build based on f0cce9c

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.11.3","generation_timestamp":"2025-01-26T22:58:07","documenter_version":"1.8.0"}}
+{"documenter":{"julia_version":"1.11.3","generation_timestamp":"2025-01-26T23:05:08","documenter_version":"1.8.0"}}

dev/ancestors/index.html

@@ -66,4 +66,4 @@
 0.0305 - true value: 0.0177
 0.0913 - true value: 0.0485
 0.0542 - true value: 0.075
-0.498 - true value: 0.589</code></pre><h2 id="Functions"><a class="docs-heading-anchor" href="#Functions">Functions</a><a id="Functions-1"></a><a class="docs-heading-anchor-permalink" href="#Functions" title="Permalink"></a></h2><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="MolecularEvolution.marginal_state_dict" href="#MolecularEvolution.marginal_state_dict"><code>MolecularEvolution.marginal_state_dict</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">marginal_state_dict(tree::FelNode, model; partition_list = 1:length(tree.message), node_message_dict = Dict{FelNode,Vector{&lt;:Partition}}())</code></pre><p>Takes in a tree and a model (which can be a single model, an array of models, or a function that maps FelNode-&gt;Array{&lt;:BranchModel}), and returns a dictionary mapping nodes to their marginal reconstructions (ie. P(state|all observations,model)). A subset of partitions can be specified by partition_list, and a dictionary can be passed in to avoid re-allocating memory, in case you&#39;re running this over and over.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/MolecularEvolution.jl/blob/52af349e3f4f6ccafa79e4bc8569c6d50d608097/src/core/algorithms/ancestors.jl#L111-L117">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="MolecularEvolution.cascading_max_state_dict" href="#MolecularEvolution.cascading_max_state_dict"><code>MolecularEvolution.cascading_max_state_dict</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">cascading_max_state_dict(tree::FelNode, model; partition_list = 1:length(tree.message), node_message_dict = Dict{FelNode,Vector{&lt;:Partition}}())</code></pre><p>Takes in a tree and a model (which can be a single model, an array of models, or a function that maps FelNode-&gt;Array{&lt;:BranchModel}), and returns a dictionary mapping nodes to their inferred ancestors under the following scheme: the state that maximizes the marginal likelihood is selected at the root, and then, for each node, the maximum likelihood state is selected conditioned on the maximized state of the parent node and the observations of all descendents. A subset of partitions can be specified by partition_list, and a dictionary can be passed in to avoid re-allocating memory, in case you&#39;re running this over and over.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/MolecularEvolution.jl/blob/52af349e3f4f6ccafa79e4bc8569c6d50d608097/src/core/algorithms/ancestors.jl#L175-L182">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="MolecularEvolution.endpoint_conditioned_sample_state_dict" href="#MolecularEvolution.endpoint_conditioned_sample_state_dict"><code>MolecularEvolution.endpoint_conditioned_sample_state_dict</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">endpoint_conditioned_sample_state_dict(tree::FelNode, model; partition_list = 1:length(tree.message), node_message_dict = Dict{FelNode,Vector{&lt;:Partition}}())</code></pre><p>Takes in a tree and a model (which can be a single model, an array of models, or a function that maps FelNode-&gt;Array{&lt;:BranchModel}), and draws samples under the model conditions on the leaf observations. These samples are stored in the node<em>message</em>dict, which is returned. A subset of partitions can be specified by partition_list, and a dictionary can be passed in to avoid re-allocating memory, in case you&#39;re running this over and over.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/MolecularEvolution.jl/blob/52af349e3f4f6ccafa79e4bc8569c6d50d608097/src/core/algorithms/ancestors.jl#L208-L214">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../optimization/">« Optimization</a><a class="docs-footer-nextpage" href="../generated/viz/">Visualization »</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="Sunday 26 January 2025 22:58">Sunday 26 January 2025</span>. Using Julia version 1.11.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+0.498 - true value: 0.589</code></pre><h2 id="Functions"><a class="docs-heading-anchor" href="#Functions">Functions</a><a id="Functions-1"></a><a class="docs-heading-anchor-permalink" href="#Functions" title="Permalink"></a></h2><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="MolecularEvolution.marginal_state_dict" href="#MolecularEvolution.marginal_state_dict"><code>MolecularEvolution.marginal_state_dict</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">marginal_state_dict(tree::FelNode, model; partition_list = 1:length(tree.message), node_message_dict = Dict{FelNode,Vector{&lt;:Partition}}())</code></pre><p>Takes in a tree and a model (which can be a single model, an array of models, or a function that maps FelNode-&gt;Array{&lt;:BranchModel}), and returns a dictionary mapping nodes to their marginal reconstructions (ie. P(state|all observations,model)). A subset of partitions can be specified by partition_list, and a dictionary can be passed in to avoid re-allocating memory, in case you&#39;re running this over and over.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/MolecularEvolution.jl/blob/f0cce9cd12ed1f65856d8e446af124fe1f153edb/src/core/algorithms/ancestors.jl#L111-L117">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="MolecularEvolution.cascading_max_state_dict" href="#MolecularEvolution.cascading_max_state_dict"><code>MolecularEvolution.cascading_max_state_dict</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">cascading_max_state_dict(tree::FelNode, model; partition_list = 1:length(tree.message), node_message_dict = Dict{FelNode,Vector{&lt;:Partition}}())</code></pre><p>Takes in a tree and a model (which can be a single model, an array of models, or a function that maps FelNode-&gt;Array{&lt;:BranchModel}), and returns a dictionary mapping nodes to their inferred ancestors under the following scheme: the state that maximizes the marginal likelihood is selected at the root, and then, for each node, the maximum likelihood state is selected conditioned on the maximized state of the parent node and the observations of all descendents. A subset of partitions can be specified by partition_list, and a dictionary can be passed in to avoid re-allocating memory, in case you&#39;re running this over and over.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/MolecularEvolution.jl/blob/f0cce9cd12ed1f65856d8e446af124fe1f153edb/src/core/algorithms/ancestors.jl#L175-L182">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="MolecularEvolution.endpoint_conditioned_sample_state_dict" href="#MolecularEvolution.endpoint_conditioned_sample_state_dict"><code>MolecularEvolution.endpoint_conditioned_sample_state_dict</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">endpoint_conditioned_sample_state_dict(tree::FelNode, model; partition_list = 1:length(tree.message), node_message_dict = Dict{FelNode,Vector{&lt;:Partition}}())</code></pre><p>Takes in a tree and a model (which can be a single model, an array of models, or a function that maps FelNode-&gt;Array{&lt;:BranchModel}), and draws samples under the model conditions on the leaf observations. These samples are stored in the node<em>message</em>dict, which is returned. A subset of partitions can be specified by partition_list, and a dictionary can be passed in to avoid re-allocating memory, in case you&#39;re running this over and over.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/MolecularEvolution.jl/blob/f0cce9cd12ed1f65856d8e446af124fe1f153edb/src/core/algorithms/ancestors.jl#L208-L214">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../optimization/">« Optimization</a><a class="docs-footer-nextpage" href="../generated/viz/">Visualization »</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="Sunday 26 January 2025 23:05">Sunday 26 January 2025</span>. Using Julia version 1.11.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/examples/index.html

@@ -371,4 +371,4 @@
     end
 end</code></pre><pre><code class="nohighlight hljs">Site 153: P(β&gt;α)=0.9074
 Site 158: P(β&gt;α)=0.9266
-Site 160: P(β&gt;α)=0.9547</code></pre><p>And let&#39;s visualize one of those sites:</p><pre><code class="language-julia hljs">gridplot(alpha_ind_vec,beta_ind_vec,grid_values, weighted_mat[:,160]./sum(weighted_mat[:,160]))</code></pre><p><img src="../figures/FUBAR_site160.svg" alt/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../framework/">« The MolecularEvolution.jl Framework</a><a class="docs-footer-nextpage" href="../IO/">Input/Output »</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="Sunday 26 January 2025 22:58">Sunday 26 January 2025</span>. Using Julia version 1.11.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+Site 160: P(β&gt;α)=0.9547</code></pre><p>And let&#39;s visualize one of those sites:</p><pre><code class="language-julia hljs">gridplot(alpha_ind_vec,beta_ind_vec,grid_values, weighted_mat[:,160]./sum(weighted_mat[:,160]))</code></pre><p><img src="../figures/FUBAR_site160.svg" alt/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../framework/">« The MolecularEvolution.jl Framework</a><a class="docs-footer-nextpage" href="../IO/">Input/Output »</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="Sunday 26 January 2025 23:05">Sunday 26 January 2025</span>. Using Julia version 1.11.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>