deploy: ae7dd5f

Author: jordibc

genindex.html

@@ -486,6 +486,8 @@ <h2 id="G">G</h2>
         <li><a href="reference/reference_taxonomy.html#ete4.NCBITaxa.get_common_names">(NCBITaxa method)</a>
 </li>
       </ul></li>
+      <li><a href="reference/reference_operations.html#ete4.core.operations.get_common_values">get_common_values() (in module ete4.core.operations)</a>
+</li>
       <li><a href="reference/reference_phylo.html#ete4.PhyloTree.get_descendant_evol_events">get_descendant_evol_events() (PhyloTree method)</a>
 </li>
       <li><a href="reference/reference_taxonomy.html#ete4.GTDBTaxa.get_descendant_taxa">get_descendant_taxa() (GTDBTaxa method)</a>
@@ -521,11 +523,11 @@ <h2 id="G">G</h2>
       <li><a href="reference/reference_taxonomy.html#ete4.NCBITaxa.get_lineage_translator">get_lineage_translator() (NCBITaxa method)</a>
 </li>
       <li><a href="reference/reference_tree.html#ete4.core.tree.Tree.get_midpoint_outgroup">get_midpoint_outgroup() (Tree method)</a>
-</li>
-      <li><a href="reference/reference_tree.html#ete4.core.tree.Tree.get_monophyletic">get_monophyletic() (Tree method)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="reference/reference_tree.html#ete4.core.tree.Tree.get_monophyletic">get_monophyletic() (Tree method)</a>
+</li>
       <li><a href="reference/reference_phylo.html#ete4.PhyloTree.get_my_evol_events">get_my_evol_events() (PhyloTree method)</a>
 </li>
       <li><a href="reference/reference_taxonomy.html#ete4.GTDBTaxa.get_name_lineage">get_name_lineage() (GTDBTaxa method)</a>
@@ -705,6 +707,8 @@ <h2 id="M">M</h2>
       <li><a href="reference/reference_smartview.html#ete4.smartview.faces.make_nodes_summary">make_nodes_summary() (in module ete4.smartview.faces)</a>
 </li>
       <li><a href="reference/reference_parsers.html#ete4.parser.newick.make_parser">make_parser() (in module ete4.parser.newick)</a>
+</li>
+      <li><a href="reference/reference_operations.html#ete4.core.operations.make_partitions">make_partitions() (in module ete4.core.operations)</a>
 </li>
       <li><a href="reference/reference_treematcher.html#ete4.treematcher.treematcher.match">match() (in module ete4.treematcher.treematcher)</a>
 
@@ -794,6 +798,8 @@ <h2 id="P">P</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="reference/reference_tree.html#ete4.core.tree.Tree.parent">parent (Tree attribute)</a>
+</li>
+      <li><a href="reference/reference_operations.html#ete4.core.operations.partition_id">partition_id() (in module ete4.core.operations)</a>
 </li>
       <li><a href="reference/reference_operations.html#ete4.core.operations.phylogenetic_diversity">phylogenetic_diversity() (in module ete4.core.operations)</a>
 </li>
@@ -881,8 +887,12 @@ <h2 id="R">R</h2>
       </ul></li>
       <li><a href="reference/reference_tree.html#ete4.core.tree.Tree.reverse_children">reverse_children() (Tree method)</a>
 </li>
-      <li><a href="reference/reference_tree.html#ete4.core.tree.Tree.robinson_foulds">robinson_foulds() (Tree method)</a>
+      <li><a href="reference/reference_operations.html#ete4.core.operations.robinson_foulds">robinson_foulds() (in module ete4.core.operations)</a>
+
+      <ul>
+        <li><a href="reference/reference_tree.html#ete4.core.tree.Tree.robinson_foulds">(Tree method)</a>
 </li>
+      </ul></li>
       <li><a href="reference/reference_tree.html#ete4.core.tree.Tree.root">root (Tree attribute)</a>
 </li>
       <li><a href="reference/reference_operations.html#ete4.core.operations.root_at">root_at() (in module ete4.core.operations)</a>

objects.inv

@@ -58,22 +58,26 @@ <h1>Reference Guide<a class="headerlink" href="#reference-guide" title="Link to
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.evolutionary_distinctness"><code class="docutils literal notranslate"><span class="pre">evolutionary_distinctness()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.farthest_descendant"><code class="docutils literal notranslate"><span class="pre">farthest_descendant()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.farthest_nodes"><code class="docutils literal notranslate"><span class="pre">farthest_nodes()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.get_common_values"><code class="docutils literal notranslate"><span class="pre">get_common_values()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.get_distance_fn"><code class="docutils literal notranslate"><span class="pre">get_distance_fn()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.insert_intermediate"><code class="docutils literal notranslate"><span class="pre">insert_intermediate()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.interchange_references"><code class="docutils literal notranslate"><span class="pre">interchange_references()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.join_branch"><code class="docutils literal notranslate"><span class="pre">join_branch()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.ladderize"><code class="docutils literal notranslate"><span class="pre">ladderize()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.make_name"><code class="docutils literal notranslate"><span class="pre">make_name()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.make_partitions"><code class="docutils literal notranslate"><span class="pre">make_partitions()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.mean_distance"><code class="docutils literal notranslate"><span class="pre">mean_distance()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.midpoint"><code class="docutils literal notranslate"><span class="pre">midpoint()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.move"><code class="docutils literal notranslate"><span class="pre">move()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.partition_id"><code class="docutils literal notranslate"><span class="pre">partition_id()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.phylogenetic_diversity"><code class="docutils literal notranslate"><span class="pre">phylogenetic_diversity()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.populate"><code class="docutils literal notranslate"><span class="pre">populate()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.populate_uniform"><code class="docutils literal notranslate"><span class="pre">populate_uniform()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.populate_yule"><code class="docutils literal notranslate"><span class="pre">populate_yule()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.rehang"><code class="docutils literal notranslate"><span class="pre">rehang()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.remove"><code class="docutils literal notranslate"><span class="pre">remove()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.resolve_polytomy"><code class="docutils literal notranslate"><span class="pre">resolve_polytomy()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.robinson_foulds"><code class="docutils literal notranslate"><span class="pre">robinson_foulds()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.root_at"><code class="docutils literal notranslate"><span class="pre">root_at()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.set_midpoint_outgroup"><code class="docutils literal notranslate"><span class="pre">set_midpoint_outgroup()</span></code></a></li>
 <li class="toctree-l2"><a class="reference internal" href="reference_operations.html#ete4.core.operations.set_outgroup"><code class="docutils literal notranslate"><span class="pre">set_outgroup()</span></code></a></li>

reference/index.html

@@ -201,6 +201,13 @@
 <dd><p>Return the farthest nodes and the diameter of the tree.</p>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="ete4.core.operations.get_common_values">
+<span class="sig-name descname"><span class="pre">get_common_values</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">t1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">t2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'name'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.get_common_values" title="Link to this definition">¶</a></dt>
+<dd><p>Return the common leaf property prop values of trees t1 and t2.</p>
+<p>If strict, raise AssertionError if t1 and t2 don’t share leaves.</p>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="ete4.core.operations.get_distance_fn">
 <span class="sig-name descname"><span class="pre">get_distance_fn</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">topological</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">asserted</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.get_distance_fn" title="Link to this definition">¶</a></dt>
@@ -275,6 +282,14 @@
 <dd><p>Return a short name corresponding to the index i.</p>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="ete4.core.operations.make_partitions">
+<span class="sig-name descname"><span class="pre">make_partitions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tree</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">common_vals</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'name'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.make_partitions" title="Link to this definition">¶</a></dt>
+<dd><p>Return a set of partitions of the given tree.</p>
+<p>A “partition” is an id for each node, based on the leaves that it
+has at each side. The id is unique no matter the topology.</p>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="ete4.core.operations.mean_distance">
 <span class="sig-name descname"><span class="pre">mean_distance</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tree</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weight_fn</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">leaf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">topological</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.mean_distance" title="Link to this definition">¶</a></dt>
@@ -314,6 +329,12 @@
 <dd><p>Change the position of the current node with respect to its parent.</p>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="ete4.core.operations.partition_id">
+<span class="sig-name descname"><span class="pre">partition_id</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">values1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">values2</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.partition_id" title="Link to this definition">¶</a></dt>
+<dd><p>Return a unique id based on the given sets of values.</p>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="ete4.core.operations.phylogenetic_diversity">
 <span class="sig-name descname"><span class="pre">phylogenetic_diversity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">tree</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">topological</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.phylogenetic_diversity" title="Link to this definition">¶</a></dt>
@@ -388,6 +409,17 @@
 </dl>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="ete4.core.operations.robinson_foulds">
+<span class="sig-name descname"><span class="pre">robinson_foulds</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">t1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">t2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">prop</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'name'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normalized</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">strict</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.robinson_foulds" title="Link to this definition">¶</a></dt>
+<dd><p>Return the Robinson-Foulds distance between trees t1 and t2.</p>
+<dl class="simple">
+<dt>The distance is A + B, where</dt><dd><p>A: number of partitions implied by the 1st tree but not the 2nd
+B: number of partitions implied by the 2nd tree but not the 1st</p>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="ete4.core.operations.root_at">
 <span class="sig-name descname"><span class="pre">root_at</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">node</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bprops</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#ete4.core.operations.root_at" title="Link to this definition">¶</a></dt>