wip: update

Author: mnneely

.quarto/cites/index.json

@@ -1 +1 @@
-{"Compare.qmd":[],"NPAG.qmd":[],"NPAG_cov.qmd":[],"data.qmd":["bealWaysFitPK2001a"],"examine.qmd":[],"index.qmd":["goutelleNonparametricMethodsPopulation2022","goutelleParametricNonparametricMethods2022","guidiParametricApproachesPopulation2022"],"intro.qmd":["knuth84"],"models.qmd":[],"objects.qmd":[],"overview.qmd":[],"plotly.qmd":[],"references.qmd":[],"summary.qmd":[],"workflow.qmd":[]}
+{"Compare.qmd":[],"NPAG.qmd":[],"NPAG_cov.qmd":[],"data.qmd":["bealWaysFitPK2001a"],"examine.qmd":[],"index.qmd":["goutelleNonparametricMethodsPopulation2022","goutelleParametricNonparametricMethods2022","guidiParametricApproachesPopulation2022"],"intro.qmd":["knuth84"],"models.qmd":[],"objects.qmd":[],"overview.qmd":[],"plotly.qmd":[],"references.qmd":[],"simulation.qmd":["goutelle_nonparametric_2022"],"summary.qmd":[],"workflow.qmd":[]}

.quarto/idx/index.qmd.json

@@ -48,7 +48,8 @@ format:
 pdf:
     documentclass: scrreprt
 
-
-
+execute:
+  env:
+    CLIPR_ALLOW: "TRUE"
 
 

_quarto.yml

@@ -3993,31 +3993,43 @@
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./NPAG.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Detailed example of a typical workflow</span></span></a>
+ <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Fit a model with NPAG</span></span></a>
+  </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./objects.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">The results</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./examine.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Examine the results</span></span></a>
+ <span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Examine results</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./NPAG_cov.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">NPAG with covariates</span></span></a>
+ <span class="menu-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">More complex models</span></span></a>
+  </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./simulation.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Simulations</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./plotly.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Plotting Details</span></span></a>
+ <span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Plotting Details</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./Compare.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Comparing models</span></span></a>
+ <span class="menu-text"><span class="chapter-number">12</span>&nbsp; <span class="chapter-title">Comparing models</span></span></a>
   </div>
 </li>
     </ul>

docs/examine.html

@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>7&nbsp; The results – Learn Pmetrics</title>
+<title>7  The results – Learn Pmetrics</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -3983,7 +3983,7 @@
     <span class="navbar-title">Learn Pmetrics</span>
     </a>
   </div>
-            <div id="quarto-search" class="" title="Search"></div>
+            <div id="quarto-search" class title="Search"></div>
           <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" role="menu" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
   <span class="navbar-toggler-icon"></span>
 </button>
@@ -4004,7 +4004,7 @@
       <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" role="button" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
-        <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./objects.html"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">The results</span></a></li></ol></nav>
+        <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./objects.html"><span class="chapter-number">7</span>  <span class="chapter-title">The results</span></a></li></ol></nav>
         <a class="flex-grow-1" role="navigation" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
     </div>
@@ -4023,67 +4023,73 @@
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./index.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Introduction</span></span></a>
+ <span class="menu-text"><span class="chapter-number">1</span>  <span class="chapter-title">Introduction</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./overview.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Overview</span></span></a>
+ <span class="menu-text"><span class="chapter-number">2</span>  <span class="chapter-title">Overview</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./workflow.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Workflow</span></span></a>
+ <span class="menu-text"><span class="chapter-number">3</span>  <span class="chapter-title">Workflow</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./data.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Data</span></span></a>
+ <span class="menu-text"><span class="chapter-number">4</span>  <span class="chapter-title">Data</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./models.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Models</span></span></a>
+ <span class="menu-text"><span class="chapter-number">5</span>  <span class="chapter-title">Models</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./NPAG.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Fit a model with NPAG</span></span></a>
+ <span class="menu-text"><span class="chapter-number">6</span>  <span class="chapter-title">Fit a model with NPAG</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./objects.html" class="sidebar-item-text sidebar-link active">
- <span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">The results</span></span></a>
+ <span class="menu-text"><span class="chapter-number">7</span>  <span class="chapter-title">The results</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./examine.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Examine results</span></span></a>
+ <span class="menu-text"><span class="chapter-number">8</span>  <span class="chapter-title">Examine results</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./NPAG_cov.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">NPAG with covariates</span></span></a>
+ <span class="menu-text"><span class="chapter-number">9</span>  <span class="chapter-title">More complex models</span></span></a>
+  </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./simulation.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">10</span>  <span class="chapter-title">Simulations</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./plotly.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Plotting Details</span></span></a>
+ <span class="menu-text"><span class="chapter-number">11</span>  <span class="chapter-title">Plotting Details</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./Compare.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">Comparing models</span></span></a>
+ <span class="menu-text"><span class="chapter-number">12</span>  <span class="chapter-title">Comparing models</span></span></a>
   </div>
 </li>
     </ul>
@@ -4105,7 +4111,7 @@ <h2 id="toc-title">On this page</h2>
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
-<h1 class="title"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">The results</span></h1>
+<h1 class="title"><span class="chapter-number">7</span>  <span class="chapter-title">The results</span></h1>
 </div>
 
 
@@ -4124,9 +4130,9 @@ <h1 class="title"><span class="chapter-number">7</span>&nbsp; <span class="chapt
 
 <section id="pm_result-details" class="level2" data-number="7.1">
 <h2 data-number="7.1" class="anchored" data-anchor-id="pm_result-details"><span class="header-section-number">7.1</span> PM_result details</h2>
-<p>After a successful NPAG/NPOD run, an R datafile is saved in the /outputs subdirectory of the newly created numerically ordered folder in the working directory. This file is called “PMout.Rdata”. These data files can be loaded by ensuring that the Runs folder is set as the working directory or using the <code>path</code> argument to <code>$fit()</code>, and then using the <span style="color: #841010; font-family: 'Arial', Arial, sans-serif; font-weight: 900;">Pmetrics</span> command <a href="https://lapkb.github.io/Pmetrics/reference/PM_load.html"><code>PM_load</code></a>.</p>
+<p>After a successful NPAG/NPOD run, an R datafile is saved in the /outputs subdirectory of the newly created numerically ordered folder in the working directory. This file is called “PMout.Rdata”. These data files can be loaded by ensuring that the Runs folder is set as the working directory or using the <code>path</code> argument to <code>$fit()</code>, and then using the <span style="color: #841010; font-family: &#39;Arial&#39;, Arial, sans-serif; font-weight: 900;">Pmetrics</span> command <a href="https://lapkb.github.io/Pmetrics/reference/PM_load.html"><code>PM_load</code></a>.</p>
 <p>There are several data objects contained within the Rdata files which are loaded, making these objects available for plotting and other analysis. This is in contrast to the Legacy method of loading objects into your global R environment, suffixed with the run number, e.g., “op.1” or “final.1”. Obscurely loading objects into memory is not good or current programming practice.</p>
-<p>Therefore, in R6 <span style="color: #841010; font-family: 'Arial', Arial, sans-serif; font-weight: 900;">Pmetrics</span>, <code>PM_load()</code> returns a <a href="https://lapkb.github.io/Pmetrics/reference/PM_result.html"><code>PM_result</code></a>object. The fields in the object are in the table below.</p>
+<p>Therefore, in R6 <span style="color: #841010; font-family: &#39;Arial&#39;, Arial, sans-serif; font-weight: 900;">Pmetrics</span>, <code>PM_load()</code> returns a <a href="https://lapkb.github.io/Pmetrics/reference/PM_result.html"><code>PM_result</code></a>object. The fields in the object are in the table below.</p>
 <div id="tcdzyubfbi" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
 <style>#tcdzyubfbi table {
 font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji';
@@ -4979,7 +4985,7 @@ <h2 data-number="7.1" class="anchored" data-anchor-id="pm_result-details"><span
 <p>To access the fields in a <code>PM_result</code> object, use the “$”.</p>
 <div class="cell">
 <div class="code-copy-outer-scaffold"><div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="co"># load the results of run1</span></span>
-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>run1 <span class="ot">&lt;-</span> <span class="fu">PM_load</span>(<span class="dv">1</span>, <span class="at">path =</span> <span class="st">"Runs"</span>)</span>
+<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>run1 <span class="ot">&lt;-</span> <span class="fu">PM_load</span>(<span class="dv">1</span>, <span class="at">path =</span> <span class="st">&quot;Runs&quot;</span>)</span>
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>run1<span class="sc">$</span>op <span class="co"># observed vs. predicted PM_op R6 object</span></span>
 <span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>run1<span class="sc">$</span>op<span class="sc">$</span>time <span class="co"># times in PM_op</span></span>
 <span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>run1<span class="sc">$</span>op<span class="sc">$</span>data <span class="co"># this accesses the whole observed vs. predicted raw data frame</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
@@ -5407,7 +5413,7 @@ <h2 data-number="7.1" class="anchored" data-anchor-id="pm_result-details"><span
 </tr>
 <tr class="odd">
 <td class="gt_row gt_left" headers="Methods"></td>
-<td class="gt_row gt_left" headers="Comments"><code>PM_result$plot("op")</code></td>
+<td class="gt_row gt_left" headers="Comments"><code>PM_result$plot(&quot;op&quot;)</code></td>
 </tr>
 <tr class="even">
 <td class="gt_row gt_left" headers="Methods"></td>
@@ -5427,7 +5433,7 @@ <h2 data-number="7.1" class="anchored" data-anchor-id="pm_result-details"><span
 </tr>
 <tr class="even">
 <td class="gt_row gt_left" headers="Methods"></td>
-<td class="gt_row gt_left" headers="Comments"><code>PM_result$summary("final")</code></td>
+<td class="gt_row gt_left" headers="Comments"><code>PM_result$summary(&quot;final&quot;)</code></td>
 </tr>
 <tr class="odd">
 <td class="gt_row gt_left" headers="Methods"></td>
@@ -5447,7 +5453,7 @@ <h2 data-number="7.1" class="anchored" data-anchor-id="pm_result-details"><span
 </tr>
 <tr class="odd">
 <td class="gt_row gt_left" headers="Methods">$auc</td>
-<td class="gt_row gt_left" headers="Comments">Calculate auc by supplying a src, e.g.&nbsp;<code>PM_result$auc("op")</code></td>
+<td class="gt_row gt_left" headers="Comments">Calculate auc by supplying a src, e.g. <code>PM_result$auc(&quot;op&quot;)</code></td>
 </tr>
 <tr class="even">
 <td class="gt_row gt_left" headers="Methods">$report</td>
@@ -5890,12 +5896,12 @@ <h2 data-number="7.1" class="anchored" data-anchor-id="pm_result-details"><span
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
       <a href="./NPAG.html" class="pagination-link" aria-label="Fit a model with NPAG">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Fit a model with NPAG</span></span>
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">6</span>  <span class="chapter-title">Fit a model with NPAG</span></span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
       <a href="./examine.html" class="pagination-link" aria-label="Examine results">
-        <span class="nav-page-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Examine results</span></span> <i class="bi bi-arrow-right-short"></i>
+        <span class="nav-page-text"><span class="chapter-number">8</span>  <span class="chapter-title">Examine results</span></span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>