Merge branch 'v1.1.2'

1 files changed, 23 insertions, 17 deletions

diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html
index a472b054..ed72ec47 100644
--- a/docs/dev/reference/endpoints.html
+++ b/docs/dev/reference/endpoints.html
@@ -23,7 +23,7 @@ advantage that the SFORB model can also be used for metabolites."><meta name="ro
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.0</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span>
       </span>
     </div>
 
@@ -32,7 +32,7 @@ advantage that the SFORB model can also be used for metabolites."><meta name="ro
   <a href="../reference/index.html">Functions and data</a>
 </li>
 <li class="dropdown">
-  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
     Articles
      
     <span class="caret"></span>
@@ -47,6 +47,9 @@ advantage that the SFORB model can also be used for metabolites."><meta name="ro
       <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
     </li>
     <li>
+      <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+    </li>
+    <li>
       <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
     </li>
     <li>
@@ -95,21 +98,24 @@ advantage that the SFORB model can also be used for metabolites.</p>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">endpoints</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">endpoints</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
     <h2>Arguments</h2>
     <dl><dt>fit</dt>
-<dd><p>An object of class <a href="mkinfit.html">mkinfit</a>, <a href="nlme.mmkin.html">nlme.mmkin</a>, <a href="saem.html">saem.mmkin</a> or
-<a href="nlmixr.mmkin.html">nlmixr.mmkin</a>. Or another object that has list components
+<dd><p>An object of class <a href="mkinfit.html">mkinfit</a>, <a href="nlme.mmkin.html">nlme.mmkin</a> or <a href="saem.html">saem.mmkin</a>,
+or another object that has list components
 mkinmod containing an <a href="mkinmod.html">mkinmod</a> degradation model, and two numeric vectors,
 bparms.optim and bparms.fixed, that contain parameter values
 for that model.</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    <p>A list with a matrix of dissipation times named distimes,
+    
+
+<p>A list with a matrix of dissipation times named distimes,
 and, if applicable, a vector of formation fractions named ff
 and, if the SFORB model was in use, a vector of eigenvalues
 of these SFORB models, equivalent to DFOP rate constants</p>
@@ -131,22 +137,22 @@ HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models</p>
 
     <div id="ref-examples">
     <h2>Examples</h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span>
-<span class="r-in">  <span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in">  <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span>  <span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $distimes</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>            DT50    DT90 DT50back</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent 1.785233 15.1479 4.559973</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-in">  <span class="co"># \dontrun{</span></span>
-<span class="r-in">    <span class="va">fit_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in">    <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit_2</span><span class="op">)</span></span>
+<span class="r-in"><span>  <span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span>    <span class="va">fit_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span>    <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit_2</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $distimes</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>            DT50     DT90 DT50back  DT50_k1  DT50_k2</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent 1.886925 21.25106 6.397207 1.508293 38.83438</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-in">    <span class="va">fit_3</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in">    <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit_3</span><span class="op">)</span></span>
+<span class="r-in"><span>    <span class="va">fit_3</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span>    <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit_3</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $ff</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent_free </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>           1 </span>
@@ -159,8 +165,8 @@ HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span>            DT50     DT90 DT50back DT50_parent_b1 DT50_parent_b2</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent 1.886925 21.25106 6.397208       1.508293       38.83438</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-in">  <span class="co"># }</span></span>
-<span class="r-in"></span>
+<span class="r-in"><span>  <span class="co"># }</span></span></span>
+<span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
   </div>
@@ -175,7 +181,7 @@ HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
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