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UofUEpiBio · Nov 22, 2024 · 2343d1a · 2343d1a
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diff --git a/agent-meat-virus-sampling_8hpp_source.html b/agent-meat-virus-sampling_8hpp_source.html
@@ -75,7 +75,7 @@
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-<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;<span class="keyword">template</span>&lt;<span class="keyword">typename</span> TSeq&gt;</div>
+<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;<span class="keyword">template</span>&lt;<span class="keyword">typename</span> TSeq = EPI_DEFAULT_TSEQ&gt;</div>
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@@ -221,7 +221,7 @@
 <div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;    </div>
 <div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;}</div>
 <div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160; </div>
-<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;<span class="keyword">template</span>&lt;<span class="keyword">typename</span> TSeq = <span class="keywordtype">int</span>&gt;</div>
+<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;<span class="keyword">template</span>&lt;<span class="keyword">typename</span> TSeq = EPI_DEFAULT_TSEQ&gt;</div>
 <div class="line"><a name="l00183"></a><span class="lineno"><a class="line" href="namespacesampler.html#a4cafc444e0a6c563f34ed5f9b5366ae4">  183</a></span>&#160;<span class="keyword">inline</span> std::function&lt;Virus&lt;TSeq&gt;*(<a class="code" href="class_agent.html">Agent&lt;TSeq&gt;</a>*,<a class="code" href="class_model.html">Model&lt;TSeq&gt;</a>*)&gt; <a class="code" href="namespacesampler.html#a4cafc444e0a6c563f34ed5f9b5366ae4">make_sample_virus_neighbors</a>(</div>
 <div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;    std::vector&lt; epiworld_fast_uint &gt; exclude = {}</div>
 <div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;)</div>
@@ -373,7 +373,7 @@
 <div class="line"><a name="l00331"></a><span class="lineno">  331</span>&#160; </div>
 <div class="line"><a name="l00332"></a><span class="lineno">  332</span>&#160;}</div>
 <div class="line"><a name="l00333"></a><span class="lineno">  333</span>&#160; </div>
-<div class="line"><a name="l00350"></a><span class="lineno">  350</span>&#160;<span class="keyword">template</span>&lt;<span class="keyword">typename</span> TSeq = <span class="keywordtype">int</span>&gt;</div>
+<div class="line"><a name="l00350"></a><span class="lineno">  350</span>&#160;<span class="keyword">template</span>&lt;<span class="keyword">typename</span> TSeq = EPI_DEFAULT_TSEQ&gt;</div>
 <div class="line"><a name="l00351"></a><span class="lineno"><a class="line" href="namespacesampler.html#ab33532e84aba976673b13d0f6758e95b">  351</a></span>&#160;<span class="keyword">inline</span> <a class="code" href="class_virus.html">Virus&lt;TSeq&gt;</a> * <a class="code" href="namespacesampler.html#ab33532e84aba976673b13d0f6758e95b">sample_virus_single</a>(<a class="code" href="class_agent.html">Agent&lt;TSeq&gt;</a> * p, <a class="code" href="class_model.html">Model&lt;TSeq&gt;</a> * m)</div>
 <div class="line"><a name="l00352"></a><span class="lineno">  352</span>&#160;{</div>
 <div class="line"><a name="l00353"></a><span class="lineno">  353</span>&#160; </div>

diff --git a/class_l_f_m_c_m_c-members.html b/class_l_f_m_c_m_c-members.html
@@ -69,6 +69,8 @@
 
 <p>This is the complete list of members for <a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a>, including all inherited members.</p>
 <table class="directory">
+  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>get_accepted_params</b>() (defined in <a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0"><td class="entry"><b>get_accepted_stats</b>() (defined in <a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>get_drawn_prob</b>() (defined in <a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0"><td class="entry"><b>get_epsilon</b>() const (defined in <a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>get_n_parameters</b>() const (defined in <a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
@@ -87,7 +89,7 @@
   <tr bgcolor="#f0f0f0"><td class="entry"><b>get_stats_mean</b>() (defined in <a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>LFMCMC</b>() (defined in <a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0"><td class="entry"><b>LFMCMC</b>(const TData &amp;observed_data_) (defined in <a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>print</b>() (defined in <a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>print</b>(size_t burnin=0u) const (defined in <a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0"><td class="entry"><b>rgamma</b>() (defined in <a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>rgamma</b>(epiworld_double alpha, epiworld_double beta) (defined in <a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0"><td class="entry"><b>rnorm</b>() (defined in <a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="class_l_f_m_c_m_c.html">LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>

diff --git a/class_l_f_m_c_m_c.html b/class_l_f_m_c_m_c.html
@@ -137,6 +137,12 @@
 <tr class="memitem:ad3cba41457c38a50bc16b5783a3b3fb5"><td class="memItemLeft" align="right" valign="top"><a id="ad3cba41457c38a50bc16b5783a3b3fb5"></a>
 std::vector&lt; TData &gt; *&#160;</td><td class="memItemRight" valign="bottom"><b>get_sampled_data</b> ()</td></tr>
 <tr class="separator:ad3cba41457c38a50bc16b5783a3b3fb5"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a798c3bf3bb2c601be3456c907d5a6ea1"><td class="memItemLeft" align="right" valign="top"><a id="a798c3bf3bb2c601be3456c907d5a6ea1"></a>
+const std::vector&lt; epiworld_double &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><b>get_accepted_params</b> ()</td></tr>
+<tr class="separator:a798c3bf3bb2c601be3456c907d5a6ea1"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:afa81c1f9d53945f97d0a3b4742cf96ec"><td class="memItemLeft" align="right" valign="top"><a id="afa81c1f9d53945f97d0a3b4742cf96ec"></a>
+const std::vector&lt; epiworld_double &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><b>get_accepted_stats</b> ()</td></tr>
+<tr class="separator:afa81c1f9d53945f97d0a3b4742cf96ec"><td class="memSeparator" colspan="2">&#160;</td></tr>
 <tr class="memitem:a7e626ab23d03daac688c7ce51e44ba23"><td class="memItemLeft" align="right" valign="top"><a id="a7e626ab23d03daac688c7ce51e44ba23"></a>
 void&#160;</td><td class="memItemRight" valign="bottom"><b>set_par_names</b> (std::vector&lt; std::string &gt; names)</td></tr>
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 std::vector&lt; epiworld_double &gt;&#160;</td><td class="memItemRight" valign="bottom"><b>get_stats_mean</b> ()</td></tr>
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-<tr class="memitem:adf46ba06d7e03b3f71aa5d9e0de44c78"><td class="memItemLeft" align="right" valign="top"><a id="adf46ba06d7e03b3f71aa5d9e0de44c78"></a>
-void&#160;</td><td class="memItemRight" valign="bottom"><b>print</b> ()</td></tr>
-<tr class="separator:adf46ba06d7e03b3f71aa5d9e0de44c78"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:aa3030ef8d08f00fdec8b2fbfa8a33628"><td class="memItemLeft" align="right" valign="top"><a id="aa3030ef8d08f00fdec8b2fbfa8a33628"></a>
+void&#160;</td><td class="memItemRight" valign="bottom"><b>print</b> (size_t burnin=0u) const</td></tr>
+<tr class="separator:aa3030ef8d08f00fdec8b2fbfa8a33628"><td class="memSeparator" colspan="2">&#160;</td></tr>
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diff --git a/class_model_s_e_i_r.html b/class_model_s_e_i_r.html
@@ -788,8 +788,8 @@ <h2 class="memtitle"><span class="permalink"><a href="#ac8fceb86169a04202b06aab7
 <div class="line">        <span class="keywordflow">return</span>;    </div>
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 <div class="ttc" id="aclass_model_s_e_i_r_html"><div class="ttname"><a href="class_model_s_e_i_r.html">ModelSEIR</a></div><div class="ttdoc">Template for a Susceptible-Exposed-Infected-Removed (SEIR) model.</div><div class="ttdef"><b>Definition:</b> seir.hpp:16</div></div>
-<div class="ttc" id="aclassepiworld_1_1_agent_html"><div class="ttname"><a href="classepiworld_1_1_agent.html">epiworld::Agent</a></div><div class="ttdoc">Agent (agents)</div><div class="ttdef"><b>Definition:</b> epiworld.hpp:13643</div></div>
-<div class="ttc" id="aclassepiworld_1_1_model_html"><div class="ttname"><a href="classepiworld_1_1_model.html">epiworld::Model</a></div><div class="ttdoc">Core class of epiworld.</div><div class="ttdef"><b>Definition:</b> epiworld.hpp:6296</div></div>
+<div class="ttc" id="aclassepiworld_1_1_agent_html"><div class="ttname"><a href="classepiworld_1_1_agent.html">epiworld::Agent</a></div><div class="ttdoc">Agent (agents)</div><div class="ttdef"><b>Definition:</b> epiworld.hpp:13673</div></div>
+<div class="ttc" id="aclassepiworld_1_1_model_html"><div class="ttname"><a href="classepiworld_1_1_model.html">epiworld::Model</a></div><div class="ttdoc">Core class of epiworld.</div><div class="ttdef"><b>Definition:</b> epiworld.hpp:6326</div></div>
 </div><!-- fragment -->
 </div>
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diff --git a/class_model_s_e_i_r_d.html b/class_model_s_e_i_r_d.html
@@ -892,8 +892,8 @@ <h2 class="memtitle"><span class="permalink"><a href="#a68a053ac9d069499381e44f7
 <div class="line">    <span class="keywordflow">return</span>;</div>
 <div class="line">  }</div>
 <div class="ttc" id="aclass_model_s_e_i_r_d_html"><div class="ttname"><a href="class_model_s_e_i_r_d.html">ModelSEIRD</a></div><div class="ttdoc">Template for a Susceptible-Exposed-Infected-Removed-Deceased (SEIRD) model.</div><div class="ttdef"><b>Definition:</b> seird.hpp:9</div></div>
-<div class="ttc" id="aclassepiworld_1_1_agent_html"><div class="ttname"><a href="classepiworld_1_1_agent.html">epiworld::Agent</a></div><div class="ttdoc">Agent (agents)</div><div class="ttdef"><b>Definition:</b> epiworld.hpp:13643</div></div>
-<div class="ttc" id="aclassepiworld_1_1_model_html"><div class="ttname"><a href="classepiworld_1_1_model.html">epiworld::Model</a></div><div class="ttdoc">Core class of epiworld.</div><div class="ttdef"><b>Definition:</b> epiworld.hpp:6296</div></div>
+<div class="ttc" id="aclassepiworld_1_1_agent_html"><div class="ttname"><a href="classepiworld_1_1_agent.html">epiworld::Agent</a></div><div class="ttdoc">Agent (agents)</div><div class="ttdef"><b>Definition:</b> epiworld.hpp:13673</div></div>
+<div class="ttc" id="aclassepiworld_1_1_model_html"><div class="ttname"><a href="classepiworld_1_1_model.html">epiworld::Model</a></div><div class="ttdoc">Core class of epiworld.</div><div class="ttdef"><b>Definition:</b> epiworld.hpp:6326</div></div>
 </div><!-- fragment -->
 </div>
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diff --git a/classepiworld_1_1_l_f_m_c_m_c-members.html b/classepiworld_1_1_l_f_m_c_m_c-members.html
@@ -73,6 +73,8 @@
 
 <p>This is the complete list of members for <a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a>, including all inherited members.</p>
 <table class="directory">
+  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>get_accepted_params</b>() (defined in <a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0"><td class="entry"><b>get_accepted_stats</b>() (defined in <a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>get_drawn_prob</b>() (defined in <a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0"><td class="entry"><b>get_epsilon</b>() const (defined in <a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>get_n_parameters</b>() const (defined in <a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
@@ -91,7 +93,7 @@
   <tr bgcolor="#f0f0f0"><td class="entry"><b>get_stats_mean</b>() (defined in <a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>LFMCMC</b>() (defined in <a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0"><td class="entry"><b>LFMCMC</b>(const TData &amp;observed_data_) (defined in <a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
-  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>print</b>() (defined in <a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
+  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>print</b>(size_t burnin=0u) const (defined in <a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0"><td class="entry"><b>rgamma</b>() (defined in <a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>rgamma</b>(epiworld_double alpha, epiworld_double beta) (defined in <a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>
   <tr bgcolor="#f0f0f0"><td class="entry"><b>rnorm</b>() (defined in <a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a>)</td><td class="entry"><a class="el" href="classepiworld_1_1_l_f_m_c_m_c.html">epiworld::LFMCMC&lt; TData &gt;</a></td><td class="entry"><span class="mlabel">inline</span></td></tr>