build based on 1a04a16

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.8.5","generation_timestamp":"2024-07-08T21:20:52","documenter_version":"1.5.0"}}
+{"documenter":{"julia_version":"1.8.5","generation_timestamp":"2024-07-17T22:42:22","documenter_version":"1.5.0"}}

dev/api/index.html

@@ -13,10 +13,11 @@
     designcheck::Bool = true,
     dropcheck::Bool = true,
     dropmissingsubj = false,
+    dropincompletesubj = false,
     info::Bool = true,
     warns::Bool = true,
     autoseq::Bool = false,
-    logt::Bool = true)</code></pre><ul><li><code>vars</code> - variabel&#39;s column(s);</li><li><code>subject</code> - subject&#39;s column;</li><li><code>period</code> - period&#39;s column;</li><li><code>formulation</code> - formulation&#39;s column;</li><li><code>sequence</code> -sequence&#39;s column;</li><li><code>stage</code> - stage&#39;s column;</li><li><code>reference</code> - reference value for <code>formulation</code> column;</li><li><code>design</code> - design: &quot;parallel&quot;, &quot;2X2&quot;, &quot;2X2X2&quot;, &quot;2X2X4&quot;, ets. (formulations X sequences X periods);</li><li><code>seqcheck</code> - check sequencs; </li><li><code>designcheck</code> - check design correctness;  </li><li><code>dropcheck</code> - dropuot check;</li><li><code>dropmissingsubj</code> - drop subjects with missing data;</li><li><code>info</code> - show information;</li><li><code>warns</code> - show warnings;</li><li><code>autoseq</code> - try to make sequence collumn;</li><li><code>logt</code> - if <code>true</code> (default) data is already log-transformed, else <code>log()</code> will be used.</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/PharmCat/MetidaBioeq.jl/blob/e48eff1f070b41c8c344a2f743ef6361230b5988/src/bioequivalence.jl#L22-L58">source</a></section></article><h3 id="MetidaBioeq.estimate"><a class="docs-heading-anchor" href="#MetidaBioeq.estimate">MetidaBioeq.estimate</a><a id="MetidaBioeq.estimate-1"></a><a class="docs-heading-anchor-permalink" href="#MetidaBioeq.estimate" title="Permalink"></a></h3><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="MetidaBioeq.estimate" href="#MetidaBioeq.estimate"><code>MetidaBioeq.estimate</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">estimate(be; estimator = &quot;auto&quot;, method = &quot;auto&quot;, supresswarn = false)</code></pre><p><code>method</code> - Model settings.</p><ul><li>if <code>method == &quot;auto&quot;</code> than method <code>A</code> used for &quot;2X2&quot; and &quot;2X2X2&quot;  designes, method <code>P</code> for &quot;parallel&quot; design and method <code>B</code> for any other.</li></ul><p><em>Methods:</em></p><ul><li><code>A</code> using GLM and model <code>@formula(var ~ formulation + period + sequence + subject)</code></li><li><code>B</code> using MixedModels and model <code>@formula(var ~ formulation + period + sequence + (1|subject))</code> or Metida and model <code>@lmmformula(v ~ formulation + period + sequence, random = 1|subject:SI)</code></li><li><code>C</code> using Metida and model <code>@lmmformula(v ~ formulation + period + sequence, random = formulation|subject:CSH, repeated = formulation|subject:DIAG)</code></li><li><code>P</code> using GLM and model <code>@formula(var ~ formulation)</code></li></ul><p><code>estimator</code> - Estimator settings.</p><ul><li>if <code>estimator == &quot;auto&quot;</code> than GLM used for &quot;parallel&quot; design; for &quot;2X2&quot; design used GLM if no droputs and MixedModels if <code>dropout == true</code>; for other designes with method <code>C</code> Metida used and MixedModel for other cases.</li></ul><p><em>Estimators:</em></p><ul><li>&quot;glm&quot; for GLM (https://juliastats.org/GLM.jl/stable/)</li><li>&quot;mm&quot; for MixedModels (https://juliastats.org/MixedModels.jl/stable/)</li><li>&quot;met&quot; for Metida (https://pharmcat.github.io/Metida.jl/stable/)</li></ul><p><em>Other autosettings:</em></p><p>If design is &quot;parallel&quot; <code>estimator</code> set as &quot;glm&quot; and <code>method</code> as &quot;P&quot;.</p><p>If design is &quot;2X2&quot; and method is &quot;P&quot; or &quot;C&quot; than if <code>estimator</code> == &quot;glm&quot; method set as &quot;A&quot; and &quot;B&quot; for other estimators. </p><p>If design not &quot;parallel&quot; or &quot;2X2&quot;: </p><p>if method not &quot;A&quot;, &quot;B&quot; or &quot;C&quot; than set as &quot;A&quot; for &quot;glm&quot; ann as B for other estimators;</p><p>if <code>estimator</code> == &quot;glm&quot; and <code>method</code> == &quot;B&quot; than <code>estimator</code> set as &quot;mm&quot;, if <code>estimator</code> == &quot;glm&quot; or &quot;mm&quot; and <code>method</code> == &quot;C&quot; than <code>estimator</code> set as &quot;met&quot;.</p><p>Reference:</p><p>EMA: <a href="https://www.ema.europa.eu/en/documents/scientific-guideline/guideline-investigation-bioequivalence-rev1_en.pdf">GUIDELINE ON THE INVESTIGATION OF BIOEQUIVALENCE</a></p><p>EMA: <a href="https://www.ema.europa.eu/en/documents/other/31-annex-i-statistical-analysis-methods-compatible-ema-bioequivalence-guideline_en.pdf">GUIDELINE ON THE INVESTIGATION OF BIOEQUIVALENCE, Annex I</a></p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/PharmCat/MetidaBioeq.jl/blob/e48eff1f070b41c8c344a2f743ef6361230b5988/src/bioequivalence.jl#L318-L363">source</a></section></article><h3 id="MetidaBioeq.result"><a class="docs-heading-anchor" href="#MetidaBioeq.result">MetidaBioeq.result</a><a id="MetidaBioeq.result-1"></a><a class="docs-heading-anchor-permalink" href="#MetidaBioeq.result" title="Permalink"></a></h3><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="MetidaBioeq.result" href="#MetidaBioeq.result"><code>MetidaBioeq.result</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">result(beres::BEResults)</code></pre><p>Returns dataframe with bioequivalence results.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/PharmCat/MetidaBioeq.jl/blob/e48eff1f070b41c8c344a2f743ef6361230b5988/src/bioequivalence.jl#L629-L633">source</a></section></article><h3 id="MetidaBioeq.makeseq"><a class="docs-heading-anchor" href="#MetidaBioeq.makeseq">MetidaBioeq.makeseq</a><a id="MetidaBioeq.makeseq-1"></a><a class="docs-heading-anchor-permalink" href="#MetidaBioeq.makeseq" title="Permalink"></a></h3><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="MetidaBioeq.makeseq" href="#MetidaBioeq.makeseq"><code>MetidaBioeq.makeseq</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">makeseq(data;
+    logt::Bool = true)</code></pre><ul><li><code>vars</code> - variabel&#39;s column(s);</li><li><code>subject</code> - subject&#39;s column;</li><li><code>period</code> - period&#39;s column;</li><li><code>formulation</code> - formulation&#39;s column;</li><li><code>sequence</code> -sequence&#39;s column;</li><li><code>stage</code> - stage&#39;s column;</li><li><code>reference</code> - reference value for <code>formulation</code> column;</li><li><code>design</code> - design: &quot;parallel&quot;, &quot;2X2&quot;, &quot;2X2X2&quot;, &quot;2X2X4&quot;, ets. (formulations X sequences X periods);</li><li><code>seqcheck</code> - check sequencs; </li><li><code>designcheck</code> - check design correctness;  </li><li><code>dropcheck</code> - dropuot check;</li><li><code>dropmissingsubj</code> - drop subjects with missing data;</li><li><code>dropincompletesubj</code> - drop subjects with no full sequence data (work only if <code>seqcheck</code> = true);</li><li><code>info</code> - show information;</li><li><code>warns</code> - show warnings;</li><li><code>autoseq</code> - try to make sequence collumn;</li><li><code>logt</code> - if <code>true</code> (default) data is already log-transformed, else <code>log()</code> will be used.</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/PharmCat/MetidaBioeq.jl/blob/1a04a16576d435bb1d93f2c218b013ea84cea3c8/src/bioequivalence.jl#L22-L60">source</a></section></article><h3 id="MetidaBioeq.estimate"><a class="docs-heading-anchor" href="#MetidaBioeq.estimate">MetidaBioeq.estimate</a><a id="MetidaBioeq.estimate-1"></a><a class="docs-heading-anchor-permalink" href="#MetidaBioeq.estimate" title="Permalink"></a></h3><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="MetidaBioeq.estimate" href="#MetidaBioeq.estimate"><code>MetidaBioeq.estimate</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">estimate(be; estimator = &quot;auto&quot;, method = &quot;auto&quot;, supresswarn = false)</code></pre><p><code>method</code> - Model settings.</p><ul><li>if <code>method == &quot;auto&quot;</code> than method <code>A</code> used for &quot;2X2&quot; and &quot;2X2X2&quot;  designes, method <code>P</code> for &quot;parallel&quot; design and method <code>B</code> for any other.</li></ul><p><em>Methods:</em></p><ul><li><code>A</code> using GLM and model <code>@formula(var ~ formulation + period + sequence + subject)</code></li><li><code>B</code> using MixedModels and model <code>@formula(var ~ formulation + period + sequence + (1|subject))</code> or Metida and model <code>@lmmformula(v ~ formulation + period + sequence, random = 1|subject:SI)</code></li><li><code>C</code> using Metida and model <code>@lmmformula(v ~ formulation + period + sequence, random = formulation|subject:CSH, repeated = formulation|subject:DIAG)</code></li><li><code>P</code> using GLM and model <code>@formula(var ~ formulation)</code></li></ul><p><code>estimator</code> - Estimator settings.</p><ul><li>if <code>estimator == &quot;auto&quot;</code> than GLM used for &quot;parallel&quot; design; for &quot;2X2&quot; design used GLM if no droputs and MixedModels if <code>dropout == true</code>; for other designes with method <code>C</code> Metida used and MixedModel for other cases.</li></ul><p><em>Estimators:</em></p><ul><li>&quot;glm&quot; for GLM (https://juliastats.org/GLM.jl/stable/)</li><li>&quot;mm&quot; for MixedModels (https://juliastats.org/MixedModels.jl/stable/)</li><li>&quot;met&quot; for Metida (https://pharmcat.github.io/Metida.jl/stable/)</li></ul><p><em>Other autosettings:</em></p><p>If design is &quot;parallel&quot; <code>estimator</code> set as &quot;glm&quot; and <code>method</code> as &quot;P&quot;.</p><p>If design is &quot;2X2&quot; and method is &quot;P&quot; or &quot;C&quot; than if <code>estimator</code> == &quot;glm&quot; method set as &quot;A&quot; and &quot;B&quot; for other estimators. </p><p>If design not &quot;parallel&quot; or &quot;2X2&quot;: </p><p>if method not &quot;A&quot;, &quot;B&quot; or &quot;C&quot; than set as &quot;A&quot; for &quot;glm&quot; ann as B for other estimators;</p><p>if <code>estimator</code> == &quot;glm&quot; and <code>method</code> == &quot;B&quot; than <code>estimator</code> set as &quot;mm&quot;, if <code>estimator</code> == &quot;glm&quot; or &quot;mm&quot; and <code>method</code> == &quot;C&quot; than <code>estimator</code> set as &quot;met&quot;.</p><p>Reference:</p><p>EMA: <a href="https://www.ema.europa.eu/en/documents/scientific-guideline/guideline-investigation-bioequivalence-rev1_en.pdf">GUIDELINE ON THE INVESTIGATION OF BIOEQUIVALENCE</a></p><p>EMA: <a href="https://www.ema.europa.eu/en/documents/other/31-annex-i-statistical-analysis-methods-compatible-ema-bioequivalence-guideline_en.pdf">GUIDELINE ON THE INVESTIGATION OF BIOEQUIVALENCE, Annex I</a></p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/PharmCat/MetidaBioeq.jl/blob/1a04a16576d435bb1d93f2c218b013ea84cea3c8/src/bioequivalence.jl#L333-L378">source</a></section></article><h3 id="MetidaBioeq.result"><a class="docs-heading-anchor" href="#MetidaBioeq.result">MetidaBioeq.result</a><a id="MetidaBioeq.result-1"></a><a class="docs-heading-anchor-permalink" href="#MetidaBioeq.result" title="Permalink"></a></h3><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="MetidaBioeq.result" href="#MetidaBioeq.result"><code>MetidaBioeq.result</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">result(beres::BEResults)</code></pre><p>Returns dataframe with bioequivalence results.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/PharmCat/MetidaBioeq.jl/blob/1a04a16576d435bb1d93f2c218b013ea84cea3c8/src/bioequivalence.jl#L644-L648">source</a></section></article><h3 id="MetidaBioeq.makeseq"><a class="docs-heading-anchor" href="#MetidaBioeq.makeseq">MetidaBioeq.makeseq</a><a id="MetidaBioeq.makeseq-1"></a><a class="docs-heading-anchor-permalink" href="#MetidaBioeq.makeseq" title="Permalink"></a></h3><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="MetidaBioeq.makeseq" href="#MetidaBioeq.makeseq"><code>MetidaBioeq.makeseq</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">makeseq(data;
     subject = :subject,
     period = :period,
-    formulation = :formulation)</code></pre><p>Make sequence vector from <code>data</code> and <code>subject</code>, <code>period</code>, <code>formulation</code> columns.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/PharmCat/MetidaBioeq.jl/blob/e48eff1f070b41c8c344a2f743ef6361230b5988/src/bioequivalence.jl#L272-L279">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../example/">« Example</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 1.5.0 on <span class="colophon-date" title="Monday 8 July 2024 21:20">Monday 8 July 2024</span>. Using Julia version 1.8.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+    formulation = :formulation)</code></pre><p>Make sequence vector from <code>data</code> and <code>subject</code>, <code>period</code>, <code>formulation</code> columns.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/PharmCat/MetidaBioeq.jl/blob/1a04a16576d435bb1d93f2c218b013ea84cea3c8/src/bioequivalence.jl#L287-L294">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../example/">« Example</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 1.5.0 on <span class="colophon-date" title="Wednesday 17 July 2024 22:42">Wednesday 17 July 2024</span>. Using Julia version 1.8.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>