <span class="key">for</span> <span class="nam">nw</span><span class="op">,</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">enumerate</span><span class="op">(</span><span class="nam">fw</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t914" class="run"><span class="n"><a href="#t914">914</a></span><span class="t"> <span class="nam">r</span> <span class="op">=</span> <span class="nam">line</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">' '</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t915" class="run"><span class="n"><a href="#t915">915</a></span><span class="t"> <span class="nam">workplace</span> <span class="op">=</span> <span class="op">[</span><span class="nam">int</span><span class="op">(</span><span class="nam">u</span><span class="op">)</span> <span class="key">for</span> <span class="nam">u</span> <span class="key">in</span> <span class="nam">r</span><span class="op">]</span> </span><span class="r"></span></p>
<p id="t916" class="pln"><span class="n"><a href="#t916">916</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t917" class="run"><span class="n"><a href="#t917">917</a></span><span class="t"> <span class="key">for</span> <span class="nam">u</span> <span class="key">in</span> <span class="nam">workplace</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t918" class="run"><span class="n"><a href="#t918">918</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'W'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">set</span><span class="op">(</span><span class="nam">workplace</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t919" class="run"><span class="n"><a href="#t919">919</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'contacts'</span><span class="op">]</span><span class="op">[</span><span class="str">'W'</span><span class="op">]</span><span class="op">.</span><span class="nam">remove</span><span class="op">(</span><span class="nam">u</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t920" class="run"><span class="n"><a href="#t920">920</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'wpid'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">nw</span> </span><span class="r"></span></p>
<p id="t921" class="run"><span class="n"><a href="#t921">921</a></span><span class="t"> <span class="key">if</span> <span class="nam">with_industry_code</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t922" class="mis show_mis"><span class="n"><a href="#t922">922</a></span><span class="t"> <span class="nam">popdict</span><span class="op">[</span><span class="nam">u</span><span class="op">]</span><span class="op">[</span><span class="str">'wpindcode'</span><span class="op">]</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">workplaces_by_industry_codes</span><span class="op">[</span><span class="nam">nw</span><span class="op">]</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t923" class="pln"><span class="n"><a href="#t923">923</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t924" class="run"><span class="n"><a href="#t924">924</a></span><span class="t"> <span class="nam">fh</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t925" class="run"><span class="n"><a href="#t925">925</a></span><span class="t"> <span class="nam">fs</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t926" class="run"><span class="n"><a href="#t926">926</a></span><span class="t"> <span class="nam">ft</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t927" class="run"><span class="n"><a href="#t927">927</a></span><span class="t"> <span class="nam">fw</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span> </span><span class="r"></span></p>
<p id="t928" class="pln"><span class="n"><a href="#t928">928</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t929" class="run"><span class="n"><a href="#t929">929</a></span><span class="t"> <span class="key">return</span> <span class="nam">popdict</span> </span><span class="r"></span></p>
<p id="t930" class="pln"><span class="n"><a href="#t930">930</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t931" class="pln"><span class="n"><a href="#t931">931</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t932" class="run"><span class="n"><a href="#t932">932</a></span><span class="t"><span class="key">def</span> <span class="nam">make_contacts_from_microstructure_objects</span><span class="op">(</span><span class="nam">age_by_uid_dic</span><span class="op">,</span> <span class="nam">homes_by_uids</span><span class="op">,</span> <span class="nam">schools_by_uids</span><span class="op">,</span> <span class="nam">teachers_by_uids</span><span class="op">,</span> <span class="nam">workplaces_by_uids</span><span class="op">,</span> <span class="nam">workplaces_by_industry_codes</span><span class="op">=</span><span class="key">None</span><span class="op">)</span><span class="op">:</span> </span><span class="r"></span></p>
<p id="t933" class="pln"><span class="n"><a href="#t933">933</a></span><span class="t"> <span class="str">"""</span> </span><span class="r"></span></p>
<p id="t934" class="pln"><span class="n"><a href="#t934">934</a></span><span class="t"><span class="str"> From microstructure objects (dictionary mapping ID to age, lists of lists in different settings, etc.), create a dictionary of individuals.</span> </span><span class="r"></span></p>
<p id="t935" class="pln"><span class="n"><a href="#t935">935</a></span><span class="t"><span class="str"> Each key is the ID of an individual which maps to a dictionary for that individual with attributes such as their age, household ID (hhid),</span> </span><span class="r"></span></p>
<p id="t936" class="pln"><span class="n"><a href="#t936">936</a></span><span class="t"><span class="str"> school ID (scid), workplace ID (wpid), workplace industry code (wpindcode) if available, and contacts in different layers.</span> </span><span class="r"></span></p>
<p id="t937" class="pln"><span class="n"><a href="#t937">937</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t938" class="pln"><span class="n"><a href="#t938">938</a></span><span class="t"><span class="str"> Args:</span> </span><span class="r"></span></p>
<p id="t939" class="pln"><span class="n"><a href="#t939">939</a></span><span class="t"><span class="str"> age_by_uid_dic (dict) : dictionary mapping id to age for all individuals in the population</span> </span><span class="r"></span></p>
<p id="t940" class="pln"><span class="n"><a href="#t940">940</a></span><span class="t"><span class="str"> homes_by_uids (list) : A list of lists where each sublist is a household and the IDs of the household members.</span> </span><span class="r"></span></p>
<p id="t941" class="pln"><span class="n"><a href="#t941">941</a></span><span class="t"><span class="str"> schools_by_uids (list) : list of lists, where each sublist represents a school and the ids of the students and teachers within it</span> </span><span class="r"></span></p>
<p id="t942" class="pln"><span class="n"><a href="#t942">942</a></span><span class="t"><span class="str"> workplaces_by_uids (list) : list of lists, where each sublist represents a workplace and the ids of the workers within it</span> </span><span class="r"></span></p>
<p id="t943" class="pln"><span class="n"><a href="#t943">943</a></span><span class="t"><span class="str"> workplaces_by_industry_codes (np.ndarray or None) : array with workplace industry code for each workplace</span> </span><span class="r"></span></p>
<p id="t944" class="pln"><span class="n"><a href="#t944">944</a></span><span class="t"> </span><span class="r"></span></p>
<p id="t945" class="pln"><span class="n"><a href="#t945">945</a></span><span class="t"><span class="str"> Returns:</span> </span><span class="r"></span></p>
<p id="t946" class="pln"><span class="n"><a href="#t946">946</a></span><span class="t"><span class="str"> A popdict of people with attributes. Dictionary keys are the IDs of individuals in the population and the values are a dictionary</span> </span><span class="r"></span></p>
<p id="t947" class="pln"><span class="n"><a href="#t947">947</a></span><span class="t"><span class="str"> for each individual with their attributes, such as age, household ID (hhid), school ID (scid), workplace ID (wpid), workplace</span> </span><span class="r"></span></p>