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, 35 insertions, 18 deletions

diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html
index 1e294eaf..d446a2a2 100644
--- a/docs/reference/nlme.mmkin.html
+++ b/docs/reference/nlme.mmkin.html
@@ -19,13 +19,13 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja
       </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">
@@ -36,6 +36,8 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja
   <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>
@@ -43,22 +45,29 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja
       <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>
@@ -66,6 +75,14 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja
     <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>
@@ -239,7 +256,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_sfo</span>, <span class="va">f_nlme_dfop</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>             Model df      AIC      BIC    logLik   Test  L.Ratio p-value</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_sfo      1  5 625.0539 637.5529 -307.5269                        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop     2  9 495.1270 517.6253 -238.5635 1 vs 2 137.9269  &lt;.0001</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop     2  9 495.1270 517.6253 -238.5635 1 vs 2 137.9268  &lt;.0001</span>
 <span class="r-in"><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">f_nlme_dfop</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Kinetic nonlinear mixed-effects model fit by maximum likelihood</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -270,7 +287,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 <span class="r-in"><span>  <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop</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 10.79857 100.7937 30.34193 4.193938 43.85443</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent 10.79857 100.7937 30.34192 4.193936 43.85441</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>  <span class="va">ds_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@@ -321,12 +338,12 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 <span class="r-in"><span>  <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</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_A1 parent_sink </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   0.2768574   0.7231426 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   0.2768575   0.7231425 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</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  11.07091 104.6320 31.49737 4.462383 46.20825</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> A1     162.30519 539.1662       NA       NA       NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent  11.07091 104.6320 31.49737 4.462384 46.20825</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> A1     162.30507 539.1658       NA       NA       NA</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>  <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu">findFunction</span><span class="op">(</span><span class="st">"varConstProp"</span><span class="op">)</span><span class="op">)</span> <span class="op">&gt;</span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span> <span class="co"># tc error model for nlme available</span></span></span>
@@ -354,7 +371,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 <span class="r-out co"><span class="r-pr">#&gt;</span> Fixed effects:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> parent_0   log_k1   log_k2 g_qlogis </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 94.04774 -1.82340 -4.16716  0.05686 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 94.04773 -1.82340 -4.16716  0.05686 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Random effects:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)</span>
@@ -368,7 +385,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Formula: ~fitted(.) </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Parameter estimates:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>      const       prop </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2.23223147 0.01262395 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2.23223593 0.01262367 </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>  <span class="va">f_2_obs</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_2</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="va">f_nlme_sfo_sfo_obs</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span>
@@ -401,7 +418,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Formula: ~1 | name </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Parameter estimates:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    parent        A1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1.0000000 0.2049995 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1.0000000 0.2049994 </span>
 <span class="r-in"><span>  <span class="va">f_nlme_dfop_sfo_obs</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>,</span></span>
 <span class="r-in"><span>    control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">5e-4</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
@@ -413,7 +430,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span>, <span class="va">f_nlme_dfop_sfo_obs</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                     Model df      AIC      BIC    logLik   Test  L.Ratio</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop_sfo         1 13 843.8547 884.6201 -408.9274                </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop_sfo_obs     2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32091</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop_sfo_obs     2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32093</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                     p-value</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop_sfo            </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop_sfo_obs  &lt;.0001</span>
@@ -433,7 +450,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 </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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