build based on 3f1e097

dev/man/bootstrap/index.html

@@ -128,4 +128,4 @@
 plot(net1, edgelabel=filter(r-&gt;r[:BS_minor_sister]&gt;5, BSn)[!,[:edge,:BS_minor_sister]]);</code></pre><p><img src="../../assets/figures/boot_net_clade_1.svg" alt="boot_net_clade 1"/> <img src="../../assets/figures/boot_net_clade_2.svg" alt="boot_net_clade 2"/></p><p>In our best network, the lineage to E is estimated as the origin of gene flow, but this is recovered in only 41% of our bootstrap networks. In another 49%, it is the lineage to A that is estimated as the <em>origin</em> of gene flow: so gene flow is estimated in the opposite direction. In this example, there is support for gene flow between (A,B) and (E,O), but there is much uncertainty about its exact placement and about its direction.</p><p>Mapping the support for major sister clades might be interesting too:</p><pre><code class="language-julia hljs">plot(net1, nodelabel=filter(r-&gt;r[:BS_major_sister]&gt;5, BSn)[!,[:node,:BS_major_sister]])</code></pre><p>The estimated heritability γ on hybrid edges in the reference network, when present in a bootstrap network, was also extracted:</p><pre><code class="language-julia-repl hljs" style="display:block;">julia&gt; BSgam[1:3,:] # first 3 rows only</code><code class="nohighlight hljs ansi" style="display:block;">3×2 Matrix{Float64}:
  0.767833  0.232167
  0.0       0.0
- 0.804412  0.195588</code></pre><p>γ=0 values are for bootstrap replicates that did not have the edge in their network. Basic summaries on γ values for a given edge, say the minor parent, could be obtained like this:</p><pre><code class="language-julia-repl hljs" style="display:block;">julia&gt; minimum(BSgam[:,2])</code><code class="nohighlight hljs ansi" style="display:block;">0.0</code><br/><code class="language-julia-repl hljs" style="display:block;">julia&gt; maximum(BSgam[:,2])</code><code class="nohighlight hljs ansi" style="display:block;">0.2321667195572249</code><br/><code class="language-julia-repl hljs" style="display:block;">julia&gt; using Statistics # for functions like mean and std (standard deviation)</code><code class="nohighlight hljs ansi" style="display:block;"></code><br/><code class="language-julia-repl hljs" style="display:block;">julia&gt; mean(BSgam[:,2])</code><code class="nohighlight hljs ansi" style="display:block;">0.062201290198789325</code><br/><code class="language-julia-repl hljs" style="display:block;">julia&gt; std(BSgam[:,2])</code><code class="nohighlight hljs ansi" style="display:block;">0.09131993802196253</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../expectedCFs/">« Extract Expected CFs</a><a class="docs-footer-nextpage" href="../multiplealleles/">Multiple Alleles »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Thursday 11 May 2023 11:43">Thursday 11 May 2023</span>. Using Julia version 1.9.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+ 0.804412  0.195588</code></pre><p>γ=0 values are for bootstrap replicates that did not have the edge in their network. Basic summaries on γ values for a given edge, say the minor parent, could be obtained like this:</p><pre><code class="language-julia-repl hljs" style="display:block;">julia&gt; minimum(BSgam[:,2])</code><code class="nohighlight hljs ansi" style="display:block;">0.0</code><br/><code class="language-julia-repl hljs" style="display:block;">julia&gt; maximum(BSgam[:,2])</code><code class="nohighlight hljs ansi" style="display:block;">0.2321667195572249</code><br/><code class="language-julia-repl hljs" style="display:block;">julia&gt; using Statistics # for functions like mean and std (standard deviation)</code><code class="nohighlight hljs ansi" style="display:block;"></code><br/><code class="language-julia-repl hljs" style="display:block;">julia&gt; mean(BSgam[:,2])</code><code class="nohighlight hljs ansi" style="display:block;">0.062201290198789325</code><br/><code class="language-julia-repl hljs" style="display:block;">julia&gt; std(BSgam[:,2])</code><code class="nohighlight hljs ansi" style="display:block;">0.09131993802196253</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../expectedCFs/">« Extract Expected CFs</a><a class="docs-footer-nextpage" href="../multiplealleles/">Multiple Alleles »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 21 August 2023 14:30">Monday 21 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/man/dist_reroot/index.html

@@ -49,4 +49,4 @@
 10 edges
 11 nodes: 6 tips, 0 hybrid nodes, 5 internal tree nodes.
 tip labels: C, D, O, E, ...
-(O,(((B,A):10.0,(C,D):10.0):0.664,E));</code></pre><p>See also function <code>displayedNetworkAt!</code> to get the network with a single reticulation of interest, and eliminate all other reticulations.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../snaq_plot/">« Network estimation and display</a><a class="docs-footer-nextpage" href="../fixednetworkoptim/">Candidate Networks »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Thursday 11 May 2023 11:43">Thursday 11 May 2023</span>. Using Julia version 1.9.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+(O,(((B,A):10.0,(C,D):10.0):0.664,E));</code></pre><p>See also function <code>displayedNetworkAt!</code> to get the network with a single reticulation of interest, and eliminate all other reticulations.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../snaq_plot/">« Network estimation and display</a><a class="docs-footer-nextpage" href="../fixednetworkoptim/">Candidate Networks »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 21 August 2023 14:30">Monday 21 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/man/expectedCFs/index.html

@@ -69,4 +69,4 @@
     geom_point(alpha=0.5, position=position_jitter(width=0.005, height=0.005)) +
     ylab("quartet CF expected from network") + xlab("quartet CF observed in gene trees") + coord_equal(ratio=1);
 # can be saved:
-ggsave(&quot;expCFs_obsvsfitted_A.svg&quot;, width=6, height=5);</code></pre><p><img src="../../assets/figures/expCFs_obsvsfitted_A.svg" alt="obsvsfitted A present or not"/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../fixednetworkoptim/">« Candidate Networks</a><a class="docs-footer-nextpage" href="../bootstrap/">Bootstrap »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Thursday 11 May 2023 11:43">Thursday 11 May 2023</span>. Using Julia version 1.9.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+ggsave(&quot;expCFs_obsvsfitted_A.svg&quot;, width=6, height=5);</code></pre><p><img src="../../assets/figures/expCFs_obsvsfitted_A.svg" alt="obsvsfitted A present or not"/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../fixednetworkoptim/">« Candidate Networks</a><a class="docs-footer-nextpage" href="../bootstrap/">Bootstrap »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 21 August 2023 14:30">Monday 21 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/man/fitDiscrete/index.html

@@ -113,4 +113,4 @@
  2</code><br/><code class="language-julia-repl hljs" style="display:block;">julia&gt; m1.label[traitmatrix[:,12]]</code><code class="nohighlight hljs ansi" style="display:block;">3-element Vector{String}:
  &quot;non-carnivory&quot;
  &quot;carnivory&quot;
- &quot;non-carnivory&quot;</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../parsimony/">« Parsimony on networks</a><a class="docs-footer-nextpage" href="../nj/">Neighbour Joining »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.24 on <span class="colophon-date" title="Thursday 11 May 2023 11:43">Thursday 11 May 2023</span>. Using Julia version 1.9.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+ &quot;non-carnivory&quot;</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../parsimony/">« Parsimony on networks</a><a class="docs-footer-nextpage" href="../nj/">Neighbour Joining »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 21 August 2023 14:30">Monday 21 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>