Merge branch 'v1.2.3_pkgdown'

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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