Fix and rebuild documentation, see NEWS

I had to fix the two pathway vignettes, as they did not work with
the released version any more. So they and the multistart vignette
which got some small fixes as well were rebuilt.

Complete rebuild of the online docs with the released version. The
documentation of the 'hierarchial_kinetics' format had to be fixed
as well.

1 files changed, 39 insertions, 22 deletions

diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 62e4bd8d..cb5039d1 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -25,13 +25,13 @@ likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/
       </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">
@@ -42,6 +42,8 @@ likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/
   <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>
@@ -49,22 +51,29 @@ likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/
       <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>
@@ -72,6 +81,14 @@ likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/
     <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>
@@ -384,17 +401,17 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class="r-in"><span><span class="co"># Use shorthand notation for parent only degradation</span></span></span>
 <span class="r-in"><span><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu">mkinfit</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"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></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> mkin version used for fitting:    1.2.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:       4.2.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Thu Nov 17 13:58:19 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Nov 17 13:58:19 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for fitting:    1.2.3 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:       4.2.3 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Thu Apr 20 07:32:45 2023 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Apr 20 07:32:45 2023 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 222 model solutions performed in 0.044 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 222 model solutions performed in 0.013 s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Error model: Constant variance </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -535,9 +552,9 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class="r-in"><span>      solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>               test relative elapsed</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3       analytical    1.000   0.570</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 deSolve_compiled    1.682   0.959</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2            eigen    2.609   1.487</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3       analytical    1.000   0.264</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 deSolve_compiled    1.197   0.316</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2            eigen    2.227   0.588</span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span></span>
@@ -564,10 +581,10 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NaNs produced</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NaNs produced</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>diag(.) had 0 or NA entries; non-finite result is doubtful</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for fitting:    1.2.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:       4.2.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Thu Nov 17 13:58:30 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Nov 17 13:58:30 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for fitting:    1.2.3 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:       4.2.3 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Thu Apr 20 07:32:49 2023 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Apr 20 07:32:49 2023 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span>
@@ -576,7 +593,7 @@ Degradation Data. <em>Environments</em> 6(12) 124
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type deSolve </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 3729 model solutions performed in 2.464 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 3729 model solutions performed in 0.694 s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Error model: Two-component variance function </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -688,7 +705,7 @@ Degradation Data. <em>Environments</em> 6(12) 124
 </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>
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