build based on 41a731e

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.0","generation_timestamp":"2024-01-01T00:28:04","documenter_version":"1.2.1"}}
+{"documenter":{"julia_version":"1.10.0","generation_timestamp":"2024-01-15T13:59:06","documenter_version":"1.2.1"}}

dev/man/adding_data/index.html

@@ -17,4 +17,4 @@
 R&quot;text&quot;([9.5, 9.5, 9.5], [4, 8.5, 10], [&quot;C&quot;, &quot;B&quot;, &quot;A&quot;])</code></pre><p><img src="../../assets/figures/side_bars.svg" alt="example3"/></p><p>Let&#39;s break this down step by step. First, we read the topology, and plot the graph normally. <code>plot</code> actually returns a value, from which we can get useful information. Below, we store the plot output in <code>res</code>, then check its first two values because they contain the default range of the x axis; <code>xmin</code> and <code>xmax</code>.</p><pre><code class="language-julia hljs">res = plot(net);
 res[1:2]</code></pre><pre class="documenter-example-output"><code class="nohighlight hljs ansi">(0.29999999999999993, 8.77)</code></pre><p>Looking at <code>xmin</code> and <code>xmax</code> returned by default, we can see that the x range is about <code>(0.3, 9)</code>. To give us extra space to work with, we can set <code>xlim</code> to <code>(0.3,10)</code>, forcing the range to be wider on the right, for annotations. We can also see that in this case there is some extra white space on the left, so that we can increase <code>xmin</code> a little bit, finally settling on <code>xlim=(1,10)</code>.</p><pre><code class="language-julia hljs">plot(net, xlim=(1, 10));</code></pre><p>Knowing the coordinates, we can now add more information to the plot through <code>RCall</code>. For this, I use the R functions <code>segments</code> and <code>text</code> to add side bars with text on them.</p><pre><code class="language-julia hljs">using RCall # add (install) the RCall package prior to &#39;using&#39; it
 R&quot;segments&quot;([9, 9, 9], [0.8, 7.8, 9.8], [9, 9, 9], [7.2, 9.2, 10.2])
-R&quot;text&quot;([9.5, 9.5, 9.5], [4, 8.5, 10], [&quot;C&quot;, &quot;B&quot;, &quot;A&quot;])</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../better_edges/">« better edges</a><a class="docs-footer-nextpage" href="../../lib/public/">public »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 1 January 2024 00:28">Monday 1 January 2024</span>. Using Julia version 1.10.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+R&quot;text&quot;([9.5, 9.5, 9.5], [4, 8.5, 10], [&quot;C&quot;, &quot;B&quot;, &quot;A&quot;])</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../better_edges/">« better edges</a><a class="docs-footer-nextpage" href="../../lib/public/">public »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 15 January 2024 13:59">Monday 15 January 2024</span>. Using Julia version 1.10.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/man/better_edges/index.html

@@ -11,4 +11,4 @@
   9 => 5.0
   8 => 3.0
   3 => 3.0
-  1 =&gt; 5.0</code><br/><code class="language-julia-repl hljs" style="display:block;">julia&gt; plot(net1, edgewidth=log_populationsize);</code><code class="nohighlight hljs ansi" style="display:block;"></code><code class="nohighlight hljs ansi" style="display:block;"></code><code class="nohighlight hljs ansi" style="display:block;"></code></pre><p><img src="../../assets/figures/edge_len_example5.svg" alt="example5"/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../untangling_edges/">« untangling edges</a><a class="docs-footer-nextpage" href="../adding_data/">adding data »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 1 January 2024 00:28">Monday 1 January 2024</span>. Using Julia version 1.10.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+  1 =&gt; 5.0</code><br/><code class="language-julia-repl hljs" style="display:block;">julia&gt; plot(net1, edgewidth=log_populationsize);</code><code class="nohighlight hljs ansi" style="display:block;"></code><code class="nohighlight hljs ansi" style="display:block;"></code><code class="nohighlight hljs ansi" style="display:block;"></code></pre><p><img src="../../assets/figures/edge_len_example5.svg" alt="example5"/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../untangling_edges/">« untangling edges</a><a class="docs-footer-nextpage" href="../adding_data/">adding data »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 15 January 2024 13:59">Monday 15 January 2024</span>. Using Julia version 1.10.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/man/getting_started/index.html

@@ -3,4 +3,4 @@
 9 edges
 9 nodes: 4 tips, 1 hybrid nodes, 4 internal tree nodes.
 tip labels: A, B, C, D
-(A,((B,#H1),(C,(D)#H1)));</code></pre><p>and call <code>plot</code>, as shown below.</p><pre><code class="language-julia hljs">plot(net);</code></pre><p><img src="../../assets/figures/gettingstarted.svg" alt="example1"/></p><p>For the function&#39;s full documentation, see here: <a href="../../lib/public/#PhyloPlots.plot-Tuple{HybridNetwork}"><code>plot</code></a>.</p><div class="admonition is-info"><header class="admonition-header">version history</header><div class="admonition-body"><p>Compared to v0.3, v1 does not support the Gadfly-based plots, and uses small-case-only argument names.</p><p>The v0.3 syntax <code>plot(net, :R; ...)</code> still works in v1.0 but is <strong>deprecated</strong>, and will be removed in a future release. For example, you can still use <code>plot(net, :R; showNodeNumber=true)</code>, but you should instead start using <code>plot(net; shownodenumber=true)</code>.</p></div></div></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../installation/">« installation</a><a class="docs-footer-nextpage" href="../untangling_edges/">untangling edges »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 1 January 2024 00:28">Monday 1 January 2024</span>. Using Julia version 1.10.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+(A,((B,#H1),(C,(D)#H1)));</code></pre><p>and call <code>plot</code>, as shown below.</p><pre><code class="language-julia hljs">plot(net);</code></pre><p><img src="../../assets/figures/gettingstarted.svg" alt="example1"/></p><p>For the function&#39;s full documentation, see here: <a href="../../lib/public/#PhyloPlots.plot-Tuple{HybridNetwork}"><code>plot</code></a>.</p><div class="admonition is-info"><header class="admonition-header">version history</header><div class="admonition-body"><p>Compared to v0.3, v1 does not support the Gadfly-based plots, and uses small-case-only argument names.</p><p>The v0.3 syntax <code>plot(net, :R; ...)</code> still works in v1.0 but is <strong>deprecated</strong>, and will be removed in a future release. For example, you can still use <code>plot(net, :R; showNodeNumber=true)</code>, but you should instead start using <code>plot(net; shownodenumber=true)</code>.</p></div></div></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../installation/">« installation</a><a class="docs-footer-nextpage" href="../untangling_edges/">untangling edges »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 15 January 2024 13:59">Monday 15 January 2024</span>. Using Julia version 1.10.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>