build based on 7ddfd09

previews/PR12/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-17T03:10:50","documenter_version":"1.4.1"}}
+{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-17T12:07:52","documenter_version":"1.4.1"}}

previews/PR12/lib/public/index.html

@@ -80,7 +80,7 @@
  (tree_edge_number = 6, pop_edge_number = 3)
  (tree_edge_number = 3, pop_edge_number = 1)
  (tree_edge_number = 1, pop_edge_number = 1)
- (tree_edge_number = 2, pop_edge_number = 1)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecileane/PhyloCoalSimulations.jl/blob/d9bc44ccf207f472b5ee0672e997ebe5af08b3ac/src/simulatecoalescent_network.jl#L9-L162">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="PhyloCoalSimulations.simulatecoalescent-Tuple{Random.AbstractRNG, PhyloNetworks.HybridNetwork, Integer, Any, Any}" href="#PhyloCoalSimulations.simulatecoalescent-Tuple{Random.AbstractRNG, PhyloNetworks.HybridNetwork, Integer, Any, Any}"><code>PhyloCoalSimulations.simulatecoalescent</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">simulatecoalescent([rng::AbstractRNG,] net, nloci, nindividuals, populationsize;
+ (tree_edge_number = 2, pop_edge_number = 1)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecileane/PhyloCoalSimulations.jl/blob/7ddfd0974ad019ce6407a497f7048aebe963bb36/src/simulatecoalescent_network.jl#L9-L162">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="PhyloCoalSimulations.simulatecoalescent-Tuple{Random.AbstractRNG, PhyloNetworks.HybridNetwork, Integer, Any, Any}" href="#PhyloCoalSimulations.simulatecoalescent-Tuple{Random.AbstractRNG, PhyloNetworks.HybridNetwork, Integer, Any, Any}"><code>PhyloCoalSimulations.simulatecoalescent</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">simulatecoalescent([rng::AbstractRNG,] net, nloci, nindividuals, populationsize;
     nodemapping=false, round_generationnumber=true,
     inheritancecorrelation=0.0)</code></pre><p>Simulate <code>nloci</code> gene trees with <code>nindividuals</code> from each species under the multispecies network coalescent, along network <code>net</code>, whose branch lengths are assumed to be in <strong>number of generations</strong>. <code>populationsize</code> should be a single number, assumed to be the (haploid) effective population size Nₑ, constant across the species phylogeny. Alternatively, <code>populationsize</code> can be a dictionary mapping the number of each edge in <code>net</code> to its Nₑ, including an extra edge number for the population above the root of the network.</p><p>Coalescent units are then calculated as <code>u=g/Nₑ</code> where <code>g</code> is the edge length in <code>net</code> (number of generations), and the coalescent model is applied using the infinite-population-size approximation.</p><p>Output: vector of gene trees with edge lengths in number of generations, calculated as <code>g=uNₑ</code> and then rounded to be an integer, unless <code>round_generationnumber</code> is false.</p><div class="admonition is-warning"><header class="admonition-header">Warning</header><div class="admonition-body"><p>When <code>populationsize</code> Nₑ is not provided as input, all edge lengths are in coalescent units. When <code>populationsize</code> is given as an argument, all edge lengths are in number of generations. The second method (using # generation and Nₑ as input) is a wrapper around the first (using coalescent units).</p></div></div><pre><code class="language-julia-repl hljs">julia&gt; using PhyloNetworks
 
@@ -104,4 +104,4 @@
 julia&gt; writeMultiTopology(genetrees, stdout) # branch lengths: number of generations
 (B:546.0,A:546.0);
 (B:3155.0,A:3155.0);
-</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecileane/PhyloCoalSimulations.jl/blob/d9bc44ccf207f472b5ee0672e997ebe5af08b3ac/src/simulatecoalescent_network.jl#L295-L349">source</a></section></article><h2 id="index"><a class="docs-heading-anchor" href="#index">index</a><a id="index-1"></a><a class="docs-heading-anchor-permalink" href="#index" title="Permalink"></a></h2><ul><li><a href="#PhyloCoalSimulations.simulatecoalescent-Tuple{Random.AbstractRNG, PhyloNetworks.HybridNetwork, Integer, Any, Any}"><code>PhyloCoalSimulations.simulatecoalescent</code></a></li><li><a href="#PhyloCoalSimulations.simulatecoalescent-Tuple{PhyloNetworks.HybridNetwork, Vararg{Any}}"><code>PhyloCoalSimulations.simulatecoalescent</code></a></li></ul></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../man/more_examples/">« more examples</a><a class="docs-footer-nextpage" href="../internal/">internals »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 17 May 2024 03:10">Friday 17 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecileane/PhyloCoalSimulations.jl/blob/7ddfd0974ad019ce6407a497f7048aebe963bb36/src/simulatecoalescent_network.jl#L295-L349">source</a></section></article><h2 id="index"><a class="docs-heading-anchor" href="#index">index</a><a id="index-1"></a><a class="docs-heading-anchor-permalink" href="#index" title="Permalink"></a></h2><ul><li><a href="#PhyloCoalSimulations.simulatecoalescent-Tuple{Random.AbstractRNG, PhyloNetworks.HybridNetwork, Integer, Any, Any}"><code>PhyloCoalSimulations.simulatecoalescent</code></a></li><li><a href="#PhyloCoalSimulations.simulatecoalescent-Tuple{PhyloNetworks.HybridNetwork, Vararg{Any}}"><code>PhyloCoalSimulations.simulatecoalescent</code></a></li></ul></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../man/more_examples/">« more examples</a><a class="docs-footer-nextpage" href="../internal/">internals »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 17 May 2024 12:07">Friday 17 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

previews/PR12/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;">((((B:200.0)H1:700.0)i1:600.0)i3:758.0,(((C:900.0)i1:600.0)i3:132.0,((A:1000.0)i2:500.0)i3:132.0):625.0);
 (((((B:200.0)H1:700.0)i1:600.0)i3:2119.0,((A:1000.0)i2:500.0)i3:2119.0):971.0,((C:900.0)i1:600.0)i3:3089.0);
-(((C:900.0)i1:600.0)i3:1203.0,(((A:1000.0)i2:500.0)i3:724.0,(((B:200.0)H1:700.0)i1:600.0)i3:724.0):479.0);</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 17 May 2024 03:10">Friday 17 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+(((C:900.0)i1:600.0)i3:1203.0,(((A:1000.0)i2:500.0)i3:724.0,(((B:200.0)H1:700.0)i1:600.0)i3:724.0):479.0);</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 17 May 2024 12:07">Friday 17 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

previews/PR12/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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 17 May 2024 03:10">Friday 17 May 2024</span>. Using Julia version 1.10.3.</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.1 on <span class="colophon-date" title="Friday 17 May 2024 12:07">Friday 17 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>