Merge branch 'v1.2.3_pkgdown'

1 files changed, 40 insertions, 10 deletions

diff --git a/docs/reference/illparms.html b/docs/reference/illparms.html
index 52f130e6..f0829482 100644
--- a/docs/reference/illparms.html
+++ b/docs/reference/illparms.html
@@ -21,13 +21,13 @@ without parameter transformations is used."><!-- mathjax --><script src="https:/
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.3</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav"><li>
-  <a href="../reference/index.html">Functions and data</a>
+  <a href="../reference/index.html">Reference</a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
@@ -38,6 +38,8 @@ without parameter transformations is used."><!-- mathjax --><script src="https:/
   <ul class="dropdown-menu" role="menu"><li>
       <a href="../articles/mkin.html">Introduction to mkin</a>
     </li>
+    <li class="divider">
+    <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li>
     <li>
       <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
     </li>
@@ -45,22 +47,29 @@ without parameter transformations is used."><!-- mathjax --><script src="https:/
       <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>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
     </li>
+    <li class="divider">
+    <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li>
     <li>
-      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+      <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a>
     </li>
     <li>
-      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+      <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
     </li>
     <li>
-      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
     </li>
     <li>
-      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+      <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a>
     </li>
     <li>
-      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+      <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
+    </li>
+    <li class="divider">
+    <li class="dropdown-header">Performance</li>
+    <li>
+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
     <li>
       <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
@@ -68,6 +77,14 @@ without parameter transformations is used."><!-- mathjax --><script src="https:/
     <li>
       <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
+    <li class="divider">
+    <li class="dropdown-header">Miscellaneous</li>
+    <li>
+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+    </li>
   </ul></li>
 <li>
   <a href="../news/index.html">News</a>
@@ -116,7 +133,14 @@ without parameter transformations is used.</p>
 <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S3 method for saem.mmkin</span></span>
-<span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, errmod <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">illparms</span><span class="op">(</span></span>
+<span>  <span class="va">object</span>,</span>
+<span>  conf.level <span class="op">=</span> <span class="fl">0.95</span>,</span>
+<span>  random <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  errmod <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  slopes <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S3 method for illparms.saem.mmkin</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
@@ -154,6 +178,12 @@ without parameter transformations is used.</p>
 <dd><p>For hierarchical fits, should error model parameters be
 tested?</p></dd>
 
+
+<dt>slopes</dt>
+<dd><p>For hierarchical <a href="saem.html">saem</a> fits using saemix as backend,
+should slope parameters in the covariate model(starting with 'beta_') be
+tested?</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
@@ -209,7 +239,7 @@ does not output anything in the case no ill-defined parameters are found.</p>
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
       </footer></div>