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, 34 insertions, 14 deletions

diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 7dfa740a..15be073c 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -21,13 +21,13 @@ components."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs
       </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 @@ components."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs
   <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 @@ components."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs
       <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 @@ components."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs
     <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>
@@ -132,7 +149,7 @@ the source compartment.
 Additionally, <code>mkinsub()</code> has an argument <code>to</code>, specifying names of
 variables to which a transfer is to be assumed in the model.
 If the argument <code>use_of_ff</code> is set to "min"
-(default) and the model for the compartment is "SFO" or "SFORB", an
+and the model for the compartment is "SFO" or "SFORB", an
 additional <code>mkinsub()</code> argument can be <code>sink = FALSE</code>, effectively
 fixing the flux to sink to zero.
 In print.mkinmod, this argument is currently not used.</p></dd>
@@ -169,7 +186,9 @@ applicable to give detailed information about the C function being built.</p></d
 <dd><p>Directory where an DLL object, if generated internally by
 <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code>, should be saved.  The DLL will only be stored in a
 permanent location for use in future sessions, if 'dll_dir' and 'name'
-are specified.</p></dd>
+are specified. This is helpful if fit objects are cached e.g. by knitr,
+as the cache remains functional across sessions if the DLL is stored in
+a user defined location.</p></dd>
 
 
 <dt>unload</dt>
@@ -247,7 +266,7 @@ in the FOCUS and NAFTA guidance documents are used.</p>
 <p>For kinetic models with more than one observed variable, a symbolic solution
 of the system of differential equations is included in the resulting
 mkinmod object in some cases, speeding up the solution.</p>
-<p>If a C compiler is found by <code><a href="https://rdrr.io/pkg/pkgbuild/man/has_compiler.html" class="external-link">pkgbuild::has_compiler()</a></code> and there
+<p>If a C compiler is found by <code><a href="https://r-lib.github.io/pkgbuild/reference/has_compiler.html" class="external-link">pkgbuild::has_compiler()</a></code> and there
 is more than one observed variable in the specification, C code is generated
 for evaluating the differential equations, compiled using
 <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code> and added to the resulting mkinmod object.</p>
@@ -310,7 +329,8 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 <span class="r-in"><span>   parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full_name <span class="op">=</span> <span class="st">"Test compound"</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>   m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>   name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Copied DLL from /tmp/Rtmp6DB2Bl/file3f5b93b53e71f.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Copied DLL from /tmp/Rtmp887oxB/file67a5068775fd4.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span>
 <span class="r-in"><span><span class="co"># Now we can save the model and restore it in a new session</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="co"># Terminate the R session here if you would like to check, and then do</span></span></span>
@@ -363,7 +383,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span>     })</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>     return(predicted)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> }</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x55556401ac50&gt;</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> &lt;environment: 0x55558a8511d0&gt;</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># If we have several parallel metabolites</span></span></span>
 <span class="r-in"><span><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span></span>
@@ -392,7 +412,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</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>
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