deploy: de6fa8c

newick_generator.html

@@ -224,9 +224,9 @@ <h3><a class="anchor" id="autotoc_md56"></a>
 <div class="ttc" id="astructquetzal_1_1format_1_1newick_1_1TreeAlign_html"><div class="ttname"><a href="structquetzal_1_1format_1_1newick_1_1TreeAlign.html">quetzal::format::newick::TreeAlign</a></div><div class="ttdoc">Set a root node branch length to zero. Remove all nested comments.</div><div class="ttdef"><b>Definition</b> from_network.hpp:180</div></div>
 </div><!-- fragment --><p>Since there are no comments stored in the labels of the generated random tree, the output of the different flavors are here quite similar:</p>
 <p><b>Output</b></p>
-<div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span>(((,),(,)),):0.0;</div>
-<div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span>(((,),(,)),);</div>
-<div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span>(((,),(,)),);</div>
+<div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span>((,),((,),)):0.0;</div>
+<div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span>((,),((,),));</div>
+<div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span>((,),((,),));</div>
 </div><!-- fragment --><hr  />
 <h3><a class="anchor" id="autotoc_md58"></a>
 Custom properties</h3>
@@ -287,7 +287,7 @@ <h3><a class="anchor" id="autotoc_md58"></a>
 <div class="ttc" id="astructedge__info_html"><div class="ttname"><a href="structedge__info.html">edge_info</a></div><div class="ttdef"><b>Definition</b> newick_parser_2.cpp:12</div></div>
 <div class="ttc" id="astructvertex__info_html"><div class="ttname"><a href="structvertex__info.html">vertex_info</a></div><div class="ttdef"><b>Definition</b> coalescence_binary_tree_2.cpp:5</div></div>
 </div><!-- fragment --><p><b>Output</b></p>
-<div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span>(Q:3,(((U:5,G:1)C:0,V:8)K:7,O:0)D:2)Q:0.0;</div>
+<div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span>(Q:1,(((L:2,C:8)Y:6,V:1)E:2,V:4)C:4)S:0.0;</div>
 </div><!-- fragment --><hr  />
 <h2><a class="anchor" id="autotoc_md60"></a>
 From a Quetzal k-ary tree</h2>
@@ -392,7 +392,7 @@ <h3><a class="anchor" id="autotoc_md64"></a>
 <div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span>2</div>
 <div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span>2</div>
 <div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span>2</div>
-<div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span>(C:6,((N:6,T:6)I:6,(E:0,N:0)T:0)K:0)C;</div>
+<div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span>((V:7,(A:6,R:0)Y:3)L:9,(Z:7,M:3)Y:9)L;</div>
 </div><!-- fragment --><hr  />
 <h2><a class="anchor" id="autotoc_md66"></a>
 Interfacing legacy code</h2>

spatial_graph_local_parameters.html

@@ -358,7 +358,7 @@ <h2><a class="anchor" id="autotoc_md121"></a>
 <div class="ttc" id="aclassquetzal_1_1geography_1_1landscape_html"><div class="ttname"><a href="classquetzal_1_1geography_1_1landscape.html">quetzal::geography::landscape</a></div><div class="ttdoc">Discrete spatio-temporal variations of a set of environmental variables.</div><div class="ttdef"><b>Definition</b> landscape.hpp:42</div></div>
 </div><!-- fragment --><p><b>Output</b></p>
 <div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span>Suitability w/ isoline ( x = 0, t = 0 ) = 0</div>
-<div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span>Suitability w/ shelter ( x = 0, t = 0 ) = 0.336296</div>
+<div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span>Suitability w/ shelter ( x = 0, t = 0 ) = 0</div>
 </div><!-- fragment --><hr  />
 <h1><a class="anchor" id="autotoc_md123"></a>
 Defining a friction model for trans-oceanic dispersal events</h1>

spatial_graph_local_process.html

@@ -313,9 +313,9 @@ <h2><a class="anchor" id="autotoc_md130"></a>
 <div class="line"><a id="l00050" name="l00050"></a><span class="lineno">   50</span>}</div>
 </div><!-- fragment --><p><b>Output</b></p>
 <div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span>Time series:</div>
-<div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span>at vertex 0 : 1 1 2 3 3 5 6 12 22 24 </div>
-<div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span>at vertex 1 : 1 1 2 3 5 7 11 13 26 47 </div>
-<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span>at vertex 2 : 1 1 3 3 6 11 22 32 46 69 </div>
+<div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span>at vertex 0 : 1 1 2 4 5 5 9 16 23 26 </div>
+<div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span>at vertex 1 : 1 1 1 2 4 5 6 8 10 10 </div>
+<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span>at vertex 2 : 1 1 1 2 4 5 9 12 21 41 </div>
 <div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span>at vertex 3 : 0 0 0 0 0 0 0 0 0 0 </div>
 <div class="line"><a id="l00006" name="l00006"></a><span class="lineno">    6</span>at vertex 4 : 0 0 0 0 0 0 0 0 0 0 </div>
 <div class="line"><a id="l00007" name="l00007"></a><span class="lineno">    7</span>at vertex 5 : 0 0 0 0 0 0 0 0 0 0 </div>
@@ -383,9 +383,9 @@ <h2><a class="anchor" id="autotoc_md132"></a>
 <div class="line"><a id="l00052" name="l00052"></a><span class="lineno">   52</span>}</div>
 </div><!-- fragment --><p><b>Output</b></p>
 <div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span>Time series:</div>
-<div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span>at vertex 0 : 1 3 15 35 205 474 967 1244 1148 1351 </div>
-<div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span>at vertex 1 : 1 2 10 35 163 733 1794 0 0 0 </div>
-<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span>at vertex 2 : 1 5 29 153 464 1220 795 978 1122 857 </div>
+<div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span>at vertex 0 : 1 4 9 19 46 212 710 1963 0 0 </div>
+<div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span>at vertex 1 : 1 4 23 83 376 853 1075 1257 856 1533 </div>
+<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span>at vertex 2 : 1 4 24 128 562 880 1071 904 1208 390 </div>
 <div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span>at vertex 3 : 0 0 0 0 0 0 0 0 0 0 </div>
 <div class="line"><a id="l00006" name="l00006"></a><span class="lineno">    6</span>at vertex 4 : 0 0 0 0 0 0 0 0 0 0 </div>
 <div class="line"><a id="l00007" name="l00007"></a><span class="lineno">    7</span>at vertex 5 : 0 0 0 0 0 0 0 0 0 0 </div>
@@ -517,9 +517,9 @@ <h2><a class="anchor" id="autotoc_md134"></a>
 </div><!-- fragment --><p><b>Output</b></p>
 <div class="fragment"><div class="line"><a id="l00001" name="l00001"></a><span class="lineno">    1</span>Time series:</div>
 <div class="line"><a id="l00002" name="l00002"></a><span class="lineno">    2</span>at vertex 0 : </div>
-<div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span>    P1 : 200 122.487 64.6055 0 0 0 0 0 0 0 </div>
-<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span>    P2 : 1 8.3598 46.1062 142.851 97.1423 88.4937 84.4821 82.3647 81.1815 80.5006 </div>
-<div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span>    P3 : 1 3.95294 10.1464 0 0 0 0 0 0 0 </div>
+<div class="line"><a id="l00003" name="l00003"></a><span class="lineno">    3</span>    P1 : 200 146.76 0 0 0 0 0 0 0 0 </div>
+<div class="line"><a id="l00004" name="l00004"></a><span class="lineno">    4</span>    P2 : 1 8.97175 51.3938 0 0 0 0 0 0 0 </div>
+<div class="line"><a id="l00005" name="l00005"></a><span class="lineno">    5</span>    P3 : 1 19.6842 282.82 0 0 0 0 0 0 0 </div>
 <div class="line"><a id="l00006" name="l00006"></a><span class="lineno">    6</span> </div>
 <div class="line"><a id="l00007" name="l00007"></a><span class="lineno">    7</span>at vertex 1 : </div>
 <div class="line"><a id="l00008" name="l00008"></a><span class="lineno">    8</span>    P1 : 0 0 0 0 0 0 0 0 0 0 </div>