build based on 0aaee38

previews/PR19/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.11.2","generation_timestamp":"2024-12-11T21:24:37","documenter_version":"1.8.0"}}
+{"documenter":{"julia_version":"1.11.2","generation_timestamp":"2024-12-11T21:42:30","documenter_version":"1.8.0"}}

previews/PR19/man/converting_coal2generation_units/index.html

@@ -27,4 +27,4 @@
 R"mtext"("red: Ne values", side=1, line=-1.5, col="red4");
 R&quot;mtext&quot;(&quot;black: edge lengths&quot;, side=1, line=-0.5);</code></pre><p><img src="../../assets/figures/net_genNe.svg" alt="species net with Ne"/></p><p>To simulate gene trees with edge lengths in generations, we can use a convenience wrapper function that takes <strong>Nₑ as an extra input</strong> to:</p><ul><li>convert edge lengths to coalescent units in the species phylogeny,</li><li>simulate gene trees with lengths in coalescent units, then</li><li>convert gene trees to have lengths in number of generations:</li></ul><pre><code class="language-julia-repl hljs" style="display:block;">julia&gt; genetree_gen = simulatecoalescent(net_gen,3,1, Ne; nodemapping=true);</code><code class="nohighlight hljs ansi" style="display:block;"></code><br/><code class="language-julia-repl hljs" style="display:block;">julia&gt; writeMultiTopology(genetree_gen, stdout) # 3 gene trees, lengths in #generations</code><code class="nohighlight hljs ansi" style="display:block;">(((A:1000.0)i2:500.0)i3:348.0,(((C:900.0)i1:600.0)i3:108.0,(((B:200.0)H1:700.0)i1:600.0)i3:108.0):241.0);
 (((A:1000.0)i2:500.0)i3:396.0,((((B:200.0)H1:700.0)i1:600.0)i3:7.0,((C:900.0)i1:600.0)i3:7.0):388.0);
-(((C:900.0)i1:600.0)i3:1261.0,(((A:1000.0)i2:500.0)i3:610.0,(((B:200.0)H1:600.0)i2:500.0)i3:610.0):651.0);</code></pre><div class="admonition is-warning"><header class="admonition-header">Warning</header><div class="admonition-body"><p>When Nₑ is given as an extra input to <code>simulatecoalescent</code>, edge lengths in the network are assumed to be in number of generations. If Nₑ is <em>not</em> given as input, then edge lengths are assumed to be in coalescent units.</p></div></div></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../mapping_genetree_to_network/">« mapping gene trees into the species network</a><a class="docs-footer-nextpage" href="../correlated_inheritance/">correlated inheritance »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Wednesday 11 December 2024 21:24">Wednesday 11 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+(((C:900.0)i1:600.0)i3:1261.0,(((A:1000.0)i2:500.0)i3:610.0,(((B:200.0)H1:600.0)i2:500.0)i3:610.0):651.0);</code></pre><div class="admonition is-warning"><header class="admonition-header">Warning</header><div class="admonition-body"><p>When Nₑ is given as an extra input to <code>simulatecoalescent</code>, edge lengths in the network are assumed to be in number of generations. If Nₑ is <em>not</em> given as input, then edge lengths are assumed to be in coalescent units.</p></div></div></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../mapping_genetree_to_network/">« mapping gene trees into the species network</a><a class="docs-footer-nextpage" href="../correlated_inheritance/">correlated inheritance »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Wednesday 11 December 2024 21:42">Wednesday 11 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

previews/PR19/man/correlated_inheritance/index.html

@@ -15,4 +15,4 @@
 
 plot(gt1, shownodelabel=true, edgelabel=el1, edgelabelcolor=el1.label, tipoffset=0.1);
 plot(gt2, shownodelabel=true, edgelabel=el2, edgelabelcolor=el2.label, tipoffset=0.1);
-plot(gt3, shownodelabel=true, edgelabel=el3, edgelabelcolor=el3.label, tipoffset=0.1);</code></pre><p><img src="../../assets/figures/net1taxon_3genetrees.svg" alt="3 gene trees on 1-taxon network with inheritance correlation"/></p><p>In all cases, any lineage has a probability γ=0.6 to come from species edge 2 (labeled in red), and probability γ=0.4 to come from species edge 3 (in green). When the inheritance correlation r increases, lineages have an increased preference to come from the same parent as other lineages (at the same locus).</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../converting_coal2generation_units/">« converting between units</a><a class="docs-footer-nextpage" href="../more_examples/">more examples »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Wednesday 11 December 2024 21:24">Wednesday 11 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+plot(gt3, shownodelabel=true, edgelabel=el3, edgelabelcolor=el3.label, tipoffset=0.1);</code></pre><p><img src="../../assets/figures/net1taxon_3genetrees.svg" alt="3 gene trees on 1-taxon network with inheritance correlation"/></p><p>In all cases, any lineage has a probability γ=0.6 to come from species edge 2 (labeled in red), and probability γ=0.4 to come from species edge 3 (in green). When the inheritance correlation r increases, lineages have an increased preference to come from the same parent as other lineages (at the same locus).</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../converting_coal2generation_units/">« converting between units</a><a class="docs-footer-nextpage" href="../more_examples/">more examples »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Wednesday 11 December 2024 21:42">Wednesday 11 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

previews/PR19/man/getting_started/index.html

@@ -31,4 +31,4 @@
 tip labels: B_3, C_3, C_2, C_1, ...
 (((B_3:0.964,C_3:0.964):0.214,(C_2:0.756,C_1:0.756):0.422):1.125,((B_1:0.595,B_2:0.595):0.849,(A_1:0.079,(A_2:0.054,A_3:0.054):0.025):1.565):0.659);</code></pre><p>We can also ask for varying numbers of individuals. For example, we simulate below 2 individuals in A and 1 individual in each of B and C, using a dictionary to map species to their number of individuals:</p><pre><code class="language-julia-repl hljs" style="display:block;">julia&gt; genetrees = simulatecoalescent(net, 1, Dict(&quot;A&quot;=&gt;2, &quot;B&quot;=&gt;1, &quot;C&quot;=&gt;1));</code><code class="nohighlight hljs ansi" style="display:block;"></code><br/><code class="language-julia-repl hljs" style="display:block;">julia&gt; writenewick(genetrees[1])</code><code class="nohighlight hljs ansi" style="display:block;">&quot;(C:1.7342183562262905,(B:1.1125494690619213,(A_2:0.39810435449985226,A_1:0.39810435449985226):0.9144451145620689):0.42166888716436934);&quot;</code></pre><p>We can set 0 individuals within a species to simulate missing data.</p><pre><code class="language-julia-repl hljs" style="display:block;">julia&gt; genetrees = simulatecoalescent(net, 3, Dict(&quot;A&quot;=&gt;2, &quot;B&quot;=&gt;1, &quot;C&quot;=&gt;0));</code><code class="nohighlight hljs ansi" style="display:block;"></code><br/><code class="language-julia-repl hljs" style="display:block;">julia&gt; writeMultiTopology(genetrees, stdout)</code><code class="nohighlight hljs ansi" style="display:block;">((A_1:0.6217550029603106,A_2:0.6217550029603106):1.8934561254937003,B:2.515211128454011);
 ((A_1:0.020216077041873223,A_2:0.020216077041873223):1.6564835196459733,B:1.6766995966878466);
-(B:1.3598531402719405,(A_2:0.5258264787632165,A_1:0.5258264787632165):1.034026661508724);</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../">« home</a><a class="docs-footer-nextpage" href="../mapping_genetree_to_network/">mapping gene trees into the species network »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Wednesday 11 December 2024 21:24">Wednesday 11 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+(B:1.3598531402719405,(A_2:0.5258264787632165,A_1:0.5258264787632165):1.034026661508724);</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../">« home</a><a class="docs-footer-nextpage" href="../mapping_genetree_to_network/">mapping gene trees into the species network »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Wednesday 11 December 2024 21:42">Wednesday 11 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

previews/PR19/man/mapping_genetree_to_network/index.html

@@ -13,4 +13,4 @@
 4 edges
 5 nodes: 3 tips, 0 hybrid nodes, 2 internal tree nodes.
 tip labels: B, C, A
-((C:1.695,A:1.695):0.979,B:2.474);</code></pre><p>The option <code>true</code> is to keep the root, even if it&#39;s of degree 2.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../getting_started/">« getting started</a><a class="docs-footer-nextpage" href="../converting_coal2generation_units/">converting between units »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Wednesday 11 December 2024 21:24">Wednesday 11 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+((C:1.695,A:1.695):0.979,B:2.474);</code></pre><p>The option <code>true</code> is to keep the root, even if it&#39;s of degree 2.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../getting_started/">« getting started</a><a class="docs-footer-nextpage" href="../converting_coal2generation_units/">converting between units »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Wednesday 11 December 2024 21:42">Wednesday 11 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>