build based on bb1a90b

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.11.2","generation_timestamp":"2024-12-19T11:15:17","documenter_version":"1.8.0"}}
+{"documenter":{"julia_version":"1.11.2","generation_timestamp":"2024-12-19T11:26:00","documenter_version":"1.8.0"}}

dev/91-developer/index.html

@@ -7,4 +7,4 @@
 pkg&gt; test</code></pre><h2 id="Working-on-a-new-issue"><a class="docs-heading-anchor" href="#Working-on-a-new-issue">Working on a new issue</a><a id="Working-on-a-new-issue-1"></a><a class="docs-heading-anchor-permalink" href="#Working-on-a-new-issue" title="Permalink"></a></h2><p>We try to keep a linear history in this repo, so it is important to keep your branches up-to-date.</p><ol><li><p>Fetch from the remote and fast-forward your local main</p><pre><code class="language-bash hljs">git fetch upstream
 git switch main
 git merge --ff-only upstream/main</code></pre></li><li><p>Branch from <code>main</code> to address the issue (see below for naming)</p><pre><code class="language-bash hljs">git switch -c 42-add-answer-universe</code></pre></li><li><p>Push the new local branch to your personal remote repository</p><pre><code class="language-bash hljs">git push -u origin 42-add-answer-universe</code></pre></li><li><p>Create a pull request to merge your remote branch into the org main.</p></li></ol><h3 id="Branch-naming"><a class="docs-heading-anchor" href="#Branch-naming">Branch naming</a><a id="Branch-naming-1"></a><a class="docs-heading-anchor-permalink" href="#Branch-naming" title="Permalink"></a></h3><ul><li>If there is an associated issue, add the issue number.</li><li>If there is no associated issue, <strong>and the changes are small</strong>, add a prefix such as &quot;typo&quot;, &quot;hotfix&quot;, &quot;small-refactor&quot;, according to the type of update.</li><li>If the changes are not small and there is no associated issue, then create the issue first, so we can properly discuss the changes.</li><li>Use dash separated imperative wording related to the issue (e.g., <code>14-add-tests</code>, <code>15-fix-model</code>, <code>16-remove-obsolete-files</code>).</li></ul><h3 id="Commit-message"><a class="docs-heading-anchor" href="#Commit-message">Commit message</a><a id="Commit-message-1"></a><a class="docs-heading-anchor-permalink" href="#Commit-message" title="Permalink"></a></h3><ul><li>Use imperative or present tense, for instance: <em>Add feature</em> or <em>Fix bug</em>.</li><li>Have informative titles.</li><li>When necessary, add a body with details.</li><li>If there are breaking changes, add the information to the commit message.</li></ul><h3 id="Before-creating-a-pull-request"><a class="docs-heading-anchor" href="#Before-creating-a-pull-request">Before creating a pull request</a><a id="Before-creating-a-pull-request-1"></a><a class="docs-heading-anchor-permalink" href="#Before-creating-a-pull-request" title="Permalink"></a></h3><div class="admonition is-success"><header class="admonition-header">Atomic git commits</header><div class="admonition-body"><p>Try to create &quot;atomic git commits&quot; (recommended reading: <a href="https://blog.esciencecenter.nl/the-utopic-git-history-d44b81c09593">The Utopic Git History</a>).</p></div></div><ul><li><p>Make sure the tests pass.</p></li><li><p>Make sure the pre-commit tests pass.</p></li><li><p>Fetch any <code>main</code> updates from upstream and rebase your branch, if necessary:</p><pre><code class="language-bash hljs">git fetch upstream
-git rebase upstream/main BRANCH_NAME</code></pre></li><li><p>Then you can open a pull request and work with the reviewer to address any issues.</p></li></ul><h2 id="Building-and-viewing-the-documentation-locally"><a class="docs-heading-anchor" href="#Building-and-viewing-the-documentation-locally">Building and viewing the documentation locally</a><a id="Building-and-viewing-the-documentation-locally-1"></a><a class="docs-heading-anchor-permalink" href="#Building-and-viewing-the-documentation-locally" title="Permalink"></a></h2><p>Following the latest suggestions, we recommend using <code>LiveServer</code> to build the documentation. Here is how you do it:</p><ol><li>Run <code>julia --project=docs</code> to open Julia in the environment of the docs.</li><li>If this is the first time building the docs<ol><li>Press <code>]</code> to enter <code>pkg</code> mode</li><li>Run <code>pkg&gt; dev .</code> to use the development version of your package</li><li>Press backspace to leave <code>pkg</code> mode</li></ol></li><li>Run <code>julia&gt; using LiveServer</code></li><li>Run <code>julia&gt; servedocs()</code></li></ol></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../90-contributing/">« Contributing guidelines</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="Thursday 19 December 2024 11:15">Thursday 19 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+git rebase upstream/main BRANCH_NAME</code></pre></li><li><p>Then you can open a pull request and work with the reviewer to address any issues.</p></li></ul><h2 id="Building-and-viewing-the-documentation-locally"><a class="docs-heading-anchor" href="#Building-and-viewing-the-documentation-locally">Building and viewing the documentation locally</a><a id="Building-and-viewing-the-documentation-locally-1"></a><a class="docs-heading-anchor-permalink" href="#Building-and-viewing-the-documentation-locally" title="Permalink"></a></h2><p>Following the latest suggestions, we recommend using <code>LiveServer</code> to build the documentation. Here is how you do it:</p><ol><li>Run <code>julia --project=docs</code> to open Julia in the environment of the docs.</li><li>If this is the first time building the docs<ol><li>Press <code>]</code> to enter <code>pkg</code> mode</li><li>Run <code>pkg&gt; dev .</code> to use the development version of your package</li><li>Press backspace to leave <code>pkg</code> mode</li></ol></li><li>Run <code>julia&gt; using LiveServer</code></li><li>Run <code>julia&gt; servedocs()</code></li></ol></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../90-contributing/">« Contributing guidelines</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="Thursday 19 December 2024 11:25">Thursday 19 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/HowTo/custom_solvers/index.html

@@ -18,4 +18,4 @@
 m = Unfold.fit(UnfoldModel, designDict, evts, dat_3d; solver = b2b_solver)
 results = coeftable(m)
 
-plot_erp(results)</code></pre><p>These are the decoding results for <code>conditionA</code> while considering <code>conditionB</code>, and vice versa.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../generated/HowTo/effects/">« Marginal effects (must read re: splines)</a><a class="docs-footer-nextpage" href="../lmm_pvalues/">P-values for mixedModels »</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="Thursday 19 December 2024 11:15">Thursday 19 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+plot_erp(results)</code></pre><p>These are the decoding results for <code>conditionA</code> while considering <code>conditionB</code>, and vice versa.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../generated/HowTo/effects/">« Marginal effects (must read re: splines)</a><a class="docs-footer-nextpage" href="../lmm_pvalues/">P-values for mixedModels »</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="Thursday 19 December 2024 11:26">Thursday 19 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/HowTo/lmm_pvalues/index.html

@@ -89,4 +89,4 @@
 scatter(f[2,1],times,df.walds,axis=(;title="walds-t pvalue",xlabel="time"))
 scatter(f[2,2],times,df.lrt,axis=(;title="lrt pvalue",xlabel="time"))
 
-f</code></pre><img src="9949f295.png" alt="Example block output"/><p>Look pretty similar! Note that the Walds-T is typically too liberal (LRT also, but to a lesser exted). Best is to use the forthcoming MixedModelsPermutations.jl or go the route via R and use KenwardRoger (data not yet published)</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../custom_solvers/">« Alternative Solvers (Robust, GPU, B2B)</a><a class="docs-footer-nextpage" href="../../generated/HowTo/unfold_io/">Save and load Unfold models »</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="Thursday 19 December 2024 11:15">Thursday 19 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+f</code></pre><img src="9949f295.png" alt="Example block output"/><p>Look pretty similar! Note that the Walds-T is typically too liberal (LRT also, but to a lesser exted). Best is to use the forthcoming MixedModelsPermutations.jl or go the route via R and use KenwardRoger (data not yet published)</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../custom_solvers/">« Alternative Solvers (Robust, GPU, B2B)</a><a class="docs-footer-nextpage" href="../../generated/HowTo/unfold_io/">Save and load Unfold models »</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="Thursday 19 December 2024 11:26">Thursday 19 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/HowTo/multiple_events/index.html

@@ -23,4 +23,4 @@
     eventcolumn = "type",
 )
 results = coeftable(m)
-plot_erp(results; stderror = true, mapping = (; col = :eventname))</code></pre><img src="632387e0.png" alt="Example block output"/></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../tutorials/lmm_overlap/">« lmmERP (overlap correction)</a><a class="docs-footer-nextpage" href="../../generated/HowTo/contrasts/">Change contrasts / coding schema »</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="Thursday 19 December 2024 11:15">Thursday 19 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+plot_erp(results; stderror = true, mapping = (; col = :eventname))</code></pre><img src="632387e0.png" alt="Example block output"/></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../tutorials/lmm_overlap/">« lmmERP (overlap correction)</a><a class="docs-footer-nextpage" href="../../generated/HowTo/contrasts/">Change contrasts / coding schema »</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="Thursday 19 December 2024 11:25">Thursday 19 December 2024</span>. Using Julia version 1.11.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>